Index

_

____() (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) __all__ (in module medcat2.cdb) (in module medcat2.config) __call__ (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) __call__() (medcat2.cat.AbstractCoreComponent method) (medcat2.cat.AddonComponent method) (medcat2.cat.CAT method) (medcat2.components.addons.addons.AddonComponent method) (medcat2.components.addons.addons.BaseComponent method) (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent method) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer method) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase method) (medcat2.components.linking.context_based_linker.AbstractCoreComponent method) (medcat2.components.linking.context_based_linker.BaseTokenizer method) (medcat2.components.linking.context_based_linker.Linker method) (medcat2.components.linking.no_action_linker.AbstractCoreComponent method) (medcat2.components.linking.no_action_linker.BaseTokenizer method) (medcat2.components.linking.no_action_linker.NoActionLinker method) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent method) (medcat2.components.ner.dict_based_ner.BaseTokenizer method) (medcat2.components.ner.dict_based_ner.NER method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.deid.DeIdModel method) (medcat2.components.ner.trf.deid.NerModel method) (medcat2.components.ner.trf.deid.TransformersNER method) (medcat2.components.ner.trf.model.CAT method) (medcat2.components.ner.trf.model.NerModel method) (medcat2.components.ner.trf.model.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer method) (medcat2.components.ner.trf.transformers_ner.CollateAndPadNER method) (medcat2.components.ner.trf.transformers_ner.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer method) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer method) (medcat2.components.ner.vocab_based_ner.NER method) (medcat2.components.normalizing.normalizer.AbstractCoreComponent method) (medcat2.components.normalizing.normalizer.BaseTokenizer method) (medcat2.components.normalizing.normalizer.TokenNormalizer method) (medcat2.components.tagging.tagger.AbstractCoreComponent method) (medcat2.components.tagging.tagger.BaseTokenizer method) (medcat2.components.tagging.tagger.TagAndSkipTagger method) (medcat2.components.types.AbstractCoreComponent method) (medcat2.components.types.BaseComponent method) (medcat2.components.types.BaseTokenizer method) (medcat2.components.types.CoreComponent method) (medcat2.pipeline.pipeline.AbstractCoreComponent method) (medcat2.pipeline.pipeline.AddonComponent method) (medcat2.pipeline.pipeline.BaseComponent method) (medcat2.pipeline.pipeline.BaseTokenizer method) (medcat2.pipeline.pipeline.CoreComponent method) (medcat2.pipeline.pipeline.DelegatingTokenizer method) (medcat2.preprocessors.cleaners.BaseTokenizer method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer method) (medcat2.tokenizing.tokenizers.BaseTokenizer method) (medcat2.utils.default_args.BaseTokenizer method) (medcat2.utils.legacy.conversion_all.CAT method) (medcat2.utils.legacy.conversion_all.NoActionLinker method) (medcat2.utils.legacy.convert_deid.BaseTokenizer method) (medcat2.utils.legacy.convert_deid.TransformersNER method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE method) (medcat2.utils.ner.data_collator.CollateAndPadNER method) __class_getitem__() (medcat2.cat.AbstractCoreComponent class method) (medcat2.cat.AddonComponent class method) (medcat2.cat.Config class method) (medcat2.cat.HashableComponet class method) (medcat2.cat.MutableDocument class method) (medcat2.cat.MutableEntity class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.AddonComponent class method) (medcat2.components.addons.addons.BaseComponent class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.addons.MutableEntity class method) (medcat2.components.addons.addons.Registry class method) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent class method) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument class method) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.AbstractCoreComponent class method) (medcat2.components.linking.context_based_linker.BaseTokenizer class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.context_based_linker.Linker class method) (medcat2.components.linking.context_based_linker.MutableDocument class method) (medcat2.components.linking.context_based_linker.MutableEntity class method) (medcat2.components.linking.no_action_linker.AbstractCoreComponent class method) (medcat2.components.linking.no_action_linker.BaseTokenizer class method) (medcat2.components.linking.no_action_linker.MutableDocument class method) (medcat2.components.linking.no_action_linker.NoActionLinker class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.linking.vector_context_model.MutableDocument class method) (medcat2.components.linking.vector_context_model.MutableEntity class method) (medcat2.components.linking.vector_context_model.MutableToken class method) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent class method) (medcat2.components.ner.dict_based_ner.BaseTokenizer class method) (medcat2.components.ner.dict_based_ner.MutableDocument class method) (medcat2.components.ner.dict_based_ner.NER class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.model.MutableDocument class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent class method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.trf.transformers_ner.MutableDocument class method) (medcat2.components.ner.trf.transformers_ner.MutableEntity class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.ner.vocab_based_annotator.MutableDocument class method) (medcat2.components.ner.vocab_based_annotator.MutableEntity class method) (medcat2.components.ner.vocab_based_annotator.MutableToken class method) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent class method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer class method) (medcat2.components.ner.vocab_based_ner.MutableDocument class method) (medcat2.components.ner.vocab_based_ner.NER class method) (medcat2.components.normalizing.normalizer.AbstractCoreComponent class method) (medcat2.components.normalizing.normalizer.BaseTokenizer class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.normalizing.normalizer.MutableDocument class method) (medcat2.components.normalizing.normalizer.TokenNormalizer class method) (medcat2.components.tagging.tagger.AbstractCoreComponent class method) (medcat2.components.tagging.tagger.BaseTokenizer class method) (medcat2.components.tagging.tagger.MutableDocument class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.components.tagging.tagger.TagAndSkipTagger class method) (medcat2.components.types.AbstractCoreComponent class method) (medcat2.components.types.BaseComponent class method) (medcat2.components.types.BaseTokenizer class method) (medcat2.components.types.CoreComponent class method) (medcat2.components.types.HashableComponet class method) (medcat2.components.types.MutableDocument class method) (medcat2.components.types.MutableEntity class method) (medcat2.components.types.Registry class method) (medcat2.components.types.TrainableComponent class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.AbstractCoreComponent class method) (medcat2.pipeline.pipeline.AddonComponent class method) (medcat2.pipeline.pipeline.BaseComponent class method) (medcat2.pipeline.pipeline.BaseTokenizer class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.pipeline.pipeline.CoreComponent class method) (medcat2.pipeline.pipeline.DelegatingTokenizer class method) (medcat2.pipeline.pipeline.MutableDocument class method) (medcat2.pipeline.pipeline.MutableEntity class method) (medcat2.pipeline.pipeline.MutableToken class method) (medcat2.pipeline.pipeline.Serialisable class method) (medcat2.preprocessors.cleaners.BaseTokenizer class method) (medcat2.preprocessors.cleaners.LCDBMaker class method) (medcat2.preprocessors.cleaners.LGeneral class method) (medcat2.preprocessors.cleaners.LPreprocessing class method) (medcat2.preprocessors.cleaners.MutableDocument class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.stats.stats.MutableDocument class method) (medcat2.stats.stats.MutableEntity class method) (medcat2.storage.serialisables.ManualSerialisable class method) (medcat2.storage.serialisables.Serialisable class method) (medcat2.storage.serialisers.ManualSerialisable class method) (medcat2.storage.serialisers.Serialisable class method) (medcat2.tokenizing.regex_impl.tokenizer.BaseDocument class method) (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity class method) (medcat2.tokenizing.regex_impl.tokenizer.BaseToken class method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument class method) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity class method) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken class method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer class method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument class method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity class method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken class method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer class method) (medcat2.tokenizing.spacy_impl.tokens.BaseDocument class method) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity class method) (medcat2.tokenizing.spacy_impl.tokens.BaseToken class method) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity class method) (medcat2.tokenizing.spacy_impl.tokens.MutableToken class method) (medcat2.tokenizing.tokenizers.BaseTokenizer class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.MutableDocument class method) (medcat2.tokenizing.tokenizers.MutableEntity class method) (medcat2.tokenizing.tokenizers.MutableToken class method) (medcat2.tokenizing.tokenizers.Registry class method) (medcat2.tokenizing.tokens.BaseDocument class method) (medcat2.tokenizing.tokens.BaseEntity class method) (medcat2.tokenizing.tokens.BaseToken class method) (medcat2.tokenizing.tokens.MutableDocument class method) (medcat2.tokenizing.tokens.MutableEntity class method) (medcat2.tokenizing.tokens.MutableToken class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.MutableDocument class method) (medcat2.trainer.MutableEntity class method) (medcat2.trainer.MutableToken class method) (medcat2.trainer.Preprocessing class method) (medcat2.trainer.TrainableComponent class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.data_utils.MutableDocument class method) (medcat2.utils.data_utils.MutableEntity class method) (medcat2.utils.default_args.BaseTokenizer class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.conversion_all.NoActionLinker class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.BaseTokenizer class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) (medcat2.utils.postprocessing.MutableDocument class method) (medcat2.utils.postprocessing.MutableEntity class method) (medcat2.utils.registry.Registry class method) __class_vars__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __contains__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cat.Vocab method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.addons.Registry method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.BasicSpellChecker method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Registry method) (medcat2.components.types.Vocab method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.registry.Registry method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) __copy__() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) 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method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisables.SerialisingStrategy method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.CoreComponentType method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.CoreComponentType method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.CoreComponentType method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method) (medcat2.utils.registry.MedCATRegistryException method) __ge__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.registry.MedCATRegistryException method) __get_pydantic_core_schema__() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) __get_pydantic_json_schema__() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) __getattr__() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.LSTM method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) __getattribute__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.registry.MedCATRegistryException method) __getitem__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.MutableDocument method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cat.Vocab method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.addons.Registry method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.MutableDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.MutableDocument method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.MutableDocument method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.MutableDocument method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.MutableDocument method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.components.ner.trf.transformers_ner.MutableDocument method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_annotator.MutableDocument method) (medcat2.components.ner.vocab_based_ner.MutableDocument method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.MutableDocument method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.MutableDocument method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.MutableDocument method) (medcat2.components.types.Registry method) (medcat2.components.types.Vocab method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.MutableDocument method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.preprocessors.cleaners.MutableDocument method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.stats.stats.MutableDocument method) (medcat2.tokenizing.regex_impl.tokenizer.BaseDocument method) (medcat2.tokenizing.regex_impl.tokenizer.Document method) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument method) (medcat2.tokenizing.spacy_impl.tokenizers.Document method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument method) (medcat2.tokenizing.spacy_impl.tokens.BaseDocument method) (medcat2.tokenizing.spacy_impl.tokens.Document method) (medcat2.tokenizing.tokenizers.MutableDocument method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.tokenizing.tokens.BaseDocument method) (medcat2.tokenizing.tokens.MutableDocument method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.trainer.MutableDocument method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.data_utils.MutableDocument method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.postprocessing.MutableDocument method) (medcat2.utils.registry.Registry method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) __getstate__() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.LSTM method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) __gt__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.registry.MedCATRegistryException method) __hash__() (medcat2.cat.AvailableSerialisers method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.linking.context_based_linker.CoreComponentType method) (medcat2.components.linking.no_action_linker.CoreComponentType method) (medcat2.components.ner.dict_based_ner.CoreComponentType method) (medcat2.components.ner.trf.deid.CoreComponentType method) (medcat2.components.ner.trf.model.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers method) (medcat2.components.ner.trf.transformers_ner.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.components.ner.vocab_based_ner.CoreComponentType method) (medcat2.components.normalizing.normalizer.CoreComponentType method) (medcat2.components.tagging.tagger.CoreComponentType method) (medcat2.components.types.CoreComponentType method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.config.config.SerialisingStrategy method) (medcat2.config.config_meta_cat.AvailableSerialisers method) (medcat2.pipeline.pipeline.AvailableSerialisers method) (medcat2.pipeline.pipeline.CoreComponentType method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.SplitType method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisables.SerialisingStrategy method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.Token method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokenizers.Token method) (medcat2.tokenizing.spacy_impl.tokens.Token method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.CoreComponentType method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.default_args.CoreComponentType method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.CoreComponentType method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method) (medcat2.utils.registry.MedCATRegistryException method) __init__() (medcat2.cat.CAT method) (medcat2.cat.CDB method) (medcat2.cat.Config method) (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.Hasher method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cat.Pipeline method) (medcat2.cat.Trainer 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(medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) __iter__() (medcat2.cat.Config method) (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.MutableDocument method) (medcat2.cat.MutableEntity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.Config method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) 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method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.registry.MedCATRegistryException method) __len__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.MutableEntity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.addons.MutableEntity method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) 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(medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.MutableEntity method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.stats.stats.MutableEntity method) (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity method) (medcat2.tokenizing.regex_impl.tokenizer.Entity method) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity method) 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method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) 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(medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __pydantic_decorators__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __pydantic_extra__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute)

__pydantic_fields_set__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __pydantic_generic_metadata__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __pydantic_init_subclass__() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) __pydantic_parent_namespace__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __pydantic_post_init__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __pydantic_private__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT 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(medcat2.config.config.Environment attribute), [1] (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel 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method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.AvailableSerialisers method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.pipeline.pipeline.CoreComponentType method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.kfold.SplitType method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.LinkingFilters method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisables.SerialisingStrategy method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) 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(medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.default_args.CoreComponentType method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.CoreComponentType method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.legacy.convert_cdb.LegacyClassNotFound method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method) (medcat2.utils.registry.MedCATRegistryException method) __repr_args__() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) 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(medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) 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attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __repr_str__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute) (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute) (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __reversed__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) __rich_repr__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute) (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute) (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __ror__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) __setattr__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) 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method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.registry.MedCATRegistryException method) __setitem__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo 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(medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) __setstate__() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.LSTM method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) 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method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) (medcat2.utils.registry.MedCATRegistryException method) __signature__ (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER 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attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute), [1] (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute), [1] (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) __sizeof__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.registry.MedCATRegistryException method) __slots__ (medcat2.cat.AbstractCoreComponent attribute) (medcat2.cat.AddonComponent attribute) (medcat2.cat.Config attribute) (medcat2.cat.HashableComponet attribute) (medcat2.cat.MutableDocument attribute) (medcat2.cat.MutableEntity attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.AddonComponent attribute) (medcat2.components.addons.addons.BaseComponent attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.addons.MutableEntity attribute) (medcat2.components.addons.addons.Registry attribute) (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument attribute) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity attribute) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.AbstractCoreComponent attribute) (medcat2.components.linking.context_based_linker.BaseTokenizer attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.linking.context_based_linker.MutableDocument attribute) (medcat2.components.linking.context_based_linker.MutableEntity attribute) (medcat2.components.linking.no_action_linker.AbstractCoreComponent attribute) (medcat2.components.linking.no_action_linker.BaseTokenizer attribute) (medcat2.components.linking.no_action_linker.MutableDocument attribute) (medcat2.components.linking.no_action_linker.NoActionLinker attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.linking.vector_context_model.MutableDocument attribute) (medcat2.components.linking.vector_context_model.MutableEntity attribute) (medcat2.components.linking.vector_context_model.MutableToken attribute) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.dict_based_ner.BaseTokenizer attribute) (medcat2.components.ner.dict_based_ner.MutableDocument attribute) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.deid.TransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.model.MutableDocument attribute) (medcat2.components.ner.trf.model.TransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent attribute) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.MutableDocument attribute) (medcat2.components.ner.trf.transformers_ner.MutableEntity attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.ner.vocab_based_annotator.MutableDocument attribute) (medcat2.components.ner.vocab_based_annotator.MutableEntity attribute) (medcat2.components.ner.vocab_based_annotator.MutableToken attribute) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.vocab_based_ner.BaseTokenizer attribute) (medcat2.components.ner.vocab_based_ner.MutableDocument attribute) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.components.normalizing.normalizer.AbstractCoreComponent attribute) (medcat2.components.normalizing.normalizer.BaseTokenizer attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.normalizing.normalizer.MutableDocument attribute) (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) (medcat2.components.tagging.tagger.AbstractCoreComponent attribute) (medcat2.components.tagging.tagger.BaseTokenizer attribute) (medcat2.components.tagging.tagger.MutableDocument attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) (medcat2.components.types.AbstractCoreComponent attribute) (medcat2.components.types.BaseComponent attribute) (medcat2.components.types.BaseTokenizer attribute) (medcat2.components.types.CoreComponent attribute) (medcat2.components.types.HashableComponet attribute) (medcat2.components.types.MutableDocument attribute) (medcat2.components.types.MutableEntity attribute) (medcat2.components.types.Registry attribute) (medcat2.components.types.TrainableComponent attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute) (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.AbstractCoreComponent attribute) (medcat2.pipeline.pipeline.AddonComponent attribute) (medcat2.pipeline.pipeline.BaseComponent attribute) (medcat2.pipeline.pipeline.BaseTokenizer attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.pipeline.pipeline.CoreComponent attribute) (medcat2.pipeline.pipeline.DelegatingTokenizer attribute) (medcat2.pipeline.pipeline.MutableDocument attribute) (medcat2.pipeline.pipeline.MutableEntity attribute) (medcat2.pipeline.pipeline.MutableToken attribute) (medcat2.pipeline.pipeline.Serialisable attribute) (medcat2.preprocessors.cleaners.BaseTokenizer attribute) (medcat2.preprocessors.cleaners.LCDBMaker attribute) (medcat2.preprocessors.cleaners.LGeneral attribute) (medcat2.preprocessors.cleaners.LPreprocessing attribute) (medcat2.preprocessors.cleaners.MutableDocument attribute) (medcat2.stats.kfold.FoldCreator attribute) (medcat2.stats.kfold.PerAnnsFoldCreator attribute) (medcat2.stats.kfold.PerCUIMetrics attribute) (medcat2.stats.kfold.PerDocsFoldCreator attribute) (medcat2.stats.kfold.SimpleFoldCreator attribute) (medcat2.stats.kfold.WeightedDocumentsCreator attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.stats.stats.MutableDocument attribute) (medcat2.stats.stats.MutableEntity attribute) (medcat2.storage.serialisables.ManualSerialisable attribute) (medcat2.storage.serialisables.Serialisable attribute) (medcat2.storage.serialisers.DillSerialiser attribute) (medcat2.storage.serialisers.ManualSerialisable attribute) (medcat2.storage.serialisers.Serialisable attribute) (medcat2.storage.serialisers.Serialiser attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseDocument attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseToken attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken attribute) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken attribute) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseDocument attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseToken attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableToken attribute) (medcat2.tokenizing.tokenizers.BaseTokenizer attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.MutableDocument attribute) (medcat2.tokenizing.tokenizers.MutableEntity attribute) (medcat2.tokenizing.tokenizers.MutableToken attribute) (medcat2.tokenizing.tokenizers.Registry attribute) (medcat2.tokenizing.tokens.BaseDocument attribute) (medcat2.tokenizing.tokens.BaseEntity attribute) (medcat2.tokenizing.tokens.BaseToken attribute) (medcat2.tokenizing.tokens.MutableDocument attribute) (medcat2.tokenizing.tokens.MutableEntity attribute) (medcat2.tokenizing.tokens.MutableToken attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.MutableDocument attribute) (medcat2.trainer.MutableEntity attribute) (medcat2.trainer.MutableToken attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.trainer.TrainableComponent attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.data_utils.MutableDocument attribute) (medcat2.utils.data_utils.MutableEntity attribute) (medcat2.utils.default_args.BaseTokenizer attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute) (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.conversion_all.NoActionLinker attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.BaseTokenizer attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_deid.TransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE attribute) (medcat2.utils.postprocessing.MutableDocument attribute) (medcat2.utils.postprocessing.MutableEntity attribute) (medcat2.utils.registry.Registry attribute) __str__() (medcat2.cat.AvailableSerialisers method) (medcat2.cat.Config method) (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.Config method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.context_based_linker.CoreComponentType method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.no_action_linker.CoreComponentType method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.dict_based_ner.CoreComponentType method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.deid.CoreComponentType method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.model.CoreComponentType method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.trf.transformers_ner.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.ner.vocab_based_ner.CoreComponentType method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.normalizing.normalizer.CoreComponentType method) (medcat2.components.tagging.tagger.CoreComponentType method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.components.types.CoreComponentType method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.SerialisingStrategy method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.AvailableSerialisers method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.AvailableSerialisers method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.pipeline.pipeline.CoreComponentType method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.kfold.SplitType method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.LinkingFilters method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisables.SerialisingStrategy method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.regex_impl.tokenizer.Document method) (medcat2.tokenizing.regex_impl.tokenizer.Entity method) (medcat2.tokenizing.regex_impl.tokenizer.Token method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Document method) (medcat2.tokenizing.spacy_impl.tokenizers.Entity method) (medcat2.tokenizing.spacy_impl.tokenizers.Token method) (medcat2.tokenizing.spacy_impl.tokens.Document method) (medcat2.tokenizing.spacy_impl.tokens.Entity method) (medcat2.tokenizing.spacy_impl.tokens.Token method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.CoreComponentType method) (medcat2.trainer.General method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.default_args.CoreComponentType method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.CoreComponentType method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method) (medcat2.utils.registry.MedCATRegistryException method) __subclasshook__() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.registry.MedCATRegistryException method) __version__ (in module medcat2) _add_concept() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) _add_concept_names() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) _add_cui_info() (in module medcat2.utils.legacy.convert_cdb) _add_full_build() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) _add_helper() (in module medcat2.stats.kfold) _add_name_info() (in module medcat2.utils.legacy.convert_cdb) _add_target_ann() (medcat2.stats.kfold.PerAnnsFoldCreator method) _add_weighted_helper() (in module medcat2.stats.kfold) _ADDON_REGISTRY (in module medcat2.components.addons.addons) _addons (medcat2.cat.Pipeline attribute) (medcat2.model_creation.cdb_maker.Pipeline attribute) (medcat2.pipeline.pipeline.Pipeline attribute) (medcat2.trainer.Pipeline attribute) _all_docs (medcat2.stats.kfold.PerDocsFoldCreator attribute) _apply() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _backward_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _backward_pre_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _buffers (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) _calculate_keys() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) _call_impl() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _callback_iterator_iterable() (in module medcat2.utils.iterutils) _check_frozen() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) _check_similarity() (medcat2.components.linking.context_based_linker.Linker method) _CITATION (in module medcat2.utils.ner.transformers_ner) _CLASS_PATH (in module medcat2.storage.schema) _clear_state() (in module medcat2.utils.cdb_state) _cls2path() (in module medcat2.storage.schema) _compiled_call_impl (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _component (medcat2.components.ner.trf.deid.TransformersNER attribute) (medcat2.components.ner.trf.model.TransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNER attribute) (medcat2.utils.legacy.convert_deid.TransformersNER attribute) _component_lock (medcat2.components.addons.meta_cat.meta_cat.MetaCAT attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCAT attribute) _components (medcat2.cat.Pipeline attribute) (medcat2.components.addons.addons.Registry attribute) (medcat2.components.types.Registry attribute) (medcat2.model_creation.cdb_maker.Pipeline attribute) (medcat2.pipeline.pipeline.Pipeline attribute) (medcat2.tokenizing.tokenizers.Registry attribute) (medcat2.trainer.Pipeline attribute) (medcat2.utils.registry.Registry attribute) _copy_and_set_values() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) _CORE_REGISTRIES (in module medcat2.components.types) _count_p_anns_norm() (medcat2.stats.stats.StatsBuilder method) _count_project() (medcat2.utils.data_utils.TestTrainSplitter method) _counter (medcat2.stats.kfold.PerAnnsFoldCreator attribute) (medcat2.stats.kfold.SimpleFoldCreator attribute) _create_annotation() (medcat2.stats.stats.StatsBuilder method) _create_annotation_2() (medcat2.stats.stats.StatsBuilder method) _create_export_with_documents() (medcat2.stats.kfold.FoldCreator method) (medcat2.stats.kfold.PerAnnsFoldCreator method) (medcat2.stats.kfold.PerDocsFoldCreator method) (medcat2.stats.kfold.SimpleFoldCreator method) (medcat2.stats.kfold.WeightedDocumentsCreator method) _create_fold() (medcat2.stats.kfold.PerAnnsFoldCreator method) (medcat2.stats.kfold.PerDocsFoldCreator method) (medcat2.stats.kfold.SimpleFoldCreator method) _create_new_project() (medcat2.stats.kfold.FoldCreator method) (medcat2.stats.kfold.PerAnnsFoldCreator method) (medcat2.stats.kfold.PerDocsFoldCreator method) (medcat2.stats.kfold.SimpleFoldCreator method) (medcat2.stats.kfold.WeightedDocumentsCreator method) _decode_string() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) _DEF_SER (in module medcat2.storage.serialisers) _def_serialiser (medcat2.components.ner.trf.deid.TransformersNER attribute) (medcat2.components.ner.trf.model.TransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNER attribute) (medcat2.utils.legacy.convert_deid.TransformersNER attribute) _DEFAULT_ADDONS (in module medcat2.components.addons.addons) _DEFAULT_LINKING (in module medcat2.components.types) _DEFAULT_NER (in module medcat2.components.types) _DEFAULT_NORMALIZERS (in module medcat2.components.types) _DEFAULT_SNOMED_TYPE_ID2NAME (in module medcat2.utils.legacy.convert_cdb) _DEFAULT_TAGGERS (in module medcat2.components.types) _DEFAULT_TOKENIZING (in module medcat2.tokenizing.tokenizers) _delegate (medcat2.tokenizing.spacy_impl.tokenizers.Document attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Entity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Token attribute) (medcat2.tokenizing.spacy_impl.tokens.Document attribute) (medcat2.tokenizing.spacy_impl.tokens.Entity attribute) (medcat2.tokenizing.spacy_impl.tokens.Token attribute) _DEP_NAME_MAPPER (in module medcat2.utils.import_utils) _DEP_PATTERN (in module medcat2.utils.import_utils) _DESCRIPTION (in module medcat2.utils.ner.transformers_ner) _doc (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.Token attribute) _doc_to_out() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) _doc_to_out_entity() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) _dumper (medcat2.cat.Hasher attribute) (medcat2.cdb.cdb.Hasher attribute) (medcat2.components.addons.meta_cat.meta_cat.Hasher attribute) (medcat2.components.ner.trf.transformers_ner.Hasher attribute) (medcat2.config.config_transformers_ner.Hasher attribute) (medcat2.utils.hasher.Hasher attribute) _empty() (medcat2.stats.stats.StatsBuilder method) _end_char_index (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) _end_index (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) _ensure_lazy_default() (medcat2.components.addons.addons.Registry method) (medcat2.components.types.Registry method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.utils.registry.Registry method) _ensure_not_training() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) _entity_from_tokens() (in module medcat2.tokenizing.regex_impl.tokenizer) _EXTRA_NAME (in module medcat2.components.addons.meta_cat) (in module medcat2.components.ner.dict_based_ner) (in module medcat2.components.ner.trf) (in module medcat2.tokenizing.spacy_impl) _file_read (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) _file_readline (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) _find_or_add_doc() (medcat2.stats.kfold.FoldCreator method) (medcat2.stats.kfold.PerAnnsFoldCreator method) (medcat2.stats.kfold.PerDocsFoldCreator method) (medcat2.stats.kfold.SimpleFoldCreator method) (medcat2.stats.kfold.WeightedDocumentsCreator method) _fix_old_style_cnf() (in module medcat2.utils.legacy.convert_meta_cat) _forward_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _forward_hooks_always_called (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _forward_hooks_with_kwargs (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _forward_pre_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _forward_pre_hooks_with_kwargs (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _generate_examples() (medcat2.utils.ner.transformers_ner.TransformersDatasetNER method) _generate_next_value_() (medcat2.cat.AvailableSerialisers method) (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.linking.context_based_linker.CoreComponentType method) (medcat2.components.linking.no_action_linker.CoreComponentType method) (medcat2.components.ner.dict_based_ner.CoreComponentType method) (medcat2.components.ner.trf.deid.CoreComponentType method) (medcat2.components.ner.trf.model.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers method) (medcat2.components.ner.trf.transformers_ner.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.components.ner.vocab_based_ner.CoreComponentType method) (medcat2.components.normalizing.normalizer.CoreComponentType method) (medcat2.components.tagging.tagger.CoreComponentType method) (medcat2.components.types.CoreComponentType method) (medcat2.config.config.SerialisingStrategy method) (medcat2.config.config_meta_cat.AvailableSerialisers method) (medcat2.pipeline.pipeline.AvailableSerialisers method) (medcat2.pipeline.pipeline.CoreComponentType method) (medcat2.stats.kfold.SplitType method) (medcat2.storage.serialisables.SerialisingStrategy method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.trainer.CoreComponentType method) (medcat2.utils.default_args.CoreComponentType method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.CoreComponentType method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method) _get_attr() (in module medcat2.utils.cdb_state) _get_backward_hooks() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _get_backward_pre_hooks() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _get_entity() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) _get_loaded_addon_path() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) _get_loaded_components_paths() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) _get_meta_cat_and_tokenizer_paths() (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) _get_name() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _get_or_empty() (medcat2.stats.stats.StatsBuilder method) _get_pref_name() (medcat2.stats.stats.StatsBuilder method) _get_reason_not_deid() (medcat2.components.ner.trf.deid.DeIdModel class method) _get_tokens() (in module medcat2.preprocessors.cleaners) _get_value() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) _ignore (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) _inference() (medcat2.components.linking.context_based_linker.Linker method) _info() (medcat2.utils.ner.transformers_ner.TransformersDatasetNER method) _init_addon() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) _init_component() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) _init_components() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) _init_data_paths() (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) _INIT_PARTS_PATH (in module medcat2.storage.schema) _init_per_fold() (medcat2.stats.kfold.PerAnnsFoldCreator method) (medcat2.stats.kfold.SimpleFoldCreator method) _init_tokenizer() (medcat2.cat.Pipeline method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) _instantiate() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) _is_deid_model() (medcat2.components.ner.trf.deid.DeIdModel class method) _is_full_backward_hook (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _is_protocol (medcat2.cat.AbstractCoreComponent attribute) (medcat2.cat.AddonComponent attribute) (medcat2.cat.HashableComponet attribute) (medcat2.cat.MutableDocument attribute) (medcat2.cat.MutableEntity attribute) (medcat2.components.addons.addons.AddonComponent attribute) (medcat2.components.addons.addons.BaseComponent attribute) (medcat2.components.addons.addons.MutableEntity attribute) (medcat2.components.addons.addons.Registry attribute) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument attribute) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity attribute) (medcat2.components.linking.context_based_linker.AbstractCoreComponent attribute) (medcat2.components.linking.context_based_linker.BaseTokenizer attribute) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.linking.context_based_linker.MutableDocument attribute) (medcat2.components.linking.context_based_linker.MutableEntity attribute) (medcat2.components.linking.no_action_linker.AbstractCoreComponent attribute) (medcat2.components.linking.no_action_linker.BaseTokenizer attribute) (medcat2.components.linking.no_action_linker.MutableDocument attribute) (medcat2.components.linking.no_action_linker.NoActionLinker attribute) (medcat2.components.linking.vector_context_model.MutableDocument attribute) (medcat2.components.linking.vector_context_model.MutableEntity attribute) (medcat2.components.linking.vector_context_model.MutableToken attribute) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.dict_based_ner.BaseTokenizer attribute) (medcat2.components.ner.dict_based_ner.MutableDocument attribute) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.trf.deid.TransformersNER attribute) (medcat2.components.ner.trf.model.MutableDocument attribute) (medcat2.components.ner.trf.model.TransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent attribute) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.MutableDocument attribute) (medcat2.components.ner.trf.transformers_ner.MutableEntity attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer attribute) (medcat2.components.ner.vocab_based_annotator.MutableDocument attribute) (medcat2.components.ner.vocab_based_annotator.MutableEntity attribute) (medcat2.components.ner.vocab_based_annotator.MutableToken attribute) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.vocab_based_ner.BaseTokenizer attribute) (medcat2.components.ner.vocab_based_ner.MutableDocument attribute) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.components.normalizing.normalizer.AbstractCoreComponent attribute) (medcat2.components.normalizing.normalizer.BaseTokenizer attribute) (medcat2.components.normalizing.normalizer.MutableDocument attribute) (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) (medcat2.components.tagging.tagger.AbstractCoreComponent attribute) (medcat2.components.tagging.tagger.BaseTokenizer attribute) (medcat2.components.tagging.tagger.MutableDocument attribute) (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) (medcat2.components.types.AbstractCoreComponent attribute) (medcat2.components.types.BaseComponent attribute) (medcat2.components.types.BaseTokenizer attribute) (medcat2.components.types.CoreComponent attribute) (medcat2.components.types.HashableComponet attribute) (medcat2.components.types.MutableDocument attribute) (medcat2.components.types.MutableEntity attribute) (medcat2.components.types.Registry attribute) (medcat2.components.types.TrainableComponent attribute) (medcat2.pipeline.pipeline.AbstractCoreComponent attribute) (medcat2.pipeline.pipeline.AddonComponent attribute) (medcat2.pipeline.pipeline.BaseComponent attribute) (medcat2.pipeline.pipeline.BaseTokenizer attribute) (medcat2.pipeline.pipeline.CoreComponent attribute) (medcat2.pipeline.pipeline.DelegatingTokenizer attribute) (medcat2.pipeline.pipeline.MutableDocument attribute) (medcat2.pipeline.pipeline.MutableEntity attribute) (medcat2.pipeline.pipeline.MutableToken attribute) (medcat2.pipeline.pipeline.Serialisable attribute) (medcat2.preprocessors.cleaners.BaseTokenizer attribute) (medcat2.preprocessors.cleaners.LCDBMaker attribute) (medcat2.preprocessors.cleaners.LGeneral attribute) (medcat2.preprocessors.cleaners.LPreprocessing attribute) (medcat2.preprocessors.cleaners.MutableDocument attribute) (medcat2.stats.stats.MutableDocument attribute) (medcat2.stats.stats.MutableEntity attribute) (medcat2.storage.serialisables.ManualSerialisable attribute) (medcat2.storage.serialisables.Serialisable attribute) (medcat2.storage.serialisers.ManualSerialisable attribute) (medcat2.storage.serialisers.Serialisable attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseDocument attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseToken attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken attribute) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken attribute) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseDocument attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseToken attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableToken attribute) (medcat2.tokenizing.tokenizers.BaseTokenizer attribute) (medcat2.tokenizing.tokenizers.MutableDocument attribute) (medcat2.tokenizing.tokenizers.MutableEntity attribute) (medcat2.tokenizing.tokenizers.MutableToken attribute) (medcat2.tokenizing.tokenizers.Registry attribute) (medcat2.tokenizing.tokens.BaseDocument attribute) (medcat2.tokenizing.tokens.BaseEntity attribute) (medcat2.tokenizing.tokens.BaseToken attribute) (medcat2.tokenizing.tokens.MutableDocument attribute) (medcat2.tokenizing.tokens.MutableEntity attribute) (medcat2.tokenizing.tokens.MutableToken attribute) (medcat2.trainer.MutableDocument attribute) (medcat2.trainer.MutableEntity attribute) (medcat2.trainer.MutableToken attribute) (medcat2.trainer.TrainableComponent attribute) (medcat2.utils.data_utils.MutableDocument attribute) (medcat2.utils.data_utils.MutableEntity attribute) (medcat2.utils.default_args.BaseTokenizer attribute) (medcat2.utils.legacy.conversion_all.NoActionLinker attribute) (medcat2.utils.legacy.convert_deid.BaseTokenizer attribute) (medcat2.utils.legacy.convert_deid.TransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) (medcat2.utils.postprocessing.MutableDocument attribute) (medcat2.utils.postprocessing.MutableEntity attribute) (medcat2.utils.registry.Registry attribute) _is_punct (medcat2.tokenizing.regex_impl.tokenizer.Token attribute) _is_runtime_protocol (medcat2.cat.AbstractCoreComponent attribute) (medcat2.cat.AddonComponent attribute) (medcat2.cat.HashableComponet attribute) (medcat2.cat.MutableDocument attribute) (medcat2.cat.MutableEntity attribute) (medcat2.components.addons.addons.AddonComponent attribute) (medcat2.components.addons.addons.BaseComponent attribute) (medcat2.components.addons.addons.MutableEntity attribute) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument attribute) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity attribute) (medcat2.components.linking.context_based_linker.AbstractCoreComponent attribute) (medcat2.components.linking.context_based_linker.BaseTokenizer attribute) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.linking.context_based_linker.MutableDocument attribute) (medcat2.components.linking.context_based_linker.MutableEntity attribute) (medcat2.components.linking.no_action_linker.AbstractCoreComponent attribute) (medcat2.components.linking.no_action_linker.BaseTokenizer attribute) (medcat2.components.linking.no_action_linker.MutableDocument attribute) (medcat2.components.linking.no_action_linker.NoActionLinker attribute) (medcat2.components.linking.vector_context_model.MutableDocument attribute) (medcat2.components.linking.vector_context_model.MutableEntity attribute) (medcat2.components.linking.vector_context_model.MutableToken attribute) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.dict_based_ner.BaseTokenizer attribute) (medcat2.components.ner.dict_based_ner.MutableDocument attribute) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.trf.deid.TransformersNER attribute) (medcat2.components.ner.trf.model.MutableDocument attribute) (medcat2.components.ner.trf.model.TransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent attribute) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.MutableDocument attribute) (medcat2.components.ner.trf.transformers_ner.MutableEntity attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer attribute) (medcat2.components.ner.vocab_based_annotator.MutableDocument attribute) (medcat2.components.ner.vocab_based_annotator.MutableEntity attribute) (medcat2.components.ner.vocab_based_annotator.MutableToken attribute) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.vocab_based_ner.BaseTokenizer attribute) (medcat2.components.ner.vocab_based_ner.MutableDocument attribute) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.components.normalizing.normalizer.AbstractCoreComponent attribute) (medcat2.components.normalizing.normalizer.BaseTokenizer attribute) (medcat2.components.normalizing.normalizer.MutableDocument attribute) (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) (medcat2.components.tagging.tagger.AbstractCoreComponent attribute) (medcat2.components.tagging.tagger.BaseTokenizer attribute) (medcat2.components.tagging.tagger.MutableDocument attribute) (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) (medcat2.components.types.AbstractCoreComponent attribute) (medcat2.components.types.BaseComponent attribute) (medcat2.components.types.BaseTokenizer attribute) (medcat2.components.types.CoreComponent attribute) (medcat2.components.types.HashableComponet attribute) (medcat2.components.types.MutableDocument attribute) (medcat2.components.types.MutableEntity attribute) (medcat2.components.types.TrainableComponent attribute) (medcat2.pipeline.pipeline.AbstractCoreComponent attribute) (medcat2.pipeline.pipeline.AddonComponent attribute) (medcat2.pipeline.pipeline.BaseComponent attribute) (medcat2.pipeline.pipeline.BaseTokenizer attribute) (medcat2.pipeline.pipeline.CoreComponent attribute) (medcat2.pipeline.pipeline.DelegatingTokenizer attribute) (medcat2.pipeline.pipeline.MutableDocument attribute) (medcat2.pipeline.pipeline.MutableEntity attribute) (medcat2.pipeline.pipeline.MutableToken attribute) (medcat2.pipeline.pipeline.Serialisable attribute) (medcat2.preprocessors.cleaners.BaseTokenizer attribute) (medcat2.preprocessors.cleaners.LCDBMaker attribute) (medcat2.preprocessors.cleaners.LGeneral attribute) (medcat2.preprocessors.cleaners.LPreprocessing attribute) (medcat2.preprocessors.cleaners.MutableDocument attribute) (medcat2.stats.stats.MutableDocument attribute) (medcat2.stats.stats.MutableEntity attribute) (medcat2.storage.serialisables.ManualSerialisable attribute) (medcat2.storage.serialisables.Serialisable attribute) (medcat2.storage.serialisers.ManualSerialisable attribute) (medcat2.storage.serialisers.Serialisable attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseDocument attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseToken attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken attribute) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken attribute) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseDocument attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity attribute) (medcat2.tokenizing.spacy_impl.tokens.BaseToken attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableToken attribute) (medcat2.tokenizing.tokenizers.BaseTokenizer attribute) (medcat2.tokenizing.tokenizers.MutableDocument attribute) (medcat2.tokenizing.tokenizers.MutableEntity attribute) (medcat2.tokenizing.tokenizers.MutableToken attribute) (medcat2.tokenizing.tokens.BaseDocument attribute) (medcat2.tokenizing.tokens.BaseEntity attribute) (medcat2.tokenizing.tokens.BaseToken attribute) (medcat2.tokenizing.tokens.MutableDocument attribute) (medcat2.tokenizing.tokens.MutableEntity attribute) (medcat2.tokenizing.tokens.MutableToken attribute) (medcat2.trainer.MutableDocument attribute) (medcat2.trainer.MutableEntity attribute) (medcat2.trainer.MutableToken attribute) (medcat2.trainer.TrainableComponent attribute) (medcat2.utils.data_utils.MutableDocument attribute) (medcat2.utils.data_utils.MutableEntity attribute) (medcat2.utils.default_args.BaseTokenizer attribute) (medcat2.utils.legacy.conversion_all.NoActionLinker attribute) (medcat2.utils.legacy.convert_deid.BaseTokenizer attribute) (medcat2.utils.legacy.convert_deid.TransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) (medcat2.utils.postprocessing.MutableDocument attribute) (medcat2.utils.postprocessing.MutableEntity attribute) _is_suitable_in_dict() (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.config.config.SerialisingStrategy method) (medcat2.storage.serialisables.SerialisingStrategy method) _is_suitable_part() (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.config.config.SerialisingStrategy method) (medcat2.storage.serialisables.SerialisingStrategy method) _iter() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) _iter_obj_items() (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.config.config.SerialisingStrategy method) (medcat2.storage.serialisables.SerialisingStrategy method) _iter_obj_values() (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.config.config.SerialisingStrategy method) (medcat2.storage.serialisables.SerialisingStrategy method) _keys_to_ignore_on_load_unexpected (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) _lazy_defaults (medcat2.components.addons.addons.Registry attribute) (medcat2.components.types.Registry attribute) (medcat2.tokenizing.tokenizers.Registry attribute) (medcat2.utils.registry.Registry attribute) _load_addon() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) _load_component() (in module medcat2.components.ner.trf.transformers_ner) _load_from_state_dict() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _load_legacy() (in module medcat2.utils.legacy.convert_meta_cat) _load_saved_core_component() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) _load_state_dict_post_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _load_state_dict_pre_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _load_tokenizer() (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) _main (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) _make_changes() (in module medcat2.utils.legacy.convert_config) _maybe_warn_non_full_backward_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _mc (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) _merge_examples() (in module medcat2.stats.kfold) _META_ANNS_PATH (in module medcat2.components.addons.meta_cat.meta_cat) _missing_() (medcat2.cat.AvailableSerialisers class method) (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy class method) (medcat2.components.linking.context_based_linker.CoreComponentType class method) (medcat2.components.linking.no_action_linker.CoreComponentType class method) (medcat2.components.ner.dict_based_ner.CoreComponentType class method) (medcat2.components.ner.trf.deid.CoreComponentType class method) (medcat2.components.ner.trf.model.CoreComponentType class method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers class method) (medcat2.components.ner.trf.transformers_ner.CoreComponentType class method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy class method) (medcat2.components.ner.vocab_based_ner.CoreComponentType class method) (medcat2.components.normalizing.normalizer.CoreComponentType class method) (medcat2.components.tagging.tagger.CoreComponentType class method) (medcat2.components.types.CoreComponentType class method) (medcat2.config.config.SerialisingStrategy class method) (medcat2.config.config_meta_cat.AvailableSerialisers class method) (medcat2.pipeline.pipeline.AvailableSerialisers class method) (medcat2.pipeline.pipeline.CoreComponentType class method) (medcat2.stats.kfold.SplitType class method) (medcat2.storage.serialisables.SerialisingStrategy class method) (medcat2.storage.serialisers.AvailableSerialisers class method) (medcat2.trainer.CoreComponentType class method) (medcat2.utils.default_args.CoreComponentType class method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers class method) (medcat2.utils.legacy.conversion_all.CoreComponentType class method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers class method) _model_state_dict (medcat2.components.addons.meta_cat.meta_cat.MetaCAT property) (medcat2.utils.legacy.convert_meta_cat.MetaCAT property) _modules (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _move_identicals() (in module medcat2.utils.legacy.convert_config) _move_partials() (in module medcat2.utils.legacy.convert_config) _name (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) _named_members() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _nlp (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer attribute) _non_persistent_buffers_set (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _parameters (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _perform_epoch() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) _pipeline (medcat2.cat.CAT attribute) (medcat2.cat.Trainer attribute) (medcat2.components.ner.trf.deid.CAT attribute) (medcat2.components.ner.trf.model.CAT attribute) (medcat2.stats.kfold.CAT attribute) (medcat2.stats.stats.CAT attribute) (medcat2.trainer.Trainer attribute) (medcat2.utils.legacy.conversion_all.CAT attribute) _pn_configs (medcat2.cat.Trainer property) (medcat2.trainer.Trainer property) _prepare_dataset() (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) _preprocess_annotations() (medcat2.stats.stats.StatsBuilder method) _preprocess_center_tokens() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) _preprocess_disamb_similarities() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) _process() (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) _process_anns_norm() (medcat2.stats.stats.StatsBuilder method) _process_doc() (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) _process_entity_inference() (medcat2.components.linking.context_based_linker.Linker method) _process_entity_nt_w_name() (medcat2.components.linking.context_based_linker.Linker method) _process_entity_train() (medcat2.components.linking.context_based_linker.Linker method) _process_p_anns() (medcat2.stats.stats.StatsBuilder method) _reapply_state() (in module medcat2.utils.cdb_state) _rebuild_automaton() (medcat2.components.ner.dict_based_ner.NER method) _rebuild_index() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) _recrate_pipe() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) _register_load_state_dict_pre_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _register_state_dict_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _relocate() (in module medcat2.utils.legacy.convert_config) _remove_names() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) _replicate_for_data_parallel() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _reset() (medcat2.utils.data_utils.TestTrainSplitter method) _reset_cui_counts() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) _reset_stats() (medcat2.stats.stats.StatsBuilder method) _reset_subnames() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) _safe_setattr() (in module medcat2.utils.legacy.convert_config) _sanitise_sets() (in module medcat2.utils.legacy.convert_config) _save_component() (in module medcat2.components.ner.trf.transformers_ner) _save_to_state_dict() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _session (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) _set_attr() (in module medcat2.utils.cdb_state) _set_meta_anns() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) _SHARE_TOKENS_PATH (in module medcat2.components.addons.meta_cat.meta_cat) _should_add_to_test() (medcat2.utils.data_utils.TestTrainSplitter method) _should_change_name() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) _similarity() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) _slow_forward() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) _split_doc_train_test() (medcat2.utils.data_utils.TestTrainSplitter method) _split_generators() (medcat2.utils.ner.transformers_ner.TransformersDatasetNER method) _start_char_index (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) _start_index (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.Token attribute) _state_dict_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _state_dict_pre_hooks (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _subnames (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) _targets() (medcat2.stats.kfold.PerAnnsFoldCreator method) _text (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.Token attribute) _text_with_ws (medcat2.tokenizing.regex_impl.tokenizer.Token attribute) _to_skip (medcat2.tokenizing.regex_impl.tokenizer.Token attribute) _token_index (medcat2.tokenizing.regex_impl.tokenizer.Token attribute) _tokenizer (medcat2.cat.Pipeline attribute) (medcat2.model_creation.cdb_maker.Pipeline attribute) (medcat2.pipeline.pipeline.Pipeline attribute) (medcat2.trainer.Pipeline attribute) _TOKENIZERS_REGISTRY (in module medcat2.tokenizing.tokenizers) _tokens (medcat2.tokenizing.regex_impl.tokenizer.Document attribute) _tokens2vecs() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) _train() (medcat2.components.linking.context_based_linker.Linker method) _train_on_doc() (medcat2.components.linking.context_based_linker.Linker method) _train_supervised_for_project() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) _train_supervised_for_project2() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) _train_unsupervised() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) _trainer (medcat2.cat.CAT attribute) (medcat2.components.ner.trf.deid.CAT attribute) (medcat2.components.ner.trf.model.CAT attribute) (medcat2.stats.kfold.CAT attribute) (medcat2.stats.stats.CAT attribute) (medcat2.utils.legacy.conversion_all.CAT attribute) _type (medcat2.components.addons.addons.Registry attribute) (medcat2.components.types.Registry attribute) (medcat2.tokenizing.tokenizers.Registry attribute) (medcat2.utils.registry.Registry attribute) _update_dict() (in module medcat2.preprocessors.cleaners) _update_installed_dependencies_recursive() (in module medcat2.utils.envsnapshot) _validate() (medcat2.utils.legacy.conversion_all.Converter method) (medcat2.utils.legacy.legacy_converter.Converter method) _version (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) _versioning() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) _weight_calculator (medcat2.stats.kfold.WeightedDocumentsCreator attribute) _weighted_docs (medcat2.stats.kfold.WeightedDocumentsCreator attribute) _wrapped_call_impl() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method)

A

AbstractCoreComponent (class in medcat2.cat) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.no_action_linker) (class in medcat2.components.ner.dict_based_ner) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.components.ner.vocab_based_ner) (class in medcat2.components.normalizing.normalizer) (class in medcat2.components.tagging.tagger) (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) AbstractManualSerialisable (class in medcat2.storage.serialisables) AbstractSerialisable (class in medcat2.cat) (class in medcat2.cdb.cdb) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.linking.vector_context_model) (class in medcat2.storage.serialisables) (class in medcat2.utils.envsnapshot) (class in medcat2.vocab) acc (medcat2.cat.Entity attribute) (medcat2.data.entities.Entity attribute) add() (medcat2.stats.kfold.PerCUIMetrics method) add_addon() (medcat2.cat.CAT method) (medcat2.cat.Pipeline method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.trainer.Pipeline method) (medcat2.utils.legacy.conversion_all.CAT method) add_and_train_concept() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) add_module() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) add_names() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) add_new_concepts() (medcat2.components.ner.trf.deid.DeIdModel method) (medcat2.components.ner.trf.deid.NerModel method) (medcat2.components.ner.trf.model.NerModel method) add_sup_training() (medcat2.config.config.ModelMeta method) (medcat2.utils.cdb_state.ModelMeta method) add_types() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) add_unsup_training() (medcat2.config.config.ModelMeta method) (medcat2.utils.cdb_state.ModelMeta method) add_vec() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) add_word() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) add_words() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method)

addl_info (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.stats.stats.StatsBuilder attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) addon_type (medcat2.cat.AddonComponent property) (medcat2.components.addons.addons.AddonComponent property) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent property) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.pipeline.pipeline.AddonComponent property) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) AddonComponent (class in medcat2.cat) (class in medcat2.components.addons.addons) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.pipeline.pipeline) addons (medcat2.config.config.Components attribute) all_ents (medcat2.cat.MutableDocument property) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument property) (medcat2.components.linking.context_based_linker.MutableDocument property) (medcat2.components.linking.no_action_linker.MutableDocument property) (medcat2.components.linking.vector_context_model.MutableDocument property) (medcat2.components.ner.dict_based_ner.MutableDocument property) (medcat2.components.ner.trf.model.MutableDocument property) (medcat2.components.ner.trf.transformers_ner.MutableDocument property) (medcat2.components.ner.vocab_based_annotator.MutableDocument property) (medcat2.components.ner.vocab_based_ner.MutableDocument property) (medcat2.components.normalizing.normalizer.MutableDocument property) (medcat2.components.tagging.tagger.MutableDocument property) (medcat2.components.types.MutableDocument property) (medcat2.pipeline.pipeline.MutableDocument property) (medcat2.preprocessors.cleaners.MutableDocument property) (medcat2.stats.stats.MutableDocument property) (medcat2.tokenizing.regex_impl.tokenizer.Document attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument property) (medcat2.tokenizing.spacy_impl.tokenizers.Document attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument property) (medcat2.tokenizing.spacy_impl.tokens.Document attribute) (medcat2.tokenizing.tokenizers.MutableDocument property) (medcat2.tokenizing.tokens.MutableDocument property) (medcat2.trainer.MutableDocument property) (medcat2.utils.data_utils.MutableDocument property) (medcat2.utils.postprocessing.MutableDocument property) ALLOWED_STATUS (medcat2.cdb.cdb.ST attribute) (medcat2.components.linking.context_based_linker.ST attribute) (medcat2.components.linking.vector_context_model.ST attribute) (medcat2.utils.defaults.StatusTypes attribute) alpha (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) always_calculate_similarity (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) annotate_name() (in module medcat2.components.ner.vocab_based_annotator) annotation_output (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.config.Config attribute) (medcat2.config.config.Config attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) AnnotationOutput (class in medcat2.config.config) annotations (medcat2.data.mctexport.MedCATTrainerExportDocument attribute) (medcat2.stats.kfold.MedCATTrainerExportDocument attribute) ANNOTATIONS (medcat2.stats.kfold.SplitType attribute) annotations (medcat2.stats.stats.MedCATTrainerExportDocument attribute) (medcat2.trainer.MedCATTrainerExportDocument attribute) (medcat2.utils.data_utils.MedCATTrainerExportDocument attribute) apply() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) apply_cdb_state() (in module medcat2.utils.cdb_state) args (medcat2.utils.legacy.convert_cdb.LegacyClassNotFound attribute) auto_save_model (medcat2.config.config_meta_cat.Train attribute) AUTOMATIC (medcat2.cdb.cdb.ST attribute) (medcat2.components.linking.context_based_linker.ST attribute) (medcat2.components.linking.vector_context_model.ST attribute) (medcat2.utils.defaults.StatusTypes attribute) automaton (medcat2.components.ner.dict_based_ner.NER attribute) AvailableSerialisers (class in medcat2.cat) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.config.config_meta_cat) (class in medcat2.pipeline.pipeline) (class in medcat2.storage.serialisers) (class in medcat2.utils.legacy.conversion_all) (class in medcat2.utils.legacy.legacy_converter) average_confidence (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute)

B

base (medcat2.cat.MutableDocument property) (medcat2.cat.MutableEntity property) (medcat2.components.addons.addons.MutableEntity property) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument property) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity property) (medcat2.components.linking.context_based_linker.MutableDocument property) (medcat2.components.linking.context_based_linker.MutableEntity property) (medcat2.components.linking.no_action_linker.MutableDocument property) (medcat2.components.linking.vector_context_model.MutableDocument property) (medcat2.components.linking.vector_context_model.MutableEntity property) (medcat2.components.linking.vector_context_model.MutableToken property) (medcat2.components.ner.dict_based_ner.MutableDocument property) (medcat2.components.ner.trf.model.MutableDocument property) (medcat2.components.ner.trf.transformers_ner.MutableDocument property) (medcat2.components.ner.trf.transformers_ner.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableDocument property) (medcat2.components.ner.vocab_based_annotator.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableToken property) (medcat2.components.ner.vocab_based_ner.MutableDocument property) (medcat2.components.normalizing.normalizer.MutableDocument property) (medcat2.components.tagging.tagger.MutableDocument property) (medcat2.components.types.MutableDocument property) (medcat2.components.types.MutableEntity property) (medcat2.pipeline.pipeline.MutableDocument property) (medcat2.pipeline.pipeline.MutableEntity property) (medcat2.pipeline.pipeline.MutableToken property) (medcat2.preprocessors.cleaners.MutableDocument property) (medcat2.stats.stats.MutableDocument property) (medcat2.stats.stats.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Document property) (medcat2.tokenizing.regex_impl.tokenizer.Entity property) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument property) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Document property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.Document property) (medcat2.tokenizing.spacy_impl.tokens.Entity property) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokens.MutableToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokenizers.MutableDocument property) (medcat2.tokenizing.tokenizers.MutableEntity property) (medcat2.tokenizing.tokenizers.MutableToken property) (medcat2.tokenizing.tokens.MutableDocument property) (medcat2.tokenizing.tokens.MutableEntity property) (medcat2.tokenizing.tokens.MutableToken property) (medcat2.trainer.MutableDocument property) (medcat2.trainer.MutableEntity property) (medcat2.trainer.MutableToken property) (medcat2.utils.data_utils.MutableDocument property) (medcat2.utils.data_utils.MutableEntity property) (medcat2.utils.postprocessing.MutableDocument property) (medcat2.utils.postprocessing.MutableEntity property)

base_tokenizer (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) BaseComponent (class in medcat2.components.addons.addons) (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) BaseDocument (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) BaseEntity (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) BaseToken (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) BaseTokenizer (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.no_action_linker) (class in medcat2.components.ner.dict_based_ner) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.components.ner.vocab_based_annotator) (class in medcat2.components.ner.vocab_based_ner) (class in medcat2.components.normalizing.normalizer) (class in medcat2.components.tagging.tagger) (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) (class in medcat2.preprocessors.cleaners) (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.tokenizers) (class in medcat2.utils.default_args) (class in medcat2.utils.legacy.convert_deid) (class in medcat2.utils.legacy.convert_meta_cat) BasicSpellChecker (class in medcat2.components.normalizing.normalizer) batch_generator() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT static method) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent static method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT static method) batch_size (medcat2.config.config_meta_cat.Train attribute) batch_size_eval (medcat2.config.config_meta_cat.General attribute) bert (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) BertForMetaAnnotation (class in medcat2.components.addons.meta_cat.models) bfloat16() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) buffers() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) BUILDER_CONFIGS (medcat2.utils.ner.transformers_ner.TransformersDatasetNER attribute)

C

C (in module medcat2.config.config) calc_matrix() (in module medcat2.utils.vocab_utils) calculate_dynamic_threshold (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) calculate_label_map() (medcat2.components.ner.trf.tokenizer.TransformersTokenizer method) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer method) call_super_init (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) callback_iterator() (in module medcat2.config.config) (in module medcat2.utils.iterutils) caller (medcat2.cat.Trainer attribute) (medcat2.trainer.Trainer attribute) candidates() (medcat2.components.normalizing.normalizer.BasicSpellChecker method) captured_state_cdb() (in module medcat2.stats.kfold) (in module medcat2.utils.cdb_state) CAT (class in medcat2.cat) (class in medcat2.components.ner.trf.deid) (class in medcat2.components.ner.trf.model) (class in medcat2.stats.kfold) (class in medcat2.stats.stats) (class in medcat2.utils.legacy.conversion_all) cat (medcat2.components.ner.trf.deid.DeIdModel attribute) (medcat2.components.ner.trf.deid.NerModel attribute) (medcat2.components.ner.trf.model.NerModel attribute) category_name (medcat2.config.config_meta_cat.General attribute) category_undersample (medcat2.config.config_meta_cat.Model attribute) category_value2id (medcat2.config.config_meta_cat.General attribute) CDB (class in medcat2.cat) (class in medcat2.cdb) (class in medcat2.cdb.cdb) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.no_action_linker) (class in medcat2.components.ner.dict_based_ner) (class in medcat2.components.ner.trf.deid) (class in medcat2.components.ner.trf.helpers) (class in medcat2.components.ner.trf.model) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.components.ner.vocab_based_annotator) (class in medcat2.components.ner.vocab_based_ner) (class in medcat2.components.normalizing.normalizer) (class in medcat2.components.tagging.tagger) (class in medcat2.components.types) (class in medcat2.model_creation.cdb_maker) (class in medcat2.pipeline.pipeline) (class in medcat2.trainer) (class in medcat2.utils.data_utils) (class in medcat2.utils.default_args) (class in medcat2.utils.legacy.convert_cdb) (class in medcat2.utils.legacy.convert_deid) (class in medcat2.utils.vocab_utils) cdb (medcat2.cat.CAT attribute) (medcat2.cat.Pipeline attribute) (medcat2.cat.Trainer attribute) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.trf.deid.CAT attribute) (medcat2.components.ner.trf.deid.DeIdModel property) (medcat2.components.ner.trf.deid.NerModel property) (medcat2.components.ner.trf.model.CAT attribute) (medcat2.components.ner.trf.model.NerModel property) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent attribute) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.model_creation.cdb_maker.Pipeline attribute) (medcat2.pipeline.pipeline.Pipeline attribute) (medcat2.stats.kfold.CAT attribute) (medcat2.stats.stats.CAT attribute) (medcat2.trainer.Pipeline attribute) (medcat2.trainer.Trainer attribute) (medcat2.utils.data_utils.TestTrainSplitter attribute) (medcat2.utils.legacy.conversion_all.CAT attribute) cdb_maker (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.config.Config attribute) (medcat2.config.config.Config attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) cdb_name (medcat2.utils.legacy.conversion_all.Converter attribute) (medcat2.utils.legacy.legacy_converter.Converter attribute) CDBInfo (in module medcat2.cdb.cdb) (in module medcat2.data.model_card) CDBMaker (class in medcat2.config.config) (class in medcat2.model_creation.cdb_maker) (class in medcat2.trainer) CDBState (in module medcat2.utils.cdb_state) char_index (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) check_filters() (medcat2.config.config.LinkingFilters method) (medcat2.stats.stats.LinkingFilters method) (medcat2.utils.filters.LinkingFilters method) check_ser_type() (medcat2.storage.serialisers.DillSerialiser method) (medcat2.storage.serialisers.Serialiser method) check_upper_case_names (medcat2.config.config.Ner attribute) children() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) chunking_overlap_window (medcat2.config.config_transformers_ner.General attribute) class_weights (medcat2.config.config_meta_cat.Train attribute) clear() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) clogger (in module medcat2.utils.legacy.legacy_converter) cls (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException attribute) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException attribute) (medcat2.tokenizing.tokens.UnregisteredDataPathException attribute) cnf_cm (medcat2.model_creation.cdb_maker.CDBMaker attribute) cnf_p (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) cntx_left (medcat2.config.config_meta_cat.General attribute) cntx_right (medcat2.config.config_meta_cat.General attribute) CollateAndPadNER (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.utils.ner.data_collator) comp_name (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) comp_order (medcat2.config.config.Components attribute) compile() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) ComponentConfig (class in medcat2.components.addons.addons) (class in medcat2.config.config) (class in medcat2.config.config_meta_cat) (class in medcat2.pipeline.pipeline) (class in medcat2.utils.default_args) Components (class in medcat2.config.config) components (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.config.Config attribute) (medcat2.config.config.Config attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.DelegatingTokenizer attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) COMPONENTS_FOLDER (in module medcat2.cat) (in module medcat2.pipeline.pipeline) (in module medcat2.utils.defaults) compute_class_weights (medcat2.config.config_meta_cat.Train attribute) confidence (medcat2.cat.MutableEntity property) (medcat2.components.addons.addons.MutableEntity property) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument attribute) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity property) (medcat2.components.linking.context_based_linker.MutableEntity property) (medcat2.components.linking.vector_context_model.MutableEntity property) (medcat2.components.ner.trf.transformers_ner.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableEntity property) (medcat2.components.types.MutableEntity property) (medcat2.data.entities.MetaAnnotation attribute) (medcat2.pipeline.pipeline.MutableEntity property) (medcat2.stats.stats.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity property) (medcat2.tokenizing.tokenizers.MutableEntity property) (medcat2.tokenizing.tokens.MutableEntity property) (medcat2.trainer.MutableEntity property) (medcat2.utils.data_utils.MutableEntity property) (medcat2.utils.postprocessing.MutableEntity property) Config (class in medcat2.cat) (class in medcat2.cdb.cdb) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.ner.trf.helpers) (class in medcat2.components.ner.trf.model) (class in medcat2.components.ner.vocab_based_annotator) (class in medcat2.components.normalizing.normalizer) (class in medcat2.config) (class in medcat2.config.config) (class in medcat2.model_creation.cdb_maker) (class in medcat2.pipeline.pipeline) (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.tokenizers) (class in medcat2.utils.default_args) (class in medcat2.utils.legacy.convert_cdb) (class in medcat2.utils.legacy.convert_config) config (medcat2.cat.AddonComponent attribute) (medcat2.cat.CAT attribute) (medcat2.cat.CDB attribute) (medcat2.cat.Pipeline attribute) (medcat2.cat.Trainer attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.addons.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.context_based_linker.ContextModel attribute) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.linking.vector_context_model.ContextModel attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.trf.deid.CAT attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.deid.DeIdModel property) (medcat2.components.ner.trf.deid.NerModel property) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CAT attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.model.NerModel property) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.components.normalizing.normalizer.BasicSpellChecker attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.model_creation.cdb_maker.CDBMaker attribute) (medcat2.model_creation.cdb_maker.Pipeline attribute) (medcat2.pipeline.pipeline.AddonComponent attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.pipeline.pipeline.Pipeline attribute) (medcat2.stats.kfold.CAT attribute) (medcat2.stats.stats.CAT attribute) (medcat2.trainer.CDB attribute) (medcat2.trainer.Pipeline attribute) (medcat2.trainer.Trainer attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.conversion_all.CAT attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCAT attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) (medcat2.utils.vocab_utils.CDB attribute) CONFIG_KEEP_IDENTICAL (in module medcat2.utils.legacy.convert_config) CONFIG_MOVE (in module medcat2.utils.legacy.convert_config) config_name (medcat2.utils.legacy.conversion_all.Converter attribute) (medcat2.utils.legacy.legacy_converter.Converter attribute) ConfigMetaCAT (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.addons.meta_cat.ml_utils) (class in medcat2.components.addons.meta_cat.models) (class in medcat2.config.config_meta_cat) (class in medcat2.pipeline.pipeline) (class in medcat2.utils.legacy.convert_meta_cat) ConfigMetaCAT.Config (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.addons.meta_cat.ml_utils) (class in medcat2.components.addons.meta_cat.models) (class in medcat2.config.config_meta_cat) (class in medcat2.pipeline.pipeline) (class in medcat2.utils.legacy.convert_meta_cat) ConfigTransformersNER (class in medcat2.components.ner.trf.deid) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.config.config_transformers_ner) (class in medcat2.utils.legacy.convert_deid) ConfigTransformersNER.Config (class in medcat2.components.ner.trf.deid) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.config.config_transformers_ner) (class in medcat2.utils.legacy.convert_deid) construct() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method)

CONTAINS_NUMBER (in module medcat2.components.normalizing.normalizer) context_center (medcat2.cat.Entity attribute) (medcat2.data.entities.Entity attribute) context_ignore_center_tokens (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) context_left (medcat2.cat.Entity attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.data.entities.Entity attribute) context_model (medcat2.components.linking.context_based_linker.Linker attribute) context_right (medcat2.cat.Entity attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.data.entities.Entity attribute) context_similarity (medcat2.cat.Entity attribute) (medcat2.cat.MutableEntity property) (medcat2.components.addons.addons.MutableEntity property) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity property) (medcat2.components.linking.context_based_linker.MutableEntity property) (medcat2.components.linking.vector_context_model.MutableEntity property) (medcat2.components.ner.trf.transformers_ner.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableEntity property) (medcat2.components.types.MutableEntity property) (medcat2.data.entities.Entity attribute) (medcat2.pipeline.pipeline.MutableEntity property) (medcat2.stats.stats.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity property) (medcat2.tokenizing.tokenizers.MutableEntity property) (medcat2.tokenizing.tokens.MutableEntity property) (medcat2.trainer.MutableEntity property) (medcat2.utils.data_utils.MutableEntity property) (medcat2.utils.postprocessing.MutableEntity property) context_vector_sizes (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) context_vector_weights (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) context_vectors (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) ContextModel (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.vector_context_model) convert() (medcat2.utils.legacy.conversion_all.Converter method) (medcat2.utils.legacy.legacy_converter.Converter method) convert_context_vectors() (in module medcat2.utils.vocab_utils) convert_data() (in module medcat2.utils.legacy.convert_cdb) convert_vec() (in module medcat2.utils.vocab_utils) convert_vocab() (in module medcat2.utils.vocab_utils) convert_vocab_vector_size() (in module medcat2.utils.vocab_utils) Converter (class in medcat2.utils.legacy.conversion_all) (class in medcat2.utils.legacy.legacy_converter) copy() (medcat2.cat.Config method) (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.Config method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.LinkingFilters method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) copy_cdb_state() (in module medcat2.utils.cdb_state) CoreComponent (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) CoreComponentType (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.no_action_linker) (class in medcat2.components.ner.dict_based_ner) (class in medcat2.components.ner.trf.deid) (class in medcat2.components.ner.trf.model) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.components.ner.vocab_based_ner) (class in medcat2.components.normalizing.normalizer) (class in medcat2.components.tagging.tagger) (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) (class in medcat2.trainer) (class in medcat2.utils.default_args) (class in medcat2.utils.legacy.conversion_all) count() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) count_all_annotations() (in module medcat2.data.mctexport) (in module medcat2.stats.kfold) count_all_docs() (in module medcat2.data.mctexport) (in module medcat2.stats.kfold) count_anns_per_concept() (in module medcat2.components.ner.trf.helpers) (in module medcat2.data.mctexport) count_train (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.cdb.NameInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.cdb.concepts.NameInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.components.linking.vector_context_model.NameInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) (medcat2.utils.cdb_state.NameInfo attribute) cpu() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) cpu_arcitecture (medcat2.config.config.Environment attribute) (medcat2.utils.envsnapshot.Environment attribute) create() (medcat2.components.ner.trf.deid.DeIdModel class method) create_addon() (in module medcat2.components.addons.addons) (in module medcat2.pipeline.pipeline) create_batch_piped_data() (in module medcat2.components.addons.meta_cat.ml_utils) create_core_component() (in module medcat2.components.types) (in module medcat2.pipeline.pipeline) create_entity() (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer method) (medcat2.components.linking.context_based_linker.BaseTokenizer method) (medcat2.components.linking.no_action_linker.BaseTokenizer method) (medcat2.components.ner.dict_based_ner.BaseTokenizer method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer method) (medcat2.components.normalizing.normalizer.BaseTokenizer method) (medcat2.components.tagging.tagger.BaseTokenizer method) (medcat2.components.types.BaseTokenizer method) (medcat2.pipeline.pipeline.BaseTokenizer method) (medcat2.pipeline.pipeline.DelegatingTokenizer method) (medcat2.preprocessors.cleaners.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer method) (medcat2.tokenizing.tokenizers.BaseTokenizer method) (medcat2.utils.default_args.BaseTokenizer method) (medcat2.utils.legacy.convert_deid.BaseTokenizer method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer method) create_eval_pipeline() (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) create_folds() (medcat2.stats.kfold.FoldCreator method) (medcat2.stats.kfold.PerAnnsFoldCreator method) (medcat2.stats.kfold.PerDocsFoldCreator method) (medcat2.stats.kfold.SimpleFoldCreator method) (medcat2.stats.kfold.WeightedDocumentsCreator method) create_main_ann() (in module medcat2.components.linking.context_based_linker) (in module medcat2.components.ner.trf.transformers_ner) (in module medcat2.utils.postprocessing) create_new() (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) create_tokenizer() (in module medcat2.pipeline.pipeline) (in module medcat2.tokenizing.tokenizers) cuda() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) cui (medcat2.cat.Entity attribute) (medcat2.cat.MutableEntity property) (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.addons.addons.MutableEntity property) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity property) (medcat2.components.linking.context_based_linker.MutableEntity property) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.components.linking.vector_context_model.MutableEntity property) (medcat2.components.ner.trf.transformers_ner.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableEntity property) (medcat2.components.types.MutableEntity property) (medcat2.data.entities.Entity attribute) (medcat2.data.mctexport.MedCATTrainerExportAnnotation attribute) (medcat2.pipeline.pipeline.MutableEntity property) (medcat2.stats.kfold.MedCATTrainerExportAnnotation attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.stats.stats.MedCATTrainerExportAnnotation attribute) (medcat2.stats.stats.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity property) (medcat2.tokenizing.tokenizers.MutableEntity property) (medcat2.tokenizing.tokens.MutableEntity property) (medcat2.trainer.MutableEntity property) (medcat2.utils.cdb_state.CUIInfo attribute) (medcat2.utils.data_utils.MutableEntity property) (medcat2.utils.postprocessing.MutableEntity property) cui2info (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.context_based_linker.ContextModel attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.linking.vector_context_model.ContextModel attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.stats.stats.StatsBuilder attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) CUI2KEYS (in module medcat2.utils.legacy.convert_cdb) cui2name (medcat2.components.ner.trf.tokenizer.TransformersTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer attribute) cui_filter (medcat2.config.config_meta_cat.Train attribute) CUIInfo (class in medcat2.cdb.cdb) (class in medcat2.cdb.concepts) (class in medcat2.components.linking.vector_context_model) (class in medcat2.stats.stats) (class in medcat2.utils.cdb_state) cuis (medcat2.cdb.cdb.TypeInfo attribute) (medcat2.cdb.concepts.TypeInfo attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.data.mctexport.MedCATTrainerExportProject attribute) (medcat2.stats.kfold.MedCATTrainerExportProject attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.stats.stats.MedCATTrainerExportProject attribute) (medcat2.trainer.MedCATTrainerExportProject attribute) (medcat2.utils.data_utils.MedCATTrainerExportProject attribute) (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.filters.MedCATTrainerExportProject attribute) (medcat2.utils.legacy.convert_cdb.TypeInfo attribute) cuis_exclude (medcat2.config.config.LinkingFilters attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.utils.filters.LinkingFilters attribute) cum_probs (medcat2.cat.Vocab attribute) (medcat2.components.addons.meta_cat.meta_cat.Vocab attribute) (medcat2.components.linking.context_based_linker.Vocab attribute) (medcat2.components.linking.no_action_linker.Vocab attribute) (medcat2.components.linking.vector_context_model.Vocab attribute) (medcat2.components.ner.dict_based_ner.Vocab attribute) (medcat2.components.ner.trf.transformers_ner.Vocab attribute) (medcat2.components.ner.vocab_based_ner.Vocab attribute) (medcat2.components.normalizing.normalizer.Vocab attribute) (medcat2.components.tagging.tagger.Vocab attribute) (medcat2.components.types.Vocab attribute) (medcat2.pipeline.pipeline.Vocab attribute) (medcat2.utils.default_args.Vocab attribute) (medcat2.utils.legacy.convert_vocab.Vocab attribute) (medcat2.utils.vocab_utils.Vocab attribute) (medcat2.vocab.Vocab attribute) custom_cnf (medcat2.config.config.Ner attribute) CustomUnpickler (class in medcat2.utils.legacy.convert_cdb) CustomUnpickler.memo (class in medcat2.utils.legacy.convert_cdb) CustomUnpickler.persistent_load (class in medcat2.utils.legacy.convert_cdb)

D

d1 (medcat2.components.addons.meta_cat.models.LSTM attribute) data (medcat2.utils.data_utils.TestTrainSplitter attribute) data_vocab (medcat2.components.normalizing.normalizer.BasicSpellChecker attribute) DEFAULT_PACK_NAME (in module medcat2.cat) (in module medcat2.utils.defaults) DEFAULT_SCHEMA_FILE (in module medcat2.storage.schema) (in module medcat2.storage.serialisers) DEFAULT_SPACY_MODEL (in module medcat2.utils.defaults) default_weighted_average() (in module medcat2.cdb.cdb) (in module medcat2.utils.defaults) deid_text() (medcat2.components.ner.trf.deid.DeIdModel method) DeIdModel (class in medcat2.components.ner.trf.deid) DelegatingTokenizer (class in medcat2.pipeline.pipeline) DEP_NAME_PATTERN (in module medcat2.utils.envsnapshot) dependencies (medcat2.config.config.Environment attribute) (medcat2.utils.envsnapshot.Environment attribute) description (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) (medcat2.utils.cdb_state.ModelMeta attribute) deserialise() (in module medcat2.cat) (in module medcat2.components.addons.meta_cat.meta_cat) (in module medcat2.components.ner.trf.transformers_ner) (in module medcat2.pipeline.pipeline) (in module medcat2.storage.serialisers) (medcat2.storage.serialisers.DillSerialiser method) (medcat2.storage.serialisers.Serialiser method) deserialise_all() (medcat2.storage.serialisers.DillSerialiser method) (medcat2.storage.serialisers.Serialiser method) deserialise_from() (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.storage.serialisables.ManualSerialisable class method) (medcat2.storage.serialisers.ManualSerialisable class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) deserialise_manually() (medcat2.storage.serialisers.DillSerialiser class method) (medcat2.storage.serialisers.Serialiser class method) detected_name (medcat2.cat.Entity attribute) (medcat2.cat.MutableEntity property) (medcat2.components.addons.addons.MutableEntity property) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity property) (medcat2.components.linking.context_based_linker.MutableEntity property) (medcat2.components.linking.vector_context_model.MutableEntity property) (medcat2.components.ner.trf.transformers_ner.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableEntity property) (medcat2.components.types.MutableEntity property) (medcat2.data.entities.Entity attribute) (medcat2.pipeline.pipeline.MutableEntity property) (medcat2.stats.stats.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity property) (medcat2.tokenizing.tokenizers.MutableEntity property) (medcat2.tokenizing.tokens.MutableEntity property) (medcat2.trainer.MutableEntity property) (medcat2.utils.data_utils.MutableEntity property) (medcat2.utils.postprocessing.MutableEntity property) devalue_linked_concepts (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) device (medcat2.config.config_meta_cat.General attribute) diacritics (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) dict() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method)

DICT_ONLY (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy attribute) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy attribute) (medcat2.config.config.SerialisingStrategy attribute) (medcat2.storage.serialisables.SerialisingStrategy attribute) dill (medcat2.cat.AvailableSerialisers attribute) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers attribute) (medcat2.config.config_meta_cat.AvailableSerialisers attribute) (medcat2.pipeline.pipeline.AvailableSerialisers attribute) (medcat2.storage.serialisers.AvailableSerialisers attribute) (medcat2.utils.legacy.conversion_all.AvailableSerialisers attribute) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers attribute) DillSerialiser (class in medcat2.storage.serialisers) disable_component_lock (medcat2.config.config_meta_cat.General attribute) disabled_components (medcat2.config.config.NLPConfig attribute) disamb_length_limit (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) disambiguate() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) dispatch (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) do_conversion() (in module medcat2.utils.legacy.legacy_converter) DO_DISAMBUGATION (medcat2.cdb.cdb.ST attribute) (medcat2.components.linking.context_based_linker.ST attribute) (medcat2.components.linking.vector_context_model.ST attribute) (medcat2.utils.defaults.StatusTypes attribute) do_not_normalize (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.preprocessors.cleaners.LPreprocessing attribute) (medcat2.trainer.Preprocessing attribute) doc_getter (medcat2.stats.stats.StatsBuilder attribute) Document (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.spacy_impl.tokens) documents (medcat2.data.mctexport.MedCATTrainerExportProject attribute) (medcat2.stats.kfold.MedCATTrainerExportProject attribute) DOCUMENTS (medcat2.stats.kfold.SplitType attribute) documents (medcat2.stats.stats.MedCATTrainerExportProject attribute) (medcat2.trainer.MedCATTrainerExportProject attribute) (medcat2.utils.data_utils.MedCATTrainerExportProject attribute) (medcat2.utils.filters.MedCATTrainerExportProject attribute) DOCUMENTS_WEIGHTED (medcat2.stats.kfold.SplitType attribute) double() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) dropout (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.config.config_meta_cat.Model attribute) dump_patches (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) dumps() (in module medcat2.utils.hasher)

E

edits1() (medcat2.components.normalizing.normalizer.BasicSpellChecker method) edits2() (medcat2.components.normalizing.normalizer.BasicSpellChecker method) edits3() (medcat2.components.normalizing.normalizer.BasicSpellChecker method) emb_grad (medcat2.config.config_meta_cat.Model attribute) embeddings (medcat2.components.addons.meta_cat.meta_cat.MetaCAT attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCAT attribute) encode() (medcat2.components.ner.trf.tokenizer.TransformersTokenizer method) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer method) encode_category_values() (in module medcat2.components.addons.meta_cat.data_utils) (in module medcat2.components.addons.meta_cat.meta_cat) encoding (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) end (medcat2.cat.Entity attribute) (medcat2.data.entities.Entity attribute) (medcat2.data.mctexport.MedCATTrainerExportAnnotation attribute) (medcat2.stats.kfold.MedCATTrainerExportAnnotation attribute) (medcat2.stats.stats.MedCATTrainerExportAnnotation attribute) end_char_index (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity property) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity property) (medcat2.tokenizing.tokens.BaseEntity property) end_index (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity property) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity property) (medcat2.tokenizing.tokens.BaseEntity property) ensure_folder_if_parent() (in module medcat2.cat) (in module medcat2.utils.fileutils) ensure_optional_extras_installed() (in module medcat2.components.addons.meta_cat) (in module medcat2.components.ner.dict_based_ner) (in module medcat2.components.ner.trf) (in module medcat2.tokenizing.spacy_impl) (in module medcat2.utils.import_utils) ensure_spacy_model() (in module medcat2.tokenizing.spacy_impl.tokenizers) (in module medcat2.tokenizing.spacy_impl.utils) ensure_tokenizer() (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase method) (medcat2.components.ner.trf.tokenizer.TransformersTokenizer method) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE method) Entities (class in medcat2.cat) (class in medcat2.components.ner.trf.model) (class in medcat2.data.entities) entities (medcat2.cat.Entities attribute) (medcat2.cat.OnlyCUIEntities attribute) (medcat2.components.ner.trf.model.Entities attribute) (medcat2.components.ner.trf.model.OnlyCUIEntities attribute) (medcat2.data.entities.Entities attribute) (medcat2.data.entities.OnlyCUIEntities attribute) Entity (class in medcat2.cat) (class in medcat2.data.entities) (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.spacy_impl.tokens) entity_from_tokens() (medcat2.cat.Pipeline method) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer method) (medcat2.components.linking.context_based_linker.BaseTokenizer method) (medcat2.components.linking.no_action_linker.BaseTokenizer method) (medcat2.components.ner.dict_based_ner.BaseTokenizer method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer method) (medcat2.components.normalizing.normalizer.BaseTokenizer method) (medcat2.components.tagging.tagger.BaseTokenizer method) (medcat2.components.types.BaseTokenizer method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.BaseTokenizer method) (medcat2.pipeline.pipeline.DelegatingTokenizer method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.preprocessors.cleaners.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer method) (medcat2.tokenizing.tokenizers.BaseTokenizer method) (medcat2.trainer.Pipeline method) (medcat2.utils.default_args.BaseTokenizer method) (medcat2.utils.legacy.convert_deid.BaseTokenizer method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer method)

ENTITY_INFO_PREFIX (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) Environment (class in medcat2.config.config) (class in medcat2.utils.envsnapshot) errors (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) eval() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) (medcat2.components.ner.trf.deid.DeIdModel method) (medcat2.components.ner.trf.deid.NerModel method) (medcat2.components.ner.trf.model.NerModel method) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) eval_model() (in module medcat2.components.addons.meta_cat.meta_cat) (in module medcat2.components.addons.meta_cat.ml_utils) exp_cat_config_name (in module medcat2.utils.legacy.convert_deid) exp_cdb_name (in module medcat2.utils.legacy.convert_deid) exp_trf_ner_config_name (in module medcat2.utils.legacy.convert_deid) expand_model_with_concepts() (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) expected_files_in_folder (medcat2.utils.legacy.conversion_all.Converter property) (medcat2.utils.legacy.legacy_converter.Converter property) EXPECTED_USEFUL_KEYS (in module medcat2.utils.legacy.convert_cdb) extra (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT.Config attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT.Config attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT.Config attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER.Config attribute) (medcat2.config.config.NLPConfig.Config attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT.Config attribute) (medcat2.config.config_meta_cat.General.Config attribute) (medcat2.config.config_meta_cat.Model.Config attribute) (medcat2.config.config_meta_cat.Train.Config attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER.Config attribute) (medcat2.config.config_transformers_ner.General.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER.Config attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT.Config attribute) extra_cui_filter (medcat2.stats.stats.StatsBuilder attribute) extra_name (medcat2.utils.import_utils.IncorrectExtraComponent attribute) (medcat2.utils.import_utils.MissingDependenciesError attribute) extra_repr() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method)

F

FAKE_TOKENIZER_PATH (in module medcat2.components.addons.meta_cat.meta_cat_tokenizers) fc1 (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) fc2 (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) fc3 (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) filter_before_disamb (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) filter_by_cui() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) filters (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) (medcat2.stats.stats.StatsBuilder attribute) final_ents (medcat2.cat.MutableDocument property) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument property) (medcat2.components.linking.context_based_linker.MutableDocument property) (medcat2.components.linking.no_action_linker.MutableDocument property) (medcat2.components.linking.vector_context_model.MutableDocument property) (medcat2.components.ner.dict_based_ner.MutableDocument property) (medcat2.components.ner.trf.model.MutableDocument property) (medcat2.components.ner.trf.transformers_ner.MutableDocument property) (medcat2.components.ner.vocab_based_annotator.MutableDocument property) (medcat2.components.ner.vocab_based_ner.MutableDocument property) (medcat2.components.normalizing.normalizer.MutableDocument property) (medcat2.components.tagging.tagger.MutableDocument property) (medcat2.components.types.MutableDocument property) (medcat2.pipeline.pipeline.MutableDocument property) (medcat2.preprocessors.cleaners.MutableDocument property) (medcat2.stats.stats.MutableDocument property) (medcat2.tokenizing.regex_impl.tokenizer.Document attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument property) (medcat2.tokenizing.spacy_impl.tokenizers.Document attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument property) (medcat2.tokenizing.spacy_impl.tokens.Document attribute) (medcat2.tokenizing.tokenizers.MutableDocument property) (medcat2.tokenizing.tokens.MutableDocument property) (medcat2.trainer.MutableDocument property) (medcat2.utils.data_utils.MutableDocument property) (medcat2.utils.postprocessing.MutableDocument property) finalise_report() (medcat2.stats.stats.StatsBuilder method) find_class() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) fix() (medcat2.components.normalizing.normalizer.BasicSpellChecker method) fix_imports (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) float() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) FloatValuedMetric (in module medcat2.stats.kfold) FocalLoss (class in medcat2.components.addons.meta_cat.ml_utils) FoldCreator (class in medcat2.stats.kfold) forward() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) from_cat() (medcat2.stats.stats.StatsBuilder class method) from_file() (medcat2.cat.AvailableSerialisers class method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers class method) (medcat2.config.config_meta_cat.AvailableSerialisers class method) (medcat2.pipeline.pipeline.AvailableSerialisers class method) (medcat2.storage.serialisers.AvailableSerialisers class method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers class method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers class method) from_orm() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method)

full_name (medcat2.cat.AbstractCoreComponent property) (medcat2.cat.AddonComponent property) (medcat2.components.addons.addons.AddonComponent property) (medcat2.components.addons.addons.BaseComponent property) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent property) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon property) (medcat2.components.linking.context_based_linker.AbstractCoreComponent property) (medcat2.components.linking.context_based_linker.Linker property) (medcat2.components.linking.no_action_linker.AbstractCoreComponent property) (medcat2.components.linking.no_action_linker.NoActionLinker property) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent property) (medcat2.components.ner.dict_based_ner.NER property) (medcat2.components.ner.trf.deid.TransformersNER property) (medcat2.components.ner.trf.model.TransformersNER property) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent property) (medcat2.components.ner.trf.transformers_ner.TransformersNER property) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent property) (medcat2.components.ner.vocab_based_ner.NER property) (medcat2.components.normalizing.normalizer.AbstractCoreComponent property) (medcat2.components.normalizing.normalizer.TokenNormalizer property) (medcat2.components.tagging.tagger.AbstractCoreComponent property) (medcat2.components.tagging.tagger.TagAndSkipTagger property) (medcat2.components.types.AbstractCoreComponent property) (medcat2.components.types.BaseComponent property) (medcat2.components.types.CoreComponent property) (medcat2.pipeline.pipeline.AbstractCoreComponent property) (medcat2.pipeline.pipeline.AddonComponent property) (medcat2.pipeline.pipeline.BaseComponent property) (medcat2.pipeline.pipeline.CoreComponent property) (medcat2.utils.legacy.conversion_all.NoActionLinker property) (medcat2.utils.legacy.convert_deid.TransformersNER property) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon property) full_unlink (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) func_has_kwarg() (in module medcat2.components.ner.trf.transformers_ner)

G

gamma (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.config.config_meta_cat.Train attribute) General (class in medcat2.config.config) (class in medcat2.config.config_meta_cat) (class in medcat2.config.config_transformers_ner) (class in medcat2.trainer) general (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.config.Config attribute) (medcat2.config.config.Config attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) General.Config (class in medcat2.config.config_meta_cat) (class in medcat2.config.config_transformers_ner) get() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) get_addon_creator() (in module medcat2.components.addons.addons) (in module medcat2.utils.default_args) get_addon_data() (medcat2.cat.MutableDocument method) (medcat2.cat.MutableEntity method) (medcat2.components.addons.addons.MutableEntity method) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument method) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity method) (medcat2.components.linking.context_based_linker.MutableDocument method) (medcat2.components.linking.context_based_linker.MutableEntity method) (medcat2.components.linking.no_action_linker.MutableDocument method) (medcat2.components.linking.vector_context_model.MutableDocument method) (medcat2.components.linking.vector_context_model.MutableEntity method) (medcat2.components.ner.dict_based_ner.MutableDocument method) (medcat2.components.ner.trf.model.MutableDocument method) (medcat2.components.ner.trf.transformers_ner.MutableDocument method) (medcat2.components.ner.trf.transformers_ner.MutableEntity method) (medcat2.components.ner.vocab_based_annotator.MutableDocument method) (medcat2.components.ner.vocab_based_annotator.MutableEntity method) (medcat2.components.ner.vocab_based_ner.MutableDocument method) (medcat2.components.normalizing.normalizer.MutableDocument method) (medcat2.components.tagging.tagger.MutableDocument method) (medcat2.components.types.MutableDocument method) (medcat2.components.types.MutableEntity method) (medcat2.pipeline.pipeline.MutableDocument method) (medcat2.pipeline.pipeline.MutableEntity method) (medcat2.preprocessors.cleaners.MutableDocument method) (medcat2.stats.stats.MutableDocument method) (medcat2.stats.stats.MutableEntity method) (medcat2.tokenizing.regex_impl.tokenizer.Document method) (medcat2.tokenizing.regex_impl.tokenizer.Entity method) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument method) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity method) (medcat2.tokenizing.spacy_impl.tokenizers.Document method) (medcat2.tokenizing.spacy_impl.tokenizers.Entity method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity method) (medcat2.tokenizing.spacy_impl.tokens.Document method) (medcat2.tokenizing.spacy_impl.tokens.Entity method) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity method) (medcat2.tokenizing.tokenizers.MutableDocument method) (medcat2.tokenizing.tokenizers.MutableEntity method) (medcat2.tokenizing.tokens.MutableDocument method) (medcat2.tokenizing.tokens.MutableEntity method) (medcat2.trainer.MutableDocument method) (medcat2.trainer.MutableEntity method) (medcat2.utils.data_utils.MutableDocument method) (medcat2.utils.data_utils.MutableEntity method) (medcat2.utils.postprocessing.MutableDocument method) (medcat2.utils.postprocessing.MutableEntity method) get_all_extra_deps_raw() (in module medcat2.utils.import_utils) get_all_serialisable_members() (in module medcat2.storage.serialisables) (in module medcat2.storage.serialisers) get_basic_info() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) get_buffer() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) get_cdb_from_old() (in module medcat2.utils.legacy.conversion_all) (in module medcat2.utils.legacy.convert_cdb) (in module medcat2.utils.legacy.convert_deid) get_cnf() (in module medcat2.utils.legacy.convert_deid) get_component() (medcat2.cat.Pipeline method) (medcat2.components.addons.addons.Registry method) (medcat2.components.types.Registry method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.trainer.Pipeline method) (medcat2.utils.registry.Registry method) get_component_creator() (in module medcat2.components.types) (in module medcat2.utils.default_args) get_config_from_nested_dict() (in module medcat2.utils.legacy.convert_cdb) (in module medcat2.utils.legacy.convert_config) get_config_from_old() (in module medcat2.utils.legacy.conversion_all) (in module medcat2.utils.legacy.convert_config) get_context_tokens() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) get_context_vectors() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) get_core_registry() (in module medcat2.components.types) get_cui2count_train() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) get_dict() (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.config.config.SerialisingStrategy method) (medcat2.storage.serialisables.SerialisingStrategy method) get_direct_dependencies() (in module medcat2.utils.envsnapshot) get_doc() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) get_doc_class() (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer method) (medcat2.components.linking.context_based_linker.BaseTokenizer method) (medcat2.components.linking.no_action_linker.BaseTokenizer method) (medcat2.components.ner.dict_based_ner.BaseTokenizer method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer method) (medcat2.components.normalizing.normalizer.BaseTokenizer method) (medcat2.components.tagging.tagger.BaseTokenizer method) (medcat2.components.types.BaseTokenizer method) (medcat2.pipeline.pipeline.BaseTokenizer method) (medcat2.pipeline.pipeline.DelegatingTokenizer method) (medcat2.preprocessors.cleaners.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer method) (medcat2.tokenizing.tokenizers.BaseTokenizer method) (medcat2.utils.default_args.BaseTokenizer method) (medcat2.utils.legacy.convert_deid.BaseTokenizer method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer method) get_entities() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.deid.DeIdModel method) (medcat2.components.ner.trf.deid.NerModel method) (medcat2.components.ner.trf.model.CAT method) (medcat2.components.ner.trf.model.NerModel method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) get_entity_class() (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer method) (medcat2.components.linking.context_based_linker.BaseTokenizer method) (medcat2.components.linking.no_action_linker.BaseTokenizer method) (medcat2.components.ner.dict_based_ner.BaseTokenizer method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer method) (medcat2.components.normalizing.normalizer.BaseTokenizer method) (medcat2.components.tagging.tagger.BaseTokenizer method) (medcat2.components.types.BaseTokenizer method) (medcat2.pipeline.pipeline.BaseTokenizer method) (medcat2.pipeline.pipeline.DelegatingTokenizer method) (medcat2.preprocessors.cleaners.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer method) (medcat2.tokenizing.tokenizers.BaseTokenizer method) (medcat2.utils.default_args.BaseTokenizer method) (medcat2.utils.legacy.convert_deid.BaseTokenizer method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer method) get_ents() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) get_environment_info() (in module medcat2.config.config) (in module medcat2.utils.envsnapshot) get_extension() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) get_extra_state() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) get_false_positives() (in module medcat2.trainer) (in module medcat2.utils.data_utils) get_fold_creator() (in module medcat2.stats.kfold) get_folder_name() (medcat2.cat.AddonComponent method) (medcat2.components.addons.addons.AddonComponent method) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.ner.trf.deid.TransformersNER method) (medcat2.components.ner.trf.model.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.TransformersNER method) (medcat2.pipeline.pipeline.AddonComponent method) (medcat2.utils.legacy.convert_deid.TransformersNER method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) get_hash() (medcat2.cat.CDB method) (medcat2.cat.HashableComponet method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.components.types.HashableComponet method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) (medcat2.utils.vocab_utils.CDB method) get_important_config_parameters() (in module medcat2.cat) (in module medcat2.config.config) get_init_args() (medcat2.cat.AbstractCoreComponent class method) (medcat2.cat.AddonComponent class method) (medcat2.components.addons.addons.AddonComponent class method) (medcat2.components.addons.addons.BaseComponent class method) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent class method) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.linking.context_based_linker.AbstractCoreComponent class method) (medcat2.components.linking.context_based_linker.BaseTokenizer class method) (medcat2.components.linking.context_based_linker.Linker class method) (medcat2.components.linking.no_action_linker.AbstractCoreComponent class method) (medcat2.components.linking.no_action_linker.BaseTokenizer class method) (medcat2.components.linking.no_action_linker.NoActionLinker class method) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent class method) (medcat2.components.ner.dict_based_ner.BaseTokenizer class method) (medcat2.components.ner.dict_based_ner.NER class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent class method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer class method) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent class method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer class method) (medcat2.components.ner.vocab_based_ner.NER class method) (medcat2.components.normalizing.normalizer.AbstractCoreComponent class method) (medcat2.components.normalizing.normalizer.BaseTokenizer class method) (medcat2.components.normalizing.normalizer.TokenNormalizer class method) (medcat2.components.tagging.tagger.AbstractCoreComponent class method) (medcat2.components.tagging.tagger.BaseTokenizer class method) (medcat2.components.tagging.tagger.TagAndSkipTagger class method) (medcat2.components.types.AbstractCoreComponent class method) (medcat2.components.types.BaseComponent class method) (medcat2.components.types.BaseTokenizer class method) (medcat2.components.types.CoreComponent class method) (medcat2.pipeline.pipeline.AbstractCoreComponent class method) (medcat2.pipeline.pipeline.AddonComponent class method) (medcat2.pipeline.pipeline.BaseComponent class method) (medcat2.pipeline.pipeline.BaseTokenizer class method) (medcat2.pipeline.pipeline.CoreComponent class method) (medcat2.pipeline.pipeline.DelegatingTokenizer class method) (medcat2.preprocessors.cleaners.BaseTokenizer class method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer class method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer class method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer class method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer class method) (medcat2.tokenizing.tokenizers.BaseTokenizer class method) (medcat2.utils.default_args.BaseTokenizer class method) (medcat2.utils.legacy.conversion_all.NoActionLinker class method) (medcat2.utils.legacy.convert_deid.BaseTokenizer class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) get_init_attrs() (medcat2.cat.AbstractSerialisable class method) (medcat2.cat.CAT class method) (medcat2.cat.CDB class method) (medcat2.cat.Config class method) (medcat2.cat.Vocab class method) (medcat2.cdb.CDB class method) (medcat2.cdb.cdb.AbstractSerialisable class method) (medcat2.cdb.cdb.CDB class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.AbstractSerialisable class method) (medcat2.components.addons.meta_cat.meta_cat.CDB class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.addons.meta_cat.meta_cat.Vocab class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.CDB class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.context_based_linker.ContextModel class method) (medcat2.components.linking.context_based_linker.Vocab class method) (medcat2.components.linking.no_action_linker.CDB class method) (medcat2.components.linking.no_action_linker.Vocab class method) (medcat2.components.linking.vector_context_model.AbstractSerialisable class method) (medcat2.components.linking.vector_context_model.ContextModel class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.linking.vector_context_model.Vocab class method) (medcat2.components.ner.dict_based_ner.CDB class method) (medcat2.components.ner.dict_based_ner.Vocab class method) (medcat2.components.ner.trf.deid.CAT class method) (medcat2.components.ner.trf.deid.CDB class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.helpers.CDB class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.CAT class method) (medcat2.components.ner.trf.model.CDB class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.CDB class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.Vocab class method) (medcat2.components.ner.vocab_based_annotator.CDB class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.ner.vocab_based_ner.CDB class method) (medcat2.components.ner.vocab_based_ner.Vocab class method) (medcat2.components.normalizing.normalizer.CDB class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.normalizing.normalizer.Vocab class method) (medcat2.components.tagging.tagger.CDB class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.components.tagging.tagger.Vocab class method) (medcat2.components.types.CDB class method) (medcat2.components.types.Vocab class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.CDB class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.CDB class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.pipeline.pipeline.Serialisable class method) (medcat2.pipeline.pipeline.Vocab class method) (medcat2.stats.kfold.CAT class method) (medcat2.stats.stats.CAT class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.storage.serialisables.AbstractManualSerialisable class method) (medcat2.storage.serialisables.AbstractSerialisable class method) (medcat2.storage.serialisables.ManualSerialisable class method) (medcat2.storage.serialisables.Serialisable class method) (medcat2.storage.serialisers.ManualSerialisable class method) (medcat2.storage.serialisers.Serialisable class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDB class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.data_utils.CDB class method) (medcat2.utils.default_args.CDB class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.default_args.Vocab class method) (medcat2.utils.envsnapshot.AbstractSerialisable class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.conversion_all.CAT class method) (medcat2.utils.legacy.convert_cdb.CDB class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.CDB class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) (medcat2.utils.legacy.convert_vocab.Vocab class method) (medcat2.utils.vocab_utils.CDB class method) (medcat2.utils.vocab_utils.Vocab class method) (medcat2.vocab.AbstractSerialisable class method) (medcat2.vocab.Vocab class method)

get_init_kwargs() (medcat2.cat.AbstractCoreComponent class method) (medcat2.cat.AddonComponent class method) (medcat2.components.addons.addons.AddonComponent class method) (medcat2.components.addons.addons.BaseComponent class method) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent class method) (medcat2.components.addons.meta_cat.meta_cat.BaseTokenizer class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.linking.context_based_linker.AbstractCoreComponent class method) (medcat2.components.linking.context_based_linker.BaseTokenizer class method) (medcat2.components.linking.context_based_linker.Linker class method) (medcat2.components.linking.no_action_linker.AbstractCoreComponent class method) (medcat2.components.linking.no_action_linker.BaseTokenizer class method) (medcat2.components.linking.no_action_linker.NoActionLinker class method) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent class method) (medcat2.components.ner.dict_based_ner.BaseTokenizer class method) (medcat2.components.ner.dict_based_ner.NER class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent class method) (medcat2.components.ner.trf.transformers_ner.BaseTokenizer class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.components.ner.vocab_based_annotator.BaseTokenizer class method) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent class method) (medcat2.components.ner.vocab_based_ner.BaseTokenizer class method) (medcat2.components.ner.vocab_based_ner.NER class method) (medcat2.components.normalizing.normalizer.AbstractCoreComponent class method) (medcat2.components.normalizing.normalizer.BaseTokenizer class method) (medcat2.components.normalizing.normalizer.TokenNormalizer class method) (medcat2.components.tagging.tagger.AbstractCoreComponent class method) (medcat2.components.tagging.tagger.BaseTokenizer class method) (medcat2.components.tagging.tagger.TagAndSkipTagger class method) (medcat2.components.types.AbstractCoreComponent class method) (medcat2.components.types.BaseComponent class method) (medcat2.components.types.BaseTokenizer class method) (medcat2.components.types.CoreComponent class method) (medcat2.pipeline.pipeline.AbstractCoreComponent class method) (medcat2.pipeline.pipeline.AddonComponent class method) (medcat2.pipeline.pipeline.BaseComponent class method) (medcat2.pipeline.pipeline.BaseTokenizer class method) (medcat2.pipeline.pipeline.CoreComponent class method) (medcat2.pipeline.pipeline.DelegatingTokenizer class method) (medcat2.preprocessors.cleaners.BaseTokenizer class method) (medcat2.tokenizing.regex_impl.tokenizer.BaseTokenizer class method) (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer class method) (medcat2.tokenizing.spacy_impl.tokenizers.BaseTokenizer class method) (medcat2.tokenizing.spacy_impl.tokenizers.SpacyTokenizer class method) (medcat2.tokenizing.tokenizers.BaseTokenizer class method) (medcat2.utils.default_args.BaseTokenizer class method) (medcat2.utils.legacy.conversion_all.NoActionLinker class method) (medcat2.utils.legacy.convert_deid.BaseTokenizer class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.BaseTokenizer class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) get_installed_dependencies() (in module medcat2.utils.envsnapshot) get_installed_extra_dependencies() (in module medcat2.utils.import_utils) get_k_fold_stats() (in module medcat2.stats.kfold) get_lr_linking() (in module medcat2.components.linking.vector_context_model) get_manually_serialised_path() (medcat2.storage.serialisers.DillSerialiser class method) (medcat2.storage.serialisers.Serialiser class method) get_mean() (medcat2.stats.kfold.PerCUIMetrics method) get_meta_cat_from_old() (in module medcat2.utils.legacy.conversion_all) (in module medcat2.utils.legacy.convert_meta_cat) get_metrics_mean() (in module medcat2.stats.kfold) get_model() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) get_model_card() (medcat2.cat.CAT method) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) get_name() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) get_name2count_train() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) get_negative_samples() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) get_new_cui_info() (in module medcat2.cdb.cdb) (in module medcat2.cdb.concepts) (in module medcat2.components.ner.trf.helpers) (in module medcat2.stats.stats) (in module medcat2.utils.legacy.convert_cdb) get_new_name_info() (in module medcat2.cdb.cdb) (in module medcat2.cdb.concepts) (in module medcat2.utils.legacy.convert_cdb) get_nr_of_annotations() (in module medcat2.data.mctexport) (in module medcat2.stats.kfold) get_output_key_val() (medcat2.cat.AddonComponent method) (medcat2.components.addons.addons.AddonComponent method) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.pipeline.pipeline.AddonComponent method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) get_pad_id() (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE method) get_parameter() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) get_parts() (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.config.config.SerialisingStrategy method) (medcat2.storage.serialisables.SerialisingStrategy method) get_per_fold_metrics() (in module medcat2.stats.kfold) get_registered_components() (in module medcat2.components.types) get_required_extra_deps() (in module medcat2.utils.import_utils) get_ser_type_file() (medcat2.storage.serialisers.DillSerialiser class method) (medcat2.storage.serialisers.Serialiser class method) get_serialiser() (in module medcat2.storage.serialisers) get_serialiser_from_folder() (in module medcat2.storage.serialisers) get_serialiser_type_from_folder() (in module medcat2.storage.serialisers) get_similarity() (in module medcat2.components.linking.vector_context_model) get_size() (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE method) get_stats() (in module medcat2.stats.kfold) (in module medcat2.stats.stats) get_std() (medcat2.stats.kfold.PerCUIMetrics method) get_strategy() (medcat2.cat.AbstractSerialisable method) (medcat2.cat.CAT method) (medcat2.cat.CDB method) (medcat2.cat.Config method) (medcat2.cat.Vocab method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.AbstractSerialisable method) (medcat2.cdb.cdb.CDB method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.AbstractSerialisable method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.AbstractSerialisable method) (medcat2.components.linking.vector_context_model.ContextModel method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.deid.TransformersNER method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.CAT method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.model.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.trf.transformers_ner.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.CDB method) (medcat2.components.types.Vocab method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.CDB method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.pipeline.pipeline.Serialisable method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.stats.stats.LinkingFilters method) (medcat2.storage.serialisables.AbstractManualSerialisable method) (medcat2.storage.serialisables.AbstractSerialisable method) (medcat2.storage.serialisables.ManualSerialisable method) (medcat2.storage.serialisables.Serialisable method) (medcat2.storage.serialisers.ManualSerialisable method) (medcat2.storage.serialisers.Serialisable method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDB method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.envsnapshot.AbstractSerialisable method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.conversion_all.CAT method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_deid.TransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.CDB method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.AbstractSerialisable method) (medcat2.vocab.Vocab method) get_submodule() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) get_tokenizer_creator() (in module medcat2.tokenizing.tokenizers) (in module medcat2.utils.default_args) get_tokens() (medcat2.cat.MutableDocument method) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument method) (medcat2.components.linking.context_based_linker.MutableDocument method) (medcat2.components.linking.no_action_linker.MutableDocument method) (medcat2.components.linking.vector_context_model.MutableDocument method) (medcat2.components.ner.dict_based_ner.MutableDocument method) (medcat2.components.ner.trf.model.MutableDocument method) (medcat2.components.ner.trf.transformers_ner.MutableDocument method) (medcat2.components.ner.vocab_based_annotator.MutableDocument method) (medcat2.components.ner.vocab_based_ner.MutableDocument method) (medcat2.components.normalizing.normalizer.MutableDocument method) (medcat2.components.tagging.tagger.MutableDocument method) (medcat2.components.types.MutableDocument method) (medcat2.pipeline.pipeline.MutableDocument method) (medcat2.preprocessors.cleaners.MutableDocument method) (medcat2.stats.stats.MutableDocument method) (medcat2.tokenizing.regex_impl.tokenizer.Document method) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument method) (medcat2.tokenizing.spacy_impl.tokenizers.Document method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument method) (medcat2.tokenizing.spacy_impl.tokens.Document method) (medcat2.tokenizing.tokenizers.MutableDocument method) (medcat2.tokenizing.tokens.MutableDocument method) (medcat2.trainer.MutableDocument method) (medcat2.utils.data_utils.MutableDocument method) (medcat2.utils.postprocessing.MutableDocument method) get_transitive_deps() (in module medcat2.utils.envsnapshot) get_trf_ner_from_old() (in module medcat2.utils.legacy.conversion_all) (in module medcat2.utils.legacy.convert_deid) get_type() (medcat2.cat.AbstractCoreComponent method) (medcat2.components.linking.context_based_linker.AbstractCoreComponent method) (medcat2.components.linking.context_based_linker.Linker method) (medcat2.components.linking.no_action_linker.AbstractCoreComponent method) (medcat2.components.linking.no_action_linker.NoActionLinker method) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent method) (medcat2.components.ner.dict_based_ner.NER method) (medcat2.components.ner.trf.deid.TransformersNER method) (medcat2.components.ner.trf.model.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent method) (medcat2.components.ner.trf.transformers_ner.TransformersNER method) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent method) (medcat2.components.ner.vocab_based_ner.NER method) (medcat2.components.normalizing.normalizer.AbstractCoreComponent method) (medcat2.components.normalizing.normalizer.TokenNormalizer method) (medcat2.components.tagging.tagger.AbstractCoreComponent method) (medcat2.components.tagging.tagger.TagAndSkipTagger method) (medcat2.components.types.AbstractCoreComponent method) (medcat2.components.types.CoreComponent method) (medcat2.pipeline.pipeline.AbstractCoreComponent method) (medcat2.pipeline.pipeline.CoreComponent method) (medcat2.utils.legacy.conversion_all.NoActionLinker method) (medcat2.utils.legacy.convert_deid.TransformersNER method) get_updated_average_confidence() (in module medcat2.components.linking.vector_context_model) get_val_and_parent_model() (in module medcat2.utils.legacy.convert_config) get_vectors() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) get_vocab_from_old() (in module medcat2.utils.legacy.conversion_all) (in module medcat2.utils.legacy.convert_vocab) group (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute)

H

half() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) has_changed_names (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) has_spacy_model() (in module medcat2.tokenizing.spacy_impl.utils) has_subname() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method)

hash (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute) HashableComponet (class in medcat2.cat) (class in medcat2.components.types) Hasher (class in medcat2.cat) (class in medcat2.cdb.cdb) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.config.config_transformers_ner) (class in medcat2.utils.hasher) hexdigest() (medcat2.cat.Hasher method) (medcat2.cdb.cdb.Hasher method) (medcat2.components.addons.meta_cat.meta_cat.Hasher method) (medcat2.components.ner.trf.transformers_ner.Hasher method) (medcat2.config.config_transformers_ner.Hasher method) (medcat2.utils.hasher.Hasher method) hf_tokenizer (medcat2.components.ner.trf.tokenizer.TransformersTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer attribute) hf_tokenizers (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE attribute) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE attribute) hidden_size (medcat2.config.config_meta_cat.Model attribute) history (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute)

I

id (medcat2.cat.Entity attribute) (medcat2.cat.MutableEntity property) (medcat2.components.addons.addons.MutableEntity property) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity property) (medcat2.components.linking.context_based_linker.MutableEntity property) (medcat2.components.linking.vector_context_model.MutableEntity property) (medcat2.components.ner.trf.transformers_ner.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableEntity property) (medcat2.components.types.MutableEntity property) (medcat2.data.entities.Entity attribute) (medcat2.data.mctexport.MedCATTrainerExportDocument attribute) (medcat2.data.mctexport.MedCATTrainerExportProject attribute) (medcat2.pipeline.pipeline.MutableEntity property) (medcat2.stats.kfold.MedCATTrainerExportDocument attribute) (medcat2.stats.kfold.MedCATTrainerExportProject attribute) (medcat2.stats.stats.MedCATTrainerExportDocument attribute) (medcat2.stats.stats.MedCATTrainerExportProject attribute) (medcat2.stats.stats.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity property) (medcat2.tokenizing.tokenizers.MutableEntity property) (medcat2.tokenizing.tokens.MutableEntity property) (medcat2.trainer.MedCATTrainerExportDocument attribute) (medcat2.trainer.MedCATTrainerExportProject attribute) (medcat2.trainer.MutableEntity property) (medcat2.utils.data_utils.MedCATTrainerExportDocument attribute) (medcat2.utils.data_utils.MedCATTrainerExportProject attribute) (medcat2.utils.data_utils.MutableEntity property) (medcat2.utils.filters.MedCATTrainerExportProject attribute) (medcat2.utils.postprocessing.MutableEntity property) id2type (medcat2.components.ner.trf.tokenizer.TransformersTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer attribute) ignore_attrs() (medcat2.cat.AbstractSerialisable class method) (medcat2.cat.CAT class method) (medcat2.cat.CDB class method) (medcat2.cat.Config class method) (medcat2.cat.Vocab class method) (medcat2.cdb.CDB class method) (medcat2.cdb.cdb.AbstractSerialisable class method) (medcat2.cdb.cdb.CDB class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.AbstractSerialisable class method) (medcat2.components.addons.meta_cat.meta_cat.CDB class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.addons.meta_cat.meta_cat.Vocab class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.CDB class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.context_based_linker.ContextModel class method) (medcat2.components.linking.context_based_linker.Vocab class method) (medcat2.components.linking.no_action_linker.CDB class method) (medcat2.components.linking.no_action_linker.Vocab class method) (medcat2.components.linking.vector_context_model.AbstractSerialisable class method) (medcat2.components.linking.vector_context_model.ContextModel class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.linking.vector_context_model.Vocab class method) (medcat2.components.ner.dict_based_ner.CDB class method) (medcat2.components.ner.dict_based_ner.Vocab class method) (medcat2.components.ner.trf.deid.CAT class method) (medcat2.components.ner.trf.deid.CDB class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.helpers.CDB class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.CAT class method) (medcat2.components.ner.trf.model.CDB class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.CDB class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.Vocab class method) (medcat2.components.ner.vocab_based_annotator.CDB class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.ner.vocab_based_ner.CDB class method) (medcat2.components.ner.vocab_based_ner.Vocab class method) (medcat2.components.normalizing.normalizer.CDB class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.normalizing.normalizer.Vocab class method) (medcat2.components.tagging.tagger.CDB class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.components.tagging.tagger.Vocab class method) (medcat2.components.types.CDB class method) (medcat2.components.types.Vocab class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.CDB class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.CDB class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.pipeline.pipeline.Serialisable class method) (medcat2.pipeline.pipeline.Vocab class method) (medcat2.stats.kfold.CAT class method) (medcat2.stats.stats.CAT class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.storage.serialisables.AbstractManualSerialisable class method) (medcat2.storage.serialisables.AbstractSerialisable class method) (medcat2.storage.serialisables.ManualSerialisable class method) (medcat2.storage.serialisables.Serialisable class method) (medcat2.storage.serialisers.ManualSerialisable class method) (medcat2.storage.serialisers.Serialisable class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDB class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.data_utils.CDB class method) (medcat2.utils.default_args.CDB class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.default_args.Vocab class method) (medcat2.utils.envsnapshot.AbstractSerialisable class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.conversion_all.CAT class method) (medcat2.utils.legacy.convert_cdb.CDB class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.CDB class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) (medcat2.utils.legacy.convert_vocab.Vocab class method) (medcat2.utils.vocab_utils.CDB class method) (medcat2.utils.vocab_utils.Vocab class method) (medcat2.vocab.AbstractSerialisable class method) (medcat2.vocab.Vocab class method) ignore_cpos (medcat2.config.config_meta_cat.Model attribute) IllegalConfigPathException IllegalConfigPathException.__cause__ (class in medcat2.utils.config_utils) IllegalConfigPathException.__context__ (class in medcat2.utils.config_utils) IllegalConfigPathException.__suppress_context__ (class in medcat2.utils.config_utils) IllegalConfigPathException.__traceback__ (class in medcat2.utils.config_utils) IllegalConfigPathException.args (class in medcat2.utils.config_utils) IllegalSchemaException, [1] IllegalSchemaException.__cause__ (class in medcat2.storage.schema) (class in medcat2.storage.serialisers) IllegalSchemaException.__context__ (class in medcat2.storage.schema) (class in medcat2.storage.serialisers) IllegalSchemaException.__suppress_context__ (class in medcat2.storage.schema) (class in medcat2.storage.serialisers) IllegalSchemaException.__traceback__ (class in medcat2.storage.schema) (class in medcat2.storage.serialisers) IllegalSchemaException.args (class in medcat2.storage.schema) (class in medcat2.storage.serialisers) in_memory_state_capture() (in module medcat2.utils.cdb_state) in_other_ontology (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) inc_or_add() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) inc_wc() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) include_in_output (medcat2.cat.AddonComponent property) (medcat2.components.addons.addons.AddonComponent property) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent property) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon property) (medcat2.pipeline.pipeline.AddonComponent property) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon property) include_properties() (medcat2.cat.AbstractSerialisable class method) (medcat2.cat.CAT class method) (medcat2.cat.CDB class method) (medcat2.cat.Config class method) (medcat2.cat.Vocab class method) (medcat2.cdb.CDB class method) (medcat2.cdb.cdb.AbstractSerialisable class method) (medcat2.cdb.cdb.CDB class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.AbstractSerialisable class method) (medcat2.components.addons.meta_cat.meta_cat.CDB class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.addons.meta_cat.meta_cat.Vocab class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.CDB class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.context_based_linker.ContextModel class method) (medcat2.components.linking.context_based_linker.Vocab class method) (medcat2.components.linking.no_action_linker.CDB class method) (medcat2.components.linking.no_action_linker.Vocab class method) (medcat2.components.linking.vector_context_model.AbstractSerialisable class method) (medcat2.components.linking.vector_context_model.ContextModel class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.linking.vector_context_model.Vocab class method) (medcat2.components.ner.dict_based_ner.CDB class method) (medcat2.components.ner.dict_based_ner.Vocab class method) (medcat2.components.ner.trf.deid.CAT class method) (medcat2.components.ner.trf.deid.CDB class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.helpers.CDB class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.CAT class method) (medcat2.components.ner.trf.model.CDB class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.CDB class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.Vocab class method) (medcat2.components.ner.vocab_based_annotator.CDB class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.ner.vocab_based_ner.CDB class method) (medcat2.components.ner.vocab_based_ner.Vocab class method) (medcat2.components.normalizing.normalizer.CDB class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.normalizing.normalizer.Vocab class method) (medcat2.components.tagging.tagger.CDB class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.components.tagging.tagger.Vocab class method) (medcat2.components.types.CDB class method) (medcat2.components.types.Vocab class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.CDB class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.CDB class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.pipeline.pipeline.Serialisable class method) (medcat2.pipeline.pipeline.Vocab class method) (medcat2.stats.kfold.CAT class method) (medcat2.stats.stats.CAT class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.storage.serialisables.AbstractManualSerialisable class method) (medcat2.storage.serialisables.AbstractSerialisable class method) (medcat2.storage.serialisables.ManualSerialisable class method) (medcat2.storage.serialisables.Serialisable class method) (medcat2.storage.serialisers.ManualSerialisable class method) (medcat2.storage.serialisers.Serialisable class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDB class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.data_utils.CDB class method) (medcat2.utils.default_args.CDB class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.default_args.Vocab class method) (medcat2.utils.envsnapshot.AbstractSerialisable class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.conversion_all.CAT class method) (medcat2.utils.legacy.convert_cdb.CDB class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.CDB class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) (medcat2.utils.legacy.convert_vocab.Vocab class method) (medcat2.utils.vocab_utils.CDB class method) (medcat2.utils.vocab_utils.Vocab class method) (medcat2.vocab.AbstractSerialisable class method) (medcat2.vocab.Vocab class method)

include_text_in_output (medcat2.config.config.AnnotationOutput attribute) IncorrectAddonLoaded IncorrectAddonLoaded.__cause__ (class in medcat2.pipeline.pipeline) IncorrectAddonLoaded.__context__ (class in medcat2.pipeline.pipeline) IncorrectAddonLoaded.__suppress_context__ (class in medcat2.pipeline.pipeline) IncorrectAddonLoaded.__traceback__ (class in medcat2.pipeline.pipeline) IncorrectAddonLoaded.args (class in medcat2.pipeline.pipeline) IncorrectArgumentsForComponent IncorrectArgumentsForComponent.__cause__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForComponent.__context__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForComponent.__suppress_context__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForComponent.__traceback__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForComponent.args (class in medcat2.pipeline.pipeline) IncorrectArgumentsForTokenizer IncorrectArgumentsForTokenizer.__cause__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForTokenizer.__context__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForTokenizer.__suppress_context__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForTokenizer.__traceback__ (class in medcat2.pipeline.pipeline) IncorrectArgumentsForTokenizer.args (class in medcat2.pipeline.pipeline) IncorrectConfigValues IncorrectConfigValues.__cause__ (class in medcat2.config.config) IncorrectConfigValues.__context__ (class in medcat2.config.config) IncorrectConfigValues.__suppress_context__ (class in medcat2.config.config) IncorrectConfigValues.__traceback__ (class in medcat2.config.config) IncorrectConfigValues.args (class in medcat2.config.config) IncorrectCoreComponent IncorrectCoreComponent.__cause__ (class in medcat2.pipeline.pipeline) IncorrectCoreComponent.__context__ (class in medcat2.pipeline.pipeline) IncorrectCoreComponent.__suppress_context__ (class in medcat2.pipeline.pipeline) IncorrectCoreComponent.__traceback__ (class in medcat2.pipeline.pipeline) IncorrectCoreComponent.args (class in medcat2.pipeline.pipeline) IncorrectExtraComponent IncorrectExtraComponent.__cause__ (class in medcat2.utils.import_utils) IncorrectExtraComponent.__context__ (class in medcat2.utils.import_utils) IncorrectExtraComponent.__suppress_context__ (class in medcat2.utils.import_utils) IncorrectExtraComponent.__traceback__ (class in medcat2.utils.import_utils) IncorrectExtraComponent.args (class in medcat2.utils.import_utils) IncorrectFolderUponLoad IncorrectFolderUponLoad.__cause__ (class in medcat2.pipeline.pipeline) IncorrectFolderUponLoad.__context__ (class in medcat2.pipeline.pipeline) IncorrectFolderUponLoad.__suppress_context__ (class in medcat2.pipeline.pipeline) IncorrectFolderUponLoad.__traceback__ (class in medcat2.pipeline.pipeline) IncorrectFolderUponLoad.args (class in medcat2.pipeline.pipeline) index (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) index2word (medcat2.cat.Vocab attribute) (medcat2.components.addons.meta_cat.meta_cat.Vocab attribute) (medcat2.components.linking.context_based_linker.Vocab attribute) (medcat2.components.linking.no_action_linker.Vocab attribute) (medcat2.components.linking.vector_context_model.Vocab attribute) (medcat2.components.ner.dict_based_ner.Vocab attribute) (medcat2.components.ner.trf.transformers_ner.Vocab attribute) (medcat2.components.ner.vocab_based_ner.Vocab attribute) (medcat2.components.normalizing.normalizer.Vocab attribute) (medcat2.components.tagging.tagger.Vocab attribute) (medcat2.components.types.Vocab attribute) (medcat2.pipeline.pipeline.Vocab attribute) (medcat2.utils.default_args.Vocab attribute) (medcat2.utils.legacy.convert_vocab.Vocab attribute) (medcat2.utils.vocab_utils.Vocab attribute) (medcat2.vocab.Vocab attribute) init_args (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) init_cumsums() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) init_kwargs (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) input_size (medcat2.config.config_meta_cat.Model attribute) IntValuedMetric (in module medcat2.stats.kfold) ipu() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) is_core() (medcat2.cat.AbstractCoreComponent method) (medcat2.cat.AddonComponent method) (medcat2.components.addons.addons.AddonComponent method) (medcat2.components.addons.addons.BaseComponent method) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.linking.context_based_linker.AbstractCoreComponent method) (medcat2.components.linking.context_based_linker.Linker method) (medcat2.components.linking.no_action_linker.AbstractCoreComponent method) (medcat2.components.linking.no_action_linker.NoActionLinker method) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent method) (medcat2.components.ner.dict_based_ner.NER method) (medcat2.components.ner.trf.deid.TransformersNER method) (medcat2.components.ner.trf.model.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent method) (medcat2.components.ner.trf.transformers_ner.TransformersNER method) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent method) (medcat2.components.ner.vocab_based_ner.NER method) (medcat2.components.normalizing.normalizer.AbstractCoreComponent method) (medcat2.components.normalizing.normalizer.TokenNormalizer method) (medcat2.components.tagging.tagger.AbstractCoreComponent method) (medcat2.components.tagging.tagger.TagAndSkipTagger method) (medcat2.components.types.AbstractCoreComponent method) (medcat2.components.types.BaseComponent method) (medcat2.components.types.CoreComponent method) (medcat2.pipeline.pipeline.AbstractCoreComponent method) (medcat2.pipeline.pipeline.AddonComponent method) (medcat2.pipeline.pipeline.BaseComponent method) (medcat2.pipeline.pipeline.CoreComponent method) (medcat2.utils.legacy.conversion_all.NoActionLinker method) (medcat2.utils.legacy.convert_deid.TransformersNER method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) is_digit (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) is_dirty (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) is_punctuation (medcat2.components.linking.vector_context_model.MutableToken property) (medcat2.components.ner.vocab_based_annotator.MutableToken property) (medcat2.pipeline.pipeline.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.MutableToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokenizers.MutableToken property) (medcat2.tokenizing.tokens.MutableToken property) (medcat2.trainer.MutableToken property) is_stop (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) is_upper (medcat2.cdb.cdb.NameDescriptor attribute) (medcat2.cdb.cdb.NameInfo attribute) (medcat2.cdb.concepts.NameInfo attribute) (medcat2.components.linking.vector_context_model.NameInfo attribute) (medcat2.components.ner.trf.transformers_ner.NameDescriptor attribute) (medcat2.preprocessors.cleaners.NameDescriptor attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) (medcat2.trainer.NameDescriptor attribute) (medcat2.utils.cdb_state.NameInfo attribute) isupper() (medcat2.tokenizing.regex_impl.tokenizer.BaseDocument method) (medcat2.tokenizing.regex_impl.tokenizer.Document method) (medcat2.tokenizing.spacy_impl.tokenizers.Document method) (medcat2.tokenizing.spacy_impl.tokens.BaseDocument method) (medcat2.tokenizing.spacy_impl.tokens.Document method) (medcat2.tokenizing.tokens.BaseDocument method) item() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) items() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) iter_addons() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) iter_all_components() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) iter_anns() (in module medcat2.data.mctexport) (in module medcat2.stats.kfold) iter_docs() (in module medcat2.data.mctexport) (in module medcat2.stats.kfold) iter_projects() (in module medcat2.data.mctexport)

J

json() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method)

K

keep_punct (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.trainer.Preprocessing attribute) KeyDefaultDict (class in medcat2.utils.import_utils) keys() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method)

known() (medcat2.components.normalizing.normalizer.BasicSpellChecker method) kwargs (medcat2.utils.legacy.convert_cdb.LegacyClassNotFound attribute)

L

label (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity property) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity property) (medcat2.tokenizing.tokens.BaseEntity property) label_map (medcat2.components.ner.trf.tokenizer.TransformersTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer attribute) last_modified (medcat2.data.mctexport.MedCATTrainerExportDocument attribute) (medcat2.stats.kfold.MedCATTrainerExportDocument attribute) (medcat2.stats.stats.MedCATTrainerExportDocument attribute) (medcat2.trainer.MedCATTrainerExportDocument attribute) (medcat2.utils.data_utils.MedCATTrainerExportDocument attribute) last_saved (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute) last_train_on (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.General attribute) LCDBMaker (class in medcat2.preprocessors.cleaners) LegacyClassNotFound (class in medcat2.utils.legacy.convert_cdb) lemma (medcat2.components.linking.vector_context_model.MutableToken property) (medcat2.components.ner.vocab_based_annotator.MutableToken property) (medcat2.pipeline.pipeline.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.MutableToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokenizers.MutableToken property) (medcat2.tokenizing.tokens.MutableToken property) (medcat2.trainer.MutableToken property) LGeneral (class in medcat2.preprocessors.cleaners) link_candidates (medcat2.cat.MutableEntity property) (medcat2.components.addons.addons.MutableEntity property) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity property) (medcat2.components.linking.context_based_linker.MutableEntity property) (medcat2.components.linking.vector_context_model.MutableEntity property) (medcat2.components.ner.trf.transformers_ner.MutableEntity property) (medcat2.components.ner.vocab_based_annotator.MutableEntity property) (medcat2.components.types.MutableEntity property) (medcat2.pipeline.pipeline.MutableEntity property) (medcat2.stats.stats.MutableEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity attribute) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity attribute) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity attribute) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity property) (medcat2.tokenizing.tokenizers.MutableEntity property) (medcat2.tokenizing.tokens.MutableEntity property) (medcat2.trainer.MutableEntity property) (medcat2.utils.data_utils.MutableEntity property) (medcat2.utils.postprocessing.MutableEntity property) Linker (class in medcat2.components.linking.context_based_linker) Linking (class in medcat2.components.linking.vector_context_model) (class in medcat2.config.config) linking (medcat2.components.linking.context_based_linker.CoreComponentType attribute) (medcat2.components.linking.no_action_linker.CoreComponentType attribute) (medcat2.components.ner.dict_based_ner.CoreComponentType attribute) (medcat2.components.ner.trf.deid.CoreComponentType attribute) (medcat2.components.ner.trf.model.CoreComponentType attribute) (medcat2.components.ner.trf.transformers_ner.CoreComponentType attribute) (medcat2.components.ner.vocab_based_ner.CoreComponentType attribute) (medcat2.components.normalizing.normalizer.CoreComponentType attribute) (medcat2.components.tagging.tagger.CoreComponentType attribute) (medcat2.components.types.CoreComponentType attribute) (medcat2.config.config.Components attribute) (medcat2.pipeline.pipeline.CoreComponentType attribute) (medcat2.trainer.CoreComponentType attribute) (medcat2.utils.default_args.CoreComponentType attribute) (medcat2.utils.legacy.conversion_all.CoreComponentType attribute) LinkingFilters (class in medcat2.config.config) (class in medcat2.stats.stats) (class in medcat2.utils.filters) list_available_tokenizers() (in module medcat2.tokenizing.tokenizers) list_components() (medcat2.components.addons.addons.Registry method) (medcat2.components.types.Registry method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.utils.registry.Registry method) load() (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase class method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase class method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase class method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT class method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE class method) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase class method) (medcat2.components.ner.trf.tokenizer.TransformersTokenizer class method) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer class method) (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase class method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT class method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE class method) load_additems() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_and_apply_cdb_state() (in module medcat2.utils.cdb_state) load_append() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_appends() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binbytes() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binbytes8() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binfloat() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binget() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binint() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binint1() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binint2() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binpersid() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binput() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binstring() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binunicode() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_binunicode8() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_build() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_bytearray8() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_cnf() (in module medcat2.utils.legacy.convert_meta_cat) load_dict() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_dup() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_empty_dictionary() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_empty_list() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_empty_set() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_empty_tuple() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method)

load_existing() (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon class method) (medcat2.components.ner.trf.deid.TransformersNER class method) (medcat2.components.ner.trf.model.TransformersNER class method) (medcat2.components.ner.trf.transformers_ner.TransformersNER class method) (medcat2.utils.legacy.convert_deid.TransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon class method) load_ext1() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_ext2() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_ext4() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_false() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_float() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_frame() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_frozenset() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_get() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_global() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_inst() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_int() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_list() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_long() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_long1() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_long4() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_long_binget() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_long_binput() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_mark() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_memoize() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_model_pack() (medcat2.cat.CAT class method) (medcat2.components.ner.trf.deid.CAT class method) (medcat2.components.ner.trf.deid.DeIdModel class method) (medcat2.components.ner.trf.deid.NerModel class method) (medcat2.components.ner.trf.model.CAT class method) (medcat2.components.ner.trf.model.NerModel class method) (medcat2.stats.kfold.CAT class method) (medcat2.stats.stats.CAT class method) (medcat2.utils.legacy.conversion_all.CAT class method) load_newobj() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_newobj_ex() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_next_buffer() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_none() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_obj() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_old_raw_data() (in module medcat2.utils.legacy.convert_cdb) load_persid() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_pop() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_pop_mark() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_proto() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_put() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_readonly_buffer() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_reduce() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_schema() (in module medcat2.storage.schema) (in module medcat2.storage.serialisers) load_setitem() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_setitems() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_short_binbytes() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_short_binstring() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_short_binunicode() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_stack_global() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_state_dict() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) load_stop() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_string() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_true() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_tuple() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_tuple1() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_tuple2() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_tuple3() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) load_unicode() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) location (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute) log_format (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) log_level (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) log_path (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) logger (in module medcat2.cat) (in module medcat2.cdb.cdb) (in module medcat2.components.addons.meta_cat.data_utils) (in module medcat2.components.addons.meta_cat.meta_cat) (in module medcat2.components.addons.meta_cat.ml_utils) (in module medcat2.components.addons.meta_cat.models) (in module medcat2.components.linking.context_based_linker) (in module medcat2.components.linking.vector_context_model) (in module medcat2.components.ner.dict_based_ner) (in module medcat2.components.ner.trf.deid) (in module medcat2.components.ner.trf.tokenizer) (in module medcat2.components.ner.trf.transformers_ner) (in module medcat2.components.ner.vocab_based_annotator) (in module medcat2.components.ner.vocab_based_ner) (in module medcat2.config.config) (in module medcat2.model_creation.cdb_maker) (in module medcat2.pipeline.pipeline) (in module medcat2.storage.serialisers) (in module medcat2.tokenizing.spacy_impl.tokens) (in module medcat2.tokenizing.spacy_impl.utils) (in module medcat2.tokenizing.tokenizers) (in module medcat2.trainer) (in module medcat2.utils.cdb_state) (in module medcat2.utils.default_args) (in module medcat2.utils.envsnapshot) (in module medcat2.utils.legacy.conversion_all) (in module medcat2.utils.legacy.convert_cdb) (in module medcat2.utils.legacy.convert_config) (in module medcat2.utils.legacy.convert_meta_cat) (in module medcat2.utils.ner.metrics) (in module medcat2.utils.registry) (in module medcat2.utils.vocab_utils) loss_funct (medcat2.config.config_meta_cat.Train attribute) lower (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) lowercase (medcat2.config.config_meta_cat.General attribute) lowercase_context (medcat2.config.config.AnnotationOutput attribute) LPreprocessing (class in medcat2.preprocessors.cleaners) lr (medcat2.config.config_meta_cat.Train attribute) LSTM (class in medcat2.components.addons.meta_cat.models)

M

m (medcat2.cat.Hasher attribute) (medcat2.cdb.cdb.Hasher attribute) (medcat2.components.addons.meta_cat.meta_cat.Hasher attribute) (medcat2.components.ner.trf.transformers_ner.Hasher attribute) (medcat2.config.config_transformers_ner.Hasher attribute) (medcat2.utils.hasher.Hasher attribute) main() (in module medcat2.utils.legacy.legacy_converter) make_mc_train_test() (in module medcat2.trainer) (in module medcat2.utils.data_utils) make_or_update_cdb() (in module medcat2.components.ner.trf.helpers) make_pretty_labels (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) MANUAL (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy attribute) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy attribute) (medcat2.config.config.SerialisingStrategy attribute) (medcat2.storage.serialisables.SerialisingStrategy attribute) MANUAL_SERIALISED_RE (in module medcat2.storage.serialisers) MANUAL_SERIALISED_TAG (in module medcat2.storage.serialisers) ManualSerialisable (class in medcat2.storage.serialisables) (class in medcat2.storage.serialisers) map_cui_to_group (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) mark_saved_now() (medcat2.config.config.ModelMeta method) (medcat2.utils.cdb_state.ModelMeta method) max_document_length (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.trainer.Preprocessing attribute) max_len (medcat2.components.ner.trf.tokenizer.TransformersTokenizer attribute) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer attribute) max_skip_tokens (medcat2.config.config.Ner attribute) MAX_TEST_FRACTION (medcat2.utils.data_utils.TestTrainSplitter attribute) maybe_annotate_name() (in module medcat2.components.ner.dict_based_ner) (in module medcat2.components.ner.vocab_based_annotator) (in module medcat2.components.ner.vocab_based_ner) mc (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon property) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon property) mct_export (medcat2.stats.kfold.FoldCreator attribute) (medcat2.stats.kfold.PerAnnsFoldCreator attribute) (medcat2.stats.kfold.PerDocsFoldCreator attribute) (medcat2.stats.kfold.SimpleFoldCreator attribute) (medcat2.stats.kfold.WeightedDocumentsCreator attribute) medcat2 module medcat2.cat module medcat2.cdb module medcat2.cdb.cdb module medcat2.cdb.concepts module medcat2.components module medcat2.components.addons module medcat2.components.addons.addons module medcat2.components.addons.meta_cat module medcat2.components.addons.meta_cat.data_utils module medcat2.components.addons.meta_cat.meta_cat module medcat2.components.addons.meta_cat.meta_cat_tokenizers module medcat2.components.addons.meta_cat.ml_utils module medcat2.components.addons.meta_cat.models module medcat2.components.linking module medcat2.components.linking.context_based_linker module medcat2.components.linking.no_action_linker module medcat2.components.linking.vector_context_model module medcat2.components.ner module medcat2.components.ner.dict_based_ner module medcat2.components.ner.trf module medcat2.components.ner.trf.deid module medcat2.components.ner.trf.helpers module medcat2.components.ner.trf.model module medcat2.components.ner.trf.tokenizer module medcat2.components.ner.trf.transformers_ner module medcat2.components.ner.vocab_based_annotator module medcat2.components.ner.vocab_based_ner module medcat2.components.normalizing module medcat2.components.normalizing.normalizer module medcat2.components.tagging module medcat2.components.tagging.tagger module medcat2.components.types module medcat2.config module medcat2.config.config module medcat2.config.config_meta_cat module medcat2.config.config_transformers_ner module medcat2.data module medcat2.data.entities module medcat2.data.mctexport module medcat2.data.model_card module medcat2.model_creation module medcat2.model_creation.cdb_maker module medcat2.pipeline module medcat2.pipeline.pipeline module medcat2.preprocessors module medcat2.preprocessors.cleaners module medcat2.stats module medcat2.stats.kfold module medcat2.stats.stats module medcat2.storage module medcat2.storage.schema module medcat2.storage.serialisables module medcat2.storage.serialisers module medcat2.tokenizing module medcat2.tokenizing.regex_impl module medcat2.tokenizing.regex_impl.tokenizer module medcat2.tokenizing.spacy_impl module medcat2.tokenizing.spacy_impl.tokenizers module medcat2.tokenizing.spacy_impl.tokens module medcat2.tokenizing.spacy_impl.utils module medcat2.tokenizing.tokenizers module medcat2.tokenizing.tokens module medcat2.trainer module medcat2.utils module medcat2.utils.cdb_state module medcat2.utils.config_utils module medcat2.utils.data_utils module medcat2.utils.default_args module medcat2.utils.defaults module medcat2.utils.envsnapshot module medcat2.utils.fileutils module medcat2.utils.filters module medcat2.utils.hasher module medcat2.utils.import_utils module medcat2.utils.iterutils module medcat2.utils.legacy module medcat2.utils.legacy.conversion_all module medcat2.utils.legacy.convert_cdb module medcat2.utils.legacy.convert_config module medcat2.utils.legacy.convert_deid module medcat2.utils.legacy.convert_meta_cat module medcat2.utils.legacy.convert_vocab module medcat2.utils.legacy.legacy_converter module medcat2.utils.matutils module medcat2.utils.ner module medcat2.utils.ner.data_collator module medcat2.utils.ner.metrics module medcat2.utils.ner.transformers_ner module medcat2.utils.postprocessing module medcat2.utils.registry module medcat2.utils.vocab_utils module medcat2.vocab module medcat_version (in module medcat2.config.config) (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute) MedCATAnnotationsConfig (class in medcat2.utils.ner.transformers_ner) MedCATRegistryException MedCATRegistryException.__cause__ (class in medcat2.utils.registry) MedCATRegistryException.__context__ (class in medcat2.utils.registry) MedCATRegistryException.__suppress_context__ (class in medcat2.utils.registry) MedCATRegistryException.__traceback__ (class in medcat2.utils.registry) MedCATRegistryException.args (class in medcat2.utils.registry) MedCATTrainerExport (class in medcat2.data.mctexport) (class in medcat2.stats.kfold) (class in medcat2.stats.stats) (class in medcat2.trainer) (class in medcat2.utils.data_utils) MedCATTrainerExportAnnotation (class in medcat2.data.mctexport) (class in medcat2.stats.kfold) (class in medcat2.stats.stats) MedCATTrainerExportDocument (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.data.mctexport) (class in medcat2.stats.kfold) (class in medcat2.stats.stats) (class in medcat2.trainer) (class in medcat2.utils.data_utils) MedCATTrainerExportProject (class in medcat2.data.mctexport) (class in medcat2.stats.kfold) (class in medcat2.stats.stats) (class in medcat2.trainer) (class in medcat2.utils.data_utils) (class in medcat2.utils.filters) MedCATTrainerExportProjectInfo (in module medcat2.data.mctexport) (in module medcat2.stats.kfold) merge_config() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) meta (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.config.Config attribute) (medcat2.config.config.Config attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) meta_anns (medcat2.cat.Entity attribute) (medcat2.data.entities.Entity attribute) MetaAnnotation (class in medcat2.data.entities) MetaCAT (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.utils.legacy.convert_meta_cat) MetaCATAddon (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.utils.legacy.convert_meta_cat) metric (medcat2.config.config_meta_cat.Train attribute) metrics() (in module medcat2.components.ner.trf.transformers_ner) (in module medcat2.utils.ner.metrics) MIN_CNT_FOR_TEST (medcat2.utils.data_utils.TestTrainSplitter attribute) min_len_normalize (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.preprocessors.cleaners.LPreprocessing attribute) (medcat2.trainer.Preprocessing attribute) min_letters_required (medcat2.config.config.CDBMaker attribute) (medcat2.preprocessors.cleaners.LCDBMaker attribute) (medcat2.trainer.CDBMaker attribute) min_name_len (medcat2.config.config.Ner attribute) MisconfiguredMetaCATException MisconfiguredMetaCATException.__cause__ (class in medcat2.components.addons.meta_cat.meta_cat) MisconfiguredMetaCATException.__context__ (class in medcat2.components.addons.meta_cat.meta_cat) MisconfiguredMetaCATException.__suppress_context__ (class in medcat2.components.addons.meta_cat.meta_cat) MisconfiguredMetaCATException.__traceback__ (class in medcat2.components.addons.meta_cat.meta_cat) MisconfiguredMetaCATException.args (class in medcat2.components.addons.meta_cat.meta_cat) missing (medcat2.utils.import_utils.MissingDependenciesError attribute) MissingDependenciesError MissingDependenciesError.__cause__ (class in medcat2.utils.import_utils) MissingDependenciesError.__context__ (class in medcat2.utils.import_utils) MissingDependenciesError.__suppress_context__ (class in medcat2.utils.import_utils) MissingDependenciesError.__traceback__ (class in medcat2.utils.import_utils) MissingDependenciesError.args (class in medcat2.utils.import_utils) Model (class in medcat2.config.config_meta_cat) model (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCAT attribute) Model.Config (class in medcat2.config.config_meta_cat) model_architecture_config (medcat2.config.config_meta_cat.Model attribute) model_computed_fields (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute) (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute) (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) model_config (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute) (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute) (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) model_construct() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) model_copy() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) model_dump() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) model_dump_json() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) model_extra (medcat2.cat.Config property) (medcat2.cdb.cdb.Config property) (medcat2.components.addons.addons.ComponentConfig property) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT property) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT property) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT property) (medcat2.components.linking.context_based_linker.Config property) (medcat2.components.linking.vector_context_model.Linking property) (medcat2.components.ner.trf.deid.ConfigTransformersNER property) (medcat2.components.ner.trf.helpers.Config property) (medcat2.components.ner.trf.model.Config property) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER property) (medcat2.components.ner.vocab_based_annotator.Config property) (medcat2.components.normalizing.normalizer.Config property) (medcat2.components.tagging.tagger.Preprocessing property) (medcat2.config.Config property) (medcat2.config.config.AnnotationOutput property) (medcat2.config.config.CDBMaker property) (medcat2.config.config.ComponentConfig property) (medcat2.config.config.Components property) (medcat2.config.config.Config property) (medcat2.config.config.Environment property) (medcat2.config.config.General property) (medcat2.config.config.Linking property) (medcat2.config.config.LinkingFilters property) (medcat2.config.config.ModelMeta property) (medcat2.config.config.Ner property) (medcat2.config.config.NLPConfig property) (medcat2.config.config.Preprocessing property) (medcat2.config.config.SerialisableBaseModel property) (medcat2.config.config.TrainingDescriptor property) (medcat2.config.config_meta_cat.ComponentConfig property) (medcat2.config.config_meta_cat.ConfigMetaCAT property) (medcat2.config.config_meta_cat.General property) (medcat2.config.config_meta_cat.Model property) (medcat2.config.config_meta_cat.SerialisableBaseModel property) (medcat2.config.config_meta_cat.Train property) (medcat2.config.config_transformers_ner.ConfigTransformersNER property) (medcat2.config.config_transformers_ner.General property) (medcat2.config.config_transformers_ner.SerialisableBaseModel property) (medcat2.model_creation.cdb_maker.Config property) (medcat2.pipeline.pipeline.ComponentConfig property) (medcat2.pipeline.pipeline.Config property) (medcat2.pipeline.pipeline.ConfigMetaCAT property) (medcat2.stats.kfold.PerCUIMetrics property) (medcat2.stats.stats.LinkingFilters property) (medcat2.tokenizing.regex_impl.tokenizer.Config property) (medcat2.tokenizing.spacy_impl.tokenizers.Config property) (medcat2.tokenizing.tokenizers.Config property) (medcat2.trainer.CDBMaker property) (medcat2.trainer.General property) (medcat2.trainer.Preprocessing property) (medcat2.utils.cdb_state.ModelMeta property) (medcat2.utils.default_args.ComponentConfig property) (medcat2.utils.default_args.Config property) (medcat2.utils.envsnapshot.Environment property) (medcat2.utils.filters.LinkingFilters property) (medcat2.utils.legacy.convert_cdb.Config property) (medcat2.utils.legacy.convert_config.Config property) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER property) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT property)

model_fields (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.addons.addons.ComponentConfig attribute) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.Config attribute) (medcat2.config.config.AnnotationOutput attribute) (medcat2.config.config.CDBMaker attribute) (medcat2.config.config.ComponentConfig attribute) (medcat2.config.config.Components attribute) (medcat2.config.config.Config attribute) (medcat2.config.config.Environment attribute) (medcat2.config.config.General attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config.LinkingFilters attribute) (medcat2.config.config.ModelMeta attribute) (medcat2.config.config.Ner attribute) (medcat2.config.config.NLPConfig attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.config.config.SerialisableBaseModel attribute) (medcat2.config.config.TrainingDescriptor attribute) (medcat2.config.config_meta_cat.ComponentConfig attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_meta_cat.SerialisableBaseModel attribute) (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.config.config_transformers_ner.SerialisableBaseModel attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.ComponentConfig attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.stats.kfold.PerCUIMetrics attribute) (medcat2.stats.stats.LinkingFilters attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.trainer.CDBMaker attribute) (medcat2.trainer.General attribute) (medcat2.trainer.Preprocessing attribute) (medcat2.utils.cdb_state.ModelMeta attribute) (medcat2.utils.default_args.ComponentConfig attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.envsnapshot.Environment attribute) (medcat2.utils.filters.LinkingFilters attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) model_fields_set (medcat2.cat.Config property) (medcat2.cdb.cdb.Config property) (medcat2.components.addons.addons.ComponentConfig property) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT property) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT property) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT property) (medcat2.components.linking.context_based_linker.Config property) (medcat2.components.linking.vector_context_model.Linking property) (medcat2.components.ner.trf.deid.ConfigTransformersNER property) (medcat2.components.ner.trf.helpers.Config property) (medcat2.components.ner.trf.model.Config property) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER property) (medcat2.components.ner.vocab_based_annotator.Config property) (medcat2.components.normalizing.normalizer.Config property) (medcat2.components.tagging.tagger.Preprocessing property) (medcat2.config.Config property) (medcat2.config.config.AnnotationOutput property) (medcat2.config.config.CDBMaker property) (medcat2.config.config.ComponentConfig property) (medcat2.config.config.Components property) (medcat2.config.config.Config property) (medcat2.config.config.Environment property) (medcat2.config.config.General property) (medcat2.config.config.Linking property) (medcat2.config.config.LinkingFilters property) (medcat2.config.config.ModelMeta property) (medcat2.config.config.Ner property) (medcat2.config.config.NLPConfig property) (medcat2.config.config.Preprocessing property) (medcat2.config.config.SerialisableBaseModel property) (medcat2.config.config.TrainingDescriptor property) (medcat2.config.config_meta_cat.ComponentConfig property) (medcat2.config.config_meta_cat.ConfigMetaCAT property) (medcat2.config.config_meta_cat.General property) (medcat2.config.config_meta_cat.Model property) (medcat2.config.config_meta_cat.SerialisableBaseModel property) (medcat2.config.config_meta_cat.Train property) (medcat2.config.config_transformers_ner.ConfigTransformersNER property) (medcat2.config.config_transformers_ner.General property) (medcat2.config.config_transformers_ner.SerialisableBaseModel property) (medcat2.model_creation.cdb_maker.Config property) (medcat2.pipeline.pipeline.ComponentConfig property) (medcat2.pipeline.pipeline.Config property) (medcat2.pipeline.pipeline.ConfigMetaCAT property) (medcat2.stats.kfold.PerCUIMetrics property) (medcat2.stats.stats.LinkingFilters property) (medcat2.tokenizing.regex_impl.tokenizer.Config property) (medcat2.tokenizing.spacy_impl.tokenizers.Config property) (medcat2.tokenizing.tokenizers.Config property) (medcat2.trainer.CDBMaker property) (medcat2.trainer.General property) (medcat2.trainer.Preprocessing property) (medcat2.utils.cdb_state.ModelMeta property) (medcat2.utils.default_args.ComponentConfig property) (medcat2.utils.default_args.Config property) (medcat2.utils.envsnapshot.Environment property) (medcat2.utils.filters.LinkingFilters property) (medcat2.utils.legacy.convert_cdb.Config property) (medcat2.utils.legacy.convert_config.Config property) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER property) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT property) model_freeze_layers (medcat2.config.config_meta_cat.Model attribute) model_json_schema() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) model_name (medcat2.config.config_meta_cat.Model attribute) (medcat2.config.config_transformers_ner.General attribute) model_parametrized_name() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) model_post_init() (medcat2.cat.Config method) (medcat2.cdb.cdb.Config method) (medcat2.components.addons.addons.ComponentConfig method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT method) (medcat2.components.linking.context_based_linker.Config method) (medcat2.components.linking.vector_context_model.Linking method) (medcat2.components.ner.trf.deid.ConfigTransformersNER method) (medcat2.components.ner.trf.helpers.Config method) (medcat2.components.ner.trf.model.Config method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER method) (medcat2.components.ner.vocab_based_annotator.Config method) (medcat2.components.normalizing.normalizer.Config method) (medcat2.components.tagging.tagger.Preprocessing method) (medcat2.config.Config method) (medcat2.config.config.AnnotationOutput method) (medcat2.config.config.CDBMaker method) (medcat2.config.config.ComponentConfig method) (medcat2.config.config.Components method) (medcat2.config.config.Config method) (medcat2.config.config.Environment method) (medcat2.config.config.General method) (medcat2.config.config.Linking method) (medcat2.config.config.LinkingFilters method) (medcat2.config.config.ModelMeta method) (medcat2.config.config.Ner method) (medcat2.config.config.NLPConfig method) (medcat2.config.config.Preprocessing method) (medcat2.config.config.SerialisableBaseModel method) (medcat2.config.config.TrainingDescriptor method) (medcat2.config.config_meta_cat.ComponentConfig method) (medcat2.config.config_meta_cat.ConfigMetaCAT method) (medcat2.config.config_meta_cat.General method) (medcat2.config.config_meta_cat.Model method) (medcat2.config.config_meta_cat.SerialisableBaseModel method) (medcat2.config.config_meta_cat.Train method) (medcat2.config.config_transformers_ner.ConfigTransformersNER method) (medcat2.config.config_transformers_ner.General method) (medcat2.config.config_transformers_ner.SerialisableBaseModel method) (medcat2.model_creation.cdb_maker.Config method) (medcat2.pipeline.pipeline.ComponentConfig method) (medcat2.pipeline.pipeline.Config method) (medcat2.pipeline.pipeline.ConfigMetaCAT method) (medcat2.stats.kfold.PerCUIMetrics method) (medcat2.stats.stats.LinkingFilters method) (medcat2.tokenizing.regex_impl.tokenizer.Config method) (medcat2.tokenizing.spacy_impl.tokenizers.Config method) (medcat2.tokenizing.tokenizers.Config method) (medcat2.trainer.CDBMaker method) (medcat2.trainer.General method) (medcat2.trainer.Preprocessing method) (medcat2.utils.cdb_state.ModelMeta method) (medcat2.utils.default_args.ComponentConfig method) (medcat2.utils.default_args.Config method) (medcat2.utils.envsnapshot.Environment method) (medcat2.utils.filters.LinkingFilters method) (medcat2.utils.legacy.convert_cdb.Config method) (medcat2.utils.legacy.convert_config.Config method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT method) model_rebuild() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) model_validate() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) model_validate_json() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) model_validate_strings() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) model_variant (medcat2.config.config_meta_cat.Model attribute) ModelCard (in module medcat2.cat) (in module medcat2.data.model_card) ModelMeta (class in medcat2.config.config) (class in medcat2.utils.cdb_state) modelname (medcat2.config.config.NLPConfig attribute) module medcat2 medcat2.cat medcat2.cdb medcat2.cdb.cdb medcat2.cdb.concepts medcat2.components medcat2.components.addons medcat2.components.addons.addons medcat2.components.addons.meta_cat medcat2.components.addons.meta_cat.data_utils medcat2.components.addons.meta_cat.meta_cat medcat2.components.addons.meta_cat.meta_cat_tokenizers medcat2.components.addons.meta_cat.ml_utils medcat2.components.addons.meta_cat.models medcat2.components.linking medcat2.components.linking.context_based_linker medcat2.components.linking.no_action_linker medcat2.components.linking.vector_context_model medcat2.components.ner medcat2.components.ner.dict_based_ner medcat2.components.ner.trf medcat2.components.ner.trf.deid medcat2.components.ner.trf.helpers medcat2.components.ner.trf.model medcat2.components.ner.trf.tokenizer medcat2.components.ner.trf.transformers_ner medcat2.components.ner.vocab_based_annotator medcat2.components.ner.vocab_based_ner medcat2.components.normalizing medcat2.components.normalizing.normalizer medcat2.components.tagging medcat2.components.tagging.tagger medcat2.components.types medcat2.config medcat2.config.config medcat2.config.config_meta_cat medcat2.config.config_transformers_ner medcat2.data medcat2.data.entities medcat2.data.mctexport medcat2.data.model_card medcat2.model_creation medcat2.model_creation.cdb_maker medcat2.pipeline medcat2.pipeline.pipeline medcat2.preprocessors medcat2.preprocessors.cleaners medcat2.stats medcat2.stats.kfold medcat2.stats.stats medcat2.storage medcat2.storage.schema medcat2.storage.serialisables medcat2.storage.serialisers medcat2.tokenizing medcat2.tokenizing.regex_impl medcat2.tokenizing.regex_impl.tokenizer medcat2.tokenizing.spacy_impl medcat2.tokenizing.spacy_impl.tokenizers medcat2.tokenizing.spacy_impl.tokens medcat2.tokenizing.spacy_impl.utils medcat2.tokenizing.tokenizers medcat2.tokenizing.tokens medcat2.trainer medcat2.utils medcat2.utils.cdb_state medcat2.utils.config_utils medcat2.utils.data_utils medcat2.utils.default_args medcat2.utils.defaults medcat2.utils.envsnapshot medcat2.utils.fileutils medcat2.utils.filters medcat2.utils.hasher medcat2.utils.import_utils medcat2.utils.iterutils medcat2.utils.legacy medcat2.utils.legacy.conversion_all medcat2.utils.legacy.convert_cdb medcat2.utils.legacy.convert_config medcat2.utils.legacy.convert_deid medcat2.utils.legacy.convert_meta_cat medcat2.utils.legacy.convert_vocab medcat2.utils.legacy.legacy_converter medcat2.utils.matutils medcat2.utils.ner medcat2.utils.ner.data_collator medcat2.utils.ner.metrics medcat2.utils.ner.transformers_ner medcat2.utils.postprocessing medcat2.utils.registry medcat2.utils.vocab_utils medcat2.vocab modules() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) MOVE_WITH_REMOVES (in module medcat2.utils.legacy.convert_config) mtia() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) multi_separator (medcat2.config.config.CDBMaker attribute) (medcat2.trainer.CDBMaker attribute) MUST_DISAMBIGATE (medcat2.cdb.cdb.ST attribute) (medcat2.components.linking.context_based_linker.ST attribute) (medcat2.components.linking.vector_context_model.ST attribute) (medcat2.utils.defaults.StatusTypes attribute) MutableDocument (class in medcat2.cat) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.no_action_linker) (class in medcat2.components.linking.vector_context_model) (class in medcat2.components.ner.dict_based_ner) (class in medcat2.components.ner.trf.model) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.components.ner.vocab_based_annotator) (class in medcat2.components.ner.vocab_based_ner) (class in medcat2.components.normalizing.normalizer) (class in medcat2.components.tagging.tagger) (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) (class in medcat2.preprocessors.cleaners) (class in medcat2.stats.stats) (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.tokenizers) (class in medcat2.tokenizing.tokens) (class in medcat2.trainer) (class in medcat2.utils.data_utils) (class in medcat2.utils.postprocessing) MutableEntity (class in medcat2.cat) (class in medcat2.components.addons.addons) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.vector_context_model) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.components.ner.vocab_based_annotator) (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) (class in medcat2.stats.stats) (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokenizers) (class in medcat2.tokenizing.tokens) (class in medcat2.trainer) (class in medcat2.utils.data_utils) (class in medcat2.utils.postprocessing) MutableToken (class in medcat2.components.linking.vector_context_model) (class in medcat2.components.ner.vocab_based_annotator) (class in medcat2.pipeline.pipeline) (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokenizers) (class in medcat2.tokenizing.tokens) (class in medcat2.trainer)

N

name (medcat2.cat.AbstractCoreComponent property) (medcat2.cat.AddonComponent property) (medcat2.cdb.cdb.NameInfo attribute) (medcat2.cdb.cdb.TypeInfo attribute) (medcat2.cdb.concepts.NameInfo attribute) (medcat2.cdb.concepts.TypeInfo attribute) (medcat2.components.addons.addons.AddonComponent property) (medcat2.components.addons.addons.BaseComponent property) (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent property) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon property) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT attribute) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE attribute) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase attribute) (medcat2.components.linking.context_based_linker.AbstractCoreComponent property) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.linking.no_action_linker.AbstractCoreComponent property) (medcat2.components.linking.no_action_linker.NoActionLinker attribute) (medcat2.components.linking.vector_context_model.NameInfo attribute) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent property) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.trf.deid.TransformersNER attribute) (medcat2.components.ner.trf.model.TransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent property) (medcat2.components.ner.trf.transformers_ner.TransformersNER attribute) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent property) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.components.normalizing.normalizer.AbstractCoreComponent property) (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) (medcat2.components.tagging.tagger.AbstractCoreComponent property) (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) (medcat2.components.types.AbstractCoreComponent property) (medcat2.components.types.BaseComponent property) (medcat2.components.types.CoreComponent property) (medcat2.config.config_transformers_ner.General attribute) (medcat2.data.entities.MetaAnnotation attribute) (medcat2.data.mctexport.MedCATTrainerExportDocument attribute) (medcat2.data.mctexport.MedCATTrainerExportProject attribute) (medcat2.pipeline.pipeline.AbstractCoreComponent property) (medcat2.pipeline.pipeline.AddonComponent property) (medcat2.pipeline.pipeline.BaseComponent property) (medcat2.pipeline.pipeline.CoreComponent property) (medcat2.stats.kfold.MedCATTrainerExportDocument attribute) (medcat2.stats.kfold.MedCATTrainerExportProject attribute) (medcat2.stats.stats.MedCATTrainerExportDocument attribute) (medcat2.stats.stats.MedCATTrainerExportProject attribute) (medcat2.trainer.MedCATTrainerExportDocument attribute) (medcat2.trainer.MedCATTrainerExportProject attribute) (medcat2.utils.cdb_state.NameInfo attribute) (medcat2.utils.data_utils.MedCATTrainerExportDocument attribute) (medcat2.utils.data_utils.MedCATTrainerExportProject attribute) (medcat2.utils.filters.MedCATTrainerExportProject attribute) (medcat2.utils.legacy.conversion_all.NoActionLinker attribute) (medcat2.utils.legacy.convert_cdb.TypeInfo attribute) (medcat2.utils.legacy.convert_deid.TransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCAT attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon property) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT attribute) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE attribute) name() (medcat2.cat.AvailableSerialisers method) (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.linking.context_based_linker.CoreComponentType method) (medcat2.components.linking.no_action_linker.CoreComponentType method) (medcat2.components.ner.dict_based_ner.CoreComponentType method) (medcat2.components.ner.trf.deid.CoreComponentType method) (medcat2.components.ner.trf.model.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers method) (medcat2.components.ner.trf.transformers_ner.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.components.ner.vocab_based_ner.CoreComponentType method) (medcat2.components.normalizing.normalizer.CoreComponentType method) (medcat2.components.tagging.tagger.CoreComponentType method) (medcat2.components.types.CoreComponentType method) (medcat2.config.config.SerialisingStrategy method) (medcat2.config.config_meta_cat.AvailableSerialisers method) (medcat2.pipeline.pipeline.AvailableSerialisers method) (medcat2.pipeline.pipeline.CoreComponentType method) (medcat2.stats.kfold.SplitType method) (medcat2.storage.serialisables.SerialisingStrategy method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.trainer.CoreComponentType method) (medcat2.utils.default_args.CoreComponentType method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.CoreComponentType method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method) name2info (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.context_based_linker.ContextModel attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.linking.vector_context_model.ContextModel attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) NAME2KEYS (in module medcat2.utils.legacy.convert_cdb) name_all_serialisable_elements() (in module medcat2.storage.serialisables) NAME_PREFIX (medcat2.cat.AbstractCoreComponent attribute) (medcat2.cat.AddonComponent attribute) (medcat2.components.addons.addons.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.components.linking.context_based_linker.AbstractCoreComponent attribute) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.linking.no_action_linker.AbstractCoreComponent attribute) (medcat2.components.linking.no_action_linker.NoActionLinker attribute) (medcat2.components.ner.dict_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.trf.deid.TransformersNER attribute) (medcat2.components.ner.trf.model.TransformersNER attribute) (medcat2.components.ner.trf.transformers_ner.AbstractCoreComponent attribute) (medcat2.components.ner.trf.transformers_ner.TransformersNER attribute) (medcat2.components.ner.vocab_based_ner.AbstractCoreComponent attribute) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.components.normalizing.normalizer.AbstractCoreComponent attribute) (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) (medcat2.components.tagging.tagger.AbstractCoreComponent attribute) (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) (medcat2.components.types.AbstractCoreComponent attribute) (medcat2.pipeline.pipeline.AbstractCoreComponent attribute) (medcat2.pipeline.pipeline.AddonComponent attribute) (medcat2.utils.legacy.conversion_all.NoActionLinker attribute) (medcat2.utils.legacy.convert_deid.TransformersNER attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute)

name_separator (medcat2.components.linking.context_based_linker.ContextModel attribute) (medcat2.components.linking.vector_context_model.ContextModel attribute) NAME_SPLITTER (medcat2.cat.AddonComponent attribute) (medcat2.components.addons.addons.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.AddonComponent attribute) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.pipeline.pipeline.AddonComponent attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute) name_versions (medcat2.config.config.CDBMaker attribute) (medcat2.preprocessors.cleaners.LCDBMaker attribute) (medcat2.trainer.CDBMaker attribute) named_buffers() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) named_children() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) named_modules() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) named_parameters() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) NameDescriptor (class in medcat2.cdb.cdb) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.preprocessors.cleaners) (class in medcat2.trainer) NameInfo (class in medcat2.cdb.cdb) (class in medcat2.cdb.concepts) (class in medcat2.components.linking.vector_context_model) (class in medcat2.utils.cdb_state) names (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) nclasses (medcat2.config.config_meta_cat.Model attribute) negative_ignore_punct_and_num (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) negative_probability (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) nepochs (medcat2.config.config_meta_cat.Train attribute) NER (class in medcat2.components.ner.dict_based_ner) (class in medcat2.components.ner.vocab_based_ner) Ner (class in medcat2.config.config) ner (medcat2.components.linking.context_based_linker.CoreComponentType attribute) (medcat2.components.linking.no_action_linker.CoreComponentType attribute) (medcat2.components.ner.dict_based_ner.CoreComponentType attribute) (medcat2.components.ner.trf.deid.CoreComponentType attribute) (medcat2.components.ner.trf.model.CoreComponentType attribute) (medcat2.components.ner.trf.transformers_ner.CoreComponentType attribute) (medcat2.components.ner.vocab_based_ner.CoreComponentType attribute) (medcat2.components.normalizing.normalizer.CoreComponentType attribute) (medcat2.components.tagging.tagger.CoreComponentType attribute) (medcat2.components.types.CoreComponentType attribute) (medcat2.config.config.Components attribute) (medcat2.pipeline.pipeline.CoreComponentType attribute) (medcat2.trainer.CoreComponentType attribute) (medcat2.utils.default_args.CoreComponentType attribute) (medcat2.utils.legacy.conversion_all.CoreComponentType attribute) ner_aggregation_strategy (medcat2.config.config_transformers_ner.General attribute) NerModel (class in medcat2.components.ner.trf.deid) (class in medcat2.components.ner.trf.model) new_model_folder (medcat2.utils.legacy.conversion_all.Converter attribute) (medcat2.utils.legacy.legacy_converter.Converter attribute) nlp (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) NLPConfig (class in medcat2.config.config) NLPConfig.Config (class in medcat2.config.config) NoActionLinker (class in medcat2.components.linking.no_action_linker) (class in medcat2.utils.legacy.conversion_all) norm (medcat2.components.linking.vector_context_model.MutableToken property) (medcat2.components.ner.vocab_based_annotator.MutableToken property) (medcat2.pipeline.pipeline.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.MutableToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokenizers.MutableToken property) (medcat2.tokenizing.tokens.MutableToken property) (medcat2.trainer.MutableToken property) nr_of_docs (medcat2.stats.kfold.PerDocsFoldCreator attribute) nr_of_folds (medcat2.stats.kfold.FoldCreator attribute) (medcat2.stats.kfold.PerAnnsFoldCreator attribute) (medcat2.stats.kfold.PerDocsFoldCreator attribute) (medcat2.stats.kfold.SimpleFoldCreator attribute) (medcat2.stats.kfold.WeightedDocumentsCreator attribute) num_directions (medcat2.config.config_meta_cat.Model attribute) num_docs (medcat2.config.config.TrainingDescriptor attribute) num_epochs (medcat2.config.config.TrainingDescriptor attribute) num_labels (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) num_layers (medcat2.config.config_meta_cat.Model attribute)

O

old_model_folder (medcat2.utils.legacy.conversion_all.Converter attribute) (medcat2.utils.legacy.legacy_converter.Converter attribute) on_disk_memory_capture() (in module medcat2.utils.cdb_state) OnlyCUIEntities (class in medcat2.cat) (class in medcat2.components.ner.trf.model) (class in medcat2.data.entities) ontology (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute) optim (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) OptionalPartNotInstalledException OptionalPartNotInstalledException.__cause__ (class in medcat2.utils.default_args)

OptionalPartNotInstalledException.__context__ (class in medcat2.utils.default_args) OptionalPartNotInstalledException.__suppress_context__ (class in medcat2.utils.default_args) OptionalPartNotInstalledException.__traceback__ (class in medcat2.utils.default_args) OptionalPartNotInstalledException.args (class in medcat2.utils.default_args) original_names (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) os (medcat2.config.config.Environment attribute) (medcat2.utils.envsnapshot.Environment attribute) output_key (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon attribute) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon attribute)

P

P (in module medcat2.utils.registry) P() (medcat2.components.normalizing.normalizer.BasicSpellChecker method) package_name (medcat2.utils.import_utils.IncorrectExtraComponent attribute) (medcat2.utils.import_utils.MissingDependenciesError attribute) pad_id (medcat2.components.ner.trf.transformers_ner.CollateAndPadNER attribute) (medcat2.utils.ner.data_collator.CollateAndPadNER attribute) padding_idx (medcat2.config.config_meta_cat.Model attribute) parameters() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) parse_file() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) parse_obj() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) parse_raw() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method)

path (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException attribute) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException attribute) (medcat2.tokenizing.tokens.UnregisteredDataPathException attribute) per_cui_status (medcat2.cdb.cdb.NameInfo attribute) (medcat2.cdb.concepts.NameInfo attribute) (medcat2.components.linking.vector_context_model.NameInfo attribute) (medcat2.utils.cdb_state.NameInfo attribute) per_doc_simple (medcat2.stats.kfold.PerDocsFoldCreator attribute) per_fold (medcat2.stats.kfold.PerAnnsFoldCreator attribute) (medcat2.stats.kfold.SimpleFoldCreator attribute) PerAnnsFoldCreator (class in medcat2.stats.kfold) PerCUIMetrics (class in medcat2.stats.kfold) PerDocsFoldCreator (class in medcat2.stats.kfold) PerDocumentTokenCache (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.vector_context_model) PH_REMOVE (in module medcat2.model_creation.cdb_maker) phase_number (medcat2.config.config_meta_cat.Model attribute) pipe() (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) pipe_batch_size_in_chars (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_transformers_ner.General attribute) Pipeline (class in medcat2.cat) (class in medcat2.model_creation.cdb_maker) (class in medcat2.pipeline.pipeline) (class in medcat2.trainer) pipeline (medcat2.model_creation.cdb_maker.CDBMaker attribute) pop() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) pop_mark() (medcat2.utils.legacy.convert_cdb.CustomUnpickler method) popitem() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) predict() (in module medcat2.components.addons.meta_cat.meta_cat) (in module medcat2.components.addons.meta_cat.ml_utils) prefer_frequent_concepts (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) prefer_primary_name (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) preferred_name (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) prepare_and_report_training() (medcat2.config.config.ModelMeta method) (medcat2.utils.cdb_state.ModelMeta method) prepare_csvs() (medcat2.model_creation.cdb_maker.CDBMaker method) prepare_document() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) prepare_for_oversampled_data() (in module medcat2.components.addons.meta_cat.data_utils) (in module medcat2.components.addons.meta_cat.meta_cat) prepare_from_json() (in module medcat2.components.addons.meta_cat.data_utils) (in module medcat2.components.addons.meta_cat.meta_cat) prepare_name() (in module medcat2.model_creation.cdb_maker) (in module medcat2.preprocessors.cleaners) (in module medcat2.trainer) Preprocessing (class in medcat2.components.tagging.tagger) (class in medcat2.config.config) (class in medcat2.trainer) preprocessing (medcat2.cat.Config attribute) (medcat2.cdb.cdb.Config attribute) (medcat2.components.linking.context_based_linker.Config attribute) (medcat2.components.ner.trf.helpers.Config attribute) (medcat2.components.ner.trf.model.Config attribute) (medcat2.components.ner.vocab_based_annotator.Config attribute) (medcat2.components.normalizing.normalizer.Config attribute) (medcat2.config.Config attribute) (medcat2.config.config.Config attribute) (medcat2.model_creation.cdb_maker.Config attribute) (medcat2.pipeline.pipeline.Config attribute) (medcat2.tokenizing.regex_impl.tokenizer.Config attribute) (medcat2.tokenizing.spacy_impl.tokenizers.Config attribute) (medcat2.tokenizing.tokenizers.Config attribute) (medcat2.utils.default_args.Config attribute) (medcat2.utils.legacy.convert_cdb.Config attribute) (medcat2.utils.legacy.convert_config.Config attribute) prerequisites (medcat2.config.config_meta_cat.Train attribute) pretty_name (medcat2.cat.Entity attribute) (medcat2.data.entities.Entity attribute) PRIMARY_STATUS (medcat2.cdb.cdb.ST attribute) (medcat2.components.linking.context_based_linker.ST attribute) (medcat2.components.linking.vector_context_model.ST attribute) (medcat2.utils.defaults.StatusTypes attribute) PRIMARY_STATUS_NO_DISAMB (medcat2.cdb.cdb.ST attribute) (medcat2.components.linking.context_based_linker.ST attribute) (medcat2.components.linking.vector_context_model.ST attribute) (medcat2.utils.defaults.StatusTypes attribute) PRIMARY_STATUS_W_DISAMB (medcat2.cdb.cdb.ST attribute) (medcat2.components.linking.context_based_linker.ST attribute) (medcat2.components.linking.vector_context_model.ST attribute) (medcat2.utils.defaults.StatusTypes attribute) print_report() (in module medcat2.components.addons.meta_cat.ml_utils) process_document() (medcat2.stats.stats.StatsBuilder method) process_project() (medcat2.stats.stats.StatsBuilder method) project_filters() (in module medcat2.stats.stats) (in module medcat2.trainer) (in module medcat2.utils.filters) project_name (medcat2.config.config.TrainingDescriptor attribute) projects (medcat2.data.mctexport.MedCATTrainerExport attribute) (medcat2.stats.kfold.MedCATTrainerExport attribute) (medcat2.stats.stats.MedCATTrainerExport attribute) (medcat2.trainer.MedCATTrainerExport attribute) (medcat2.utils.data_utils.MedCATTrainerExport attribute) proto (medcat2.utils.legacy.convert_cdb.CustomUnpickler attribute) provider (medcat2.config.config.NLPConfig attribute) punct_checker (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) python_version (medcat2.config.config.Environment attribute) (medcat2.utils.envsnapshot.Environment attribute)

R

random_replacement_unsupervised (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) RAW_FILE (medcat2.storage.serialisers.DillSerialiser attribute) (medcat2.storage.serialisers.Serialiser attribute) raw_name (medcat2.cdb.cdb.NameDescriptor attribute) (medcat2.components.ner.trf.transformers_ner.NameDescriptor attribute) (medcat2.preprocessors.cleaners.NameDescriptor attribute) (medcat2.trainer.NameDescriptor attribute) REGEX (medcat2.tokenizing.regex_impl.tokenizer.RegexTokenizer attribute) RegexTokenizer (class in medcat2.tokenizing.regex_impl.tokenizer) register() (medcat2.components.addons.addons.Registry method) (medcat2.components.types.Registry method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.utils.registry.Registry method) register_addon() (in module medcat2.components.addons.addons) register_addon_path() (medcat2.cat.MutableDocument class method) (medcat2.cat.MutableEntity class method) (medcat2.components.addons.addons.MutableEntity class method) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument class method) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity class method) (medcat2.components.linking.context_based_linker.MutableDocument class method) (medcat2.components.linking.context_based_linker.MutableEntity class method) (medcat2.components.linking.no_action_linker.MutableDocument class method) (medcat2.components.linking.vector_context_model.MutableDocument class method) (medcat2.components.linking.vector_context_model.MutableEntity class method) (medcat2.components.ner.dict_based_ner.MutableDocument class method) (medcat2.components.ner.trf.model.MutableDocument class method) (medcat2.components.ner.trf.transformers_ner.MutableDocument class method) (medcat2.components.ner.trf.transformers_ner.MutableEntity class method) (medcat2.components.ner.vocab_based_annotator.MutableDocument class method) (medcat2.components.ner.vocab_based_annotator.MutableEntity class method) (medcat2.components.ner.vocab_based_ner.MutableDocument class method) (medcat2.components.normalizing.normalizer.MutableDocument class method) (medcat2.components.tagging.tagger.MutableDocument class method) (medcat2.components.types.MutableDocument class method) (medcat2.components.types.MutableEntity class method) (medcat2.pipeline.pipeline.MutableDocument class method) (medcat2.pipeline.pipeline.MutableEntity class method) (medcat2.preprocessors.cleaners.MutableDocument class method) (medcat2.stats.stats.MutableDocument class method) (medcat2.stats.stats.MutableEntity class method) (medcat2.tokenizing.regex_impl.tokenizer.Document class method) (medcat2.tokenizing.regex_impl.tokenizer.Entity class method) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument class method) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity class method) (medcat2.tokenizing.spacy_impl.tokenizers.Document class method) (medcat2.tokenizing.spacy_impl.tokenizers.Entity class method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument class method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity class method) (medcat2.tokenizing.spacy_impl.tokens.Document class method) (medcat2.tokenizing.spacy_impl.tokens.Entity class method) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity class method) (medcat2.tokenizing.tokenizers.MutableDocument class method) (medcat2.tokenizing.tokenizers.MutableEntity class method) (medcat2.tokenizing.tokens.MutableDocument class method) (medcat2.tokenizing.tokens.MutableEntity class method) (medcat2.trainer.MutableDocument class method) (medcat2.trainer.MutableEntity class method) (medcat2.utils.data_utils.MutableDocument class method) (medcat2.utils.data_utils.MutableEntity class method) (medcat2.utils.postprocessing.MutableDocument class method) (medcat2.utils.postprocessing.MutableEntity class method) register_all_defaults() (medcat2.components.addons.addons.Registry method) (medcat2.components.types.Registry method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.utils.registry.Registry method) register_backward_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_buffer() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_core_component() (in module medcat2.components.types) register_forward_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_forward_pre_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_full_backward_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_full_backward_pre_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_load_state_dict_post_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_load_state_dict_pre_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_module() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_parameter() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_state_dict_post_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_state_dict_pre_hook() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) register_tokenizer() (in module medcat2.tokenizing.tokenizers) Registry (class in medcat2.components.addons.addons) (class in medcat2.components.types) (class in medcat2.tokenizing.tokenizers) (class in medcat2.utils.registry)

relu (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) remove_all_vectors() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) remove_cui() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) remove_parenthesis (medcat2.config.config.CDBMaker attribute) (medcat2.trainer.CDBMaker attribute) remove_words_below_cnt() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) replace_center (medcat2.config.config_meta_cat.General attribute) replace_entities_in_text() (in module medcat2.components.ner.trf.deid) (in module medcat2.components.ner.trf.helpers) requires_grad_() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) reset_cdb() (medcat2.model_creation.cdb_maker.CDBMaker method) reset_counts() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) reset_cui_training() (in module medcat2.cdb.cdb) (in module medcat2.cdb.concepts) reset_training() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) rnn (medcat2.components.addons.meta_cat.models.LSTM attribute)

S

save() (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase method) (medcat2.components.ner.trf.deid.TransformersNER method) (medcat2.components.ner.trf.model.TransformersNER method) (medcat2.components.ner.trf.tokenizer.TransformersTokenizer method) (medcat2.components.ner.trf.transformers_ner.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.TransformersTokenizer method) (medcat2.utils.legacy.convert_deid.TransformersNER method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE method) save_and_reuse_tokens (medcat2.config.config_meta_cat.General attribute) save_cdb_state() (in module medcat2.utils.cdb_state) save_components() (medcat2.cat.Pipeline method) (medcat2.model_creation.cdb_maker.Pipeline method) (medcat2.pipeline.pipeline.Pipeline method) (medcat2.trainer.Pipeline method) save_model_pack() (medcat2.cat.CAT method) (medcat2.components.ner.trf.deid.CAT method) (medcat2.components.ner.trf.model.CAT method) (medcat2.stats.kfold.CAT method) (medcat2.stats.stats.CAT method) (medcat2.utils.legacy.conversion_all.CAT method) save_schema() (in module medcat2.storage.schema) (in module medcat2.storage.serialisers) save_ser_type_file() (medcat2.storage.serialisers.DillSerialiser method) (medcat2.storage.serialisers.Serialiser method) saved_environ (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute) schema() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) schema_json() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) score_average (medcat2.config.config_meta_cat.Train attribute) seed (medcat2.config.config_meta_cat.General attribute) (medcat2.config.config_transformers_ner.General attribute) separator (medcat2.config.config.General attribute) (medcat2.preprocessors.cleaners.LGeneral attribute) (medcat2.trainer.General attribute) ser_type (medcat2.storage.serialisers.DillSerialiser attribute) (medcat2.storage.serialisers.Serialiser property) (medcat2.utils.legacy.conversion_all.Converter attribute) (medcat2.utils.legacy.legacy_converter.Converter attribute) SER_TYPE_FILE (in module medcat2.storage.serialisers) Serialisable (class in medcat2.pipeline.pipeline) (class in medcat2.storage.serialisables) (class in medcat2.storage.serialisers) SERIALISABLE_ONLY (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy attribute) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy attribute) (medcat2.config.config.SerialisingStrategy attribute) (medcat2.storage.serialisables.SerialisingStrategy attribute) SerialisableBaseModel (class in medcat2.config.config) (class in medcat2.config.config_meta_cat) (class in medcat2.config.config_transformers_ner) SERIALISABLES_AND_DICT (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy attribute) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy attribute) (medcat2.config.config.SerialisingStrategy attribute) (medcat2.storage.serialisables.SerialisingStrategy attribute) serialise() (in module medcat2.cat) (in module medcat2.components.addons.meta_cat.meta_cat) (in module medcat2.components.ner.trf.transformers_ner) (in module medcat2.pipeline.pipeline) (in module medcat2.storage.serialisers) (medcat2.storage.serialisers.DillSerialiser method) (medcat2.storage.serialisers.Serialiser method) serialise_all() (medcat2.storage.serialisers.DillSerialiser method) (medcat2.storage.serialisers.Serialiser method) serialise_to() (medcat2.components.addons.meta_cat.meta_cat.MetaCATAddon method) (medcat2.components.ner.trf.deid.TransformersNER method) (medcat2.components.ner.trf.model.TransformersNER method) (medcat2.components.ner.trf.transformers_ner.TransformersNER method) (medcat2.storage.serialisables.ManualSerialisable method) (medcat2.storage.serialisers.ManualSerialisable method) (medcat2.utils.legacy.convert_deid.TransformersNER method) (medcat2.utils.legacy.convert_meta_cat.MetaCATAddon method)

Serialiser (class in medcat2.storage.serialisers) serialiser (medcat2.config.config_meta_cat.General attribute) SerialisingStrategy (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.config.config) (class in medcat2.storage.serialisables) set_addon_data() (medcat2.cat.MutableDocument method) (medcat2.cat.MutableEntity method) (medcat2.components.addons.addons.MutableEntity method) (medcat2.components.addons.meta_cat.meta_cat.MutableDocument method) (medcat2.components.addons.meta_cat.meta_cat.MutableEntity method) (medcat2.components.linking.context_based_linker.MutableDocument method) (medcat2.components.linking.context_based_linker.MutableEntity method) (medcat2.components.linking.no_action_linker.MutableDocument method) (medcat2.components.linking.vector_context_model.MutableDocument method) (medcat2.components.linking.vector_context_model.MutableEntity method) (medcat2.components.ner.dict_based_ner.MutableDocument method) (medcat2.components.ner.trf.model.MutableDocument method) (medcat2.components.ner.trf.transformers_ner.MutableDocument method) (medcat2.components.ner.trf.transformers_ner.MutableEntity method) (medcat2.components.ner.vocab_based_annotator.MutableDocument method) (medcat2.components.ner.vocab_based_annotator.MutableEntity method) (medcat2.components.ner.vocab_based_ner.MutableDocument method) (medcat2.components.normalizing.normalizer.MutableDocument method) (medcat2.components.tagging.tagger.MutableDocument method) (medcat2.components.types.MutableDocument method) (medcat2.components.types.MutableEntity method) (medcat2.pipeline.pipeline.MutableDocument method) (medcat2.pipeline.pipeline.MutableEntity method) (medcat2.preprocessors.cleaners.MutableDocument method) (medcat2.stats.stats.MutableDocument method) (medcat2.stats.stats.MutableEntity method) (medcat2.tokenizing.regex_impl.tokenizer.Document method) (medcat2.tokenizing.regex_impl.tokenizer.Entity method) (medcat2.tokenizing.regex_impl.tokenizer.MutableDocument method) (medcat2.tokenizing.regex_impl.tokenizer.MutableEntity method) (medcat2.tokenizing.spacy_impl.tokenizers.Document method) (medcat2.tokenizing.spacy_impl.tokenizers.Entity method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableDocument method) (medcat2.tokenizing.spacy_impl.tokenizers.MutableEntity method) (medcat2.tokenizing.spacy_impl.tokens.Document method) (medcat2.tokenizing.spacy_impl.tokens.Entity method) (medcat2.tokenizing.spacy_impl.tokens.MutableEntity method) (medcat2.tokenizing.tokenizers.MutableDocument method) (medcat2.tokenizing.tokenizers.MutableEntity method) (medcat2.tokenizing.tokens.MutableDocument method) (medcat2.tokenizing.tokens.MutableEntity method) (medcat2.trainer.MutableDocument method) (medcat2.trainer.MutableEntity method) (medcat2.utils.data_utils.MutableDocument method) (medcat2.utils.data_utils.MutableEntity method) (medcat2.utils.postprocessing.MutableDocument method) (medcat2.utils.postprocessing.MutableEntity method) set_addon_defaults() (in module medcat2.pipeline.pipeline) (in module medcat2.utils.default_args) set_all_seeds() (in module medcat2.components.addons.meta_cat.meta_cat) (in module medcat2.components.addons.meta_cat.ml_utils) (in module medcat2.components.ner.trf.transformers_ner) set_components_defaults() (in module medcat2.pipeline.pipeline) (in module medcat2.utils.default_args) set_extra_state() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) SET_IDENTIFIER (in module medcat2.utils.legacy.convert_config) set_submodule() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) set_tokenizer_defaults() (in module medcat2.pipeline.pipeline) (in module medcat2.utils.default_args) setdefault() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method) share_memory() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) should_save (medcat2.components.ner.trf.deid.TransformersNER property) (medcat2.components.ner.trf.model.TransformersNER property) (medcat2.components.ner.trf.transformers_ner.TransformersNER property) (medcat2.utils.legacy.convert_deid.TransformersNER property) show_nested_entities (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) shuffle_data (medcat2.config.config_meta_cat.Train attribute) similarity() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) similarity_threshold (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) similarity_threshold_type (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) simple_hash (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) SimpleFoldCreator (class in medcat2.stats.kfold) skip_stopwords (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.trainer.Preprocessing attribute) snames (medcat2.cdb.cdb.NameDescriptor attribute) (medcat2.components.ner.trf.transformers_ner.NameDescriptor attribute) (medcat2.preprocessors.cleaners.NameDescriptor attribute) (medcat2.trainer.NameDescriptor attribute) softmax (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) source_value (medcat2.cat.Entity attribute) (medcat2.data.entities.Entity attribute) spacy_split_all() (in module medcat2.tokenizing.spacy_impl.tokenizers) SpacyTokenizer (class in medcat2.tokenizing.spacy_impl.tokenizers) span_group (medcat2.config.config_meta_cat.General attribute) spell_check (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) spell_check_deep (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) spell_check_len_limit (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) spell_checker (medcat2.components.normalizing.normalizer.TokenNormalizer attribute) split() (medcat2.utils.data_utils.TestTrainSplitter method) split_list_train_test() (in module medcat2.components.addons.meta_cat.ml_utils) SplitType (class in medcat2.stats.kfold) ST (class in medcat2.cdb.cdb) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.vector_context_model) start (medcat2.cat.Entity attribute) (medcat2.data.entities.Entity attribute) (medcat2.data.mctexport.MedCATTrainerExportAnnotation attribute) (medcat2.stats.kfold.MedCATTrainerExportAnnotation attribute) (medcat2.stats.stats.MedCATTrainerExportAnnotation attribute) start_char_index (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity property) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity property) (medcat2.tokenizing.tokens.BaseEntity property) start_index (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity property) (medcat2.tokenizing.regex_impl.tokenizer.Entity property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity property) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity property) (medcat2.tokenizing.spacy_impl.tokens.Entity property) (medcat2.tokenizing.tokens.BaseEntity property) state_dict() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) StatsBuilder (class in medcat2.stats.stats) StatusTypes (class in medcat2.utils.defaults) stopwords (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.trainer.Preprocessing attribute) subnames (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) subsample_after (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) sup_trained (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute)

T

T (in module medcat2.config.config) (in module medcat2.utils.iterutils) T_destination (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) tag (medcat2.components.linking.vector_context_model.MutableToken property) (medcat2.components.ner.vocab_based_annotator.MutableToken property) (medcat2.pipeline.pipeline.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.MutableToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokenizers.MutableToken property) (medcat2.tokenizing.tokens.MutableToken property) (medcat2.trainer.MutableToken property) TagAndSkipTagger (class in medcat2.components.tagging.tagger) tagging (medcat2.components.linking.context_based_linker.CoreComponentType attribute) (medcat2.components.linking.no_action_linker.CoreComponentType attribute) (medcat2.components.ner.dict_based_ner.CoreComponentType attribute) (medcat2.components.ner.trf.deid.CoreComponentType attribute) (medcat2.components.ner.trf.model.CoreComponentType attribute) (medcat2.components.ner.trf.transformers_ner.CoreComponentType attribute) (medcat2.components.ner.vocab_based_ner.CoreComponentType attribute) (medcat2.components.normalizing.normalizer.CoreComponentType attribute) (medcat2.components.tagging.tagger.CoreComponentType attribute) (medcat2.components.types.CoreComponentType attribute) (medcat2.config.config.Components attribute) (medcat2.pipeline.pipeline.CoreComponentType attribute) (medcat2.trainer.CoreComponentType attribute) (medcat2.utils.default_args.CoreComponentType attribute) (medcat2.utils.legacy.conversion_all.CoreComponentType attribute) tags (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) temp_changed_config() (in module medcat2.trainer) (in module medcat2.utils.config_utils) (in module medcat2.utils.filters) test_size (medcat2.config.config_meta_cat.Train attribute) (medcat2.config.config_transformers_ner.General attribute) (medcat2.utils.data_utils.TestTrainSplitter attribute) TestTrainSplitter (class in medcat2.utils.data_utils) text (medcat2.cat.Entities attribute) (medcat2.cat.OnlyCUIEntities attribute) (medcat2.components.ner.trf.model.Entities attribute) (medcat2.components.ner.trf.model.OnlyCUIEntities attribute) (medcat2.data.entities.Entities attribute) (medcat2.data.entities.OnlyCUIEntities attribute) (medcat2.data.mctexport.MedCATTrainerExportDocument attribute) (medcat2.stats.kfold.MedCATTrainerExportDocument attribute) (medcat2.stats.stats.MedCATTrainerExportDocument attribute) (medcat2.tokenizing.regex_impl.tokenizer.BaseDocument property) (medcat2.tokenizing.regex_impl.tokenizer.BaseEntity property) (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Document attribute) (medcat2.tokenizing.regex_impl.tokenizer.Entity property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Document property) (medcat2.tokenizing.spacy_impl.tokenizers.Entity property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseDocument property) (medcat2.tokenizing.spacy_impl.tokens.BaseEntity property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Document property) (medcat2.tokenizing.spacy_impl.tokens.Entity property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseDocument property) (medcat2.tokenizing.tokens.BaseEntity property) (medcat2.tokenizing.tokens.BaseToken property) (medcat2.trainer.MedCATTrainerExportDocument attribute) (medcat2.utils.data_utils.MedCATTrainerExportDocument attribute) text_versions (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) text_with_ws (medcat2.tokenizing.regex_impl.tokenizer.BaseToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.BaseToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokens.BaseToken property) to() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) to_empty() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) TO_RENAME (in module medcat2.utils.legacy.convert_cdb) to_skip (medcat2.components.linking.vector_context_model.MutableToken property) (medcat2.components.ner.vocab_based_annotator.MutableToken property) (medcat2.pipeline.pipeline.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.MutableToken property) (medcat2.tokenizing.regex_impl.tokenizer.Token property) (medcat2.tokenizing.spacy_impl.tokenizers.MutableToken property) (medcat2.tokenizing.spacy_impl.tokenizers.Token property) (medcat2.tokenizing.spacy_impl.tokens.MutableToken property) (medcat2.tokenizing.spacy_impl.tokens.Token property) (medcat2.tokenizing.tokenizers.MutableToken property) (medcat2.tokenizing.tokens.MutableToken property) (medcat2.trainer.MutableToken property) Token (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokenizers) (class in medcat2.tokenizing.spacy_impl.tokens) token_counts (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) token_normalizing (medcat2.components.linking.context_based_linker.CoreComponentType attribute) (medcat2.components.linking.no_action_linker.CoreComponentType attribute) (medcat2.components.ner.dict_based_ner.CoreComponentType attribute) (medcat2.components.ner.trf.deid.CoreComponentType attribute) (medcat2.components.ner.trf.model.CoreComponentType attribute) (medcat2.components.ner.trf.transformers_ner.CoreComponentType attribute) (medcat2.components.ner.vocab_based_ner.CoreComponentType attribute) (medcat2.components.normalizing.normalizer.CoreComponentType attribute) (medcat2.components.tagging.tagger.CoreComponentType attribute) (medcat2.components.types.CoreComponentType attribute) (medcat2.config.config.Components attribute) (medcat2.pipeline.pipeline.CoreComponentType attribute) (medcat2.trainer.CoreComponentType attribute) (medcat2.utils.default_args.CoreComponentType attribute) (medcat2.utils.legacy.conversion_all.CoreComponentType attribute) token_to_id() (medcat2.components.addons.meta_cat.data_utils.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat2.components.addons.meta_cat.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat2.components.addons.meta_cat.ml_utils.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBase method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBERT method) (medcat2.utils.legacy.convert_meta_cat.TokenizerWrapperBPE method)

tokenizer (medcat2.cat.Pipeline property) (medcat2.components.addons.meta_cat.meta_cat.MetaCAT attribute) (medcat2.components.ner.dict_based_ner.NER attribute) (medcat2.components.ner.vocab_based_ner.NER attribute) (medcat2.model_creation.cdb_maker.Pipeline property) (medcat2.pipeline.pipeline.DelegatingTokenizer attribute) (medcat2.pipeline.pipeline.Pipeline property) (medcat2.trainer.Pipeline property) (medcat2.utils.legacy.convert_meta_cat.MetaCAT attribute) tokenizer_name (medcat2.config.config_meta_cat.General attribute) tokenizer_with_tag (medcat2.cat.Pipeline property) (medcat2.model_creation.cdb_maker.Pipeline property) (medcat2.pipeline.pipeline.Pipeline property) (medcat2.trainer.Pipeline property) TokenizerWrapperBase (class in medcat2.components.addons.meta_cat.data_utils) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.addons.meta_cat.meta_cat_tokenizers) (class in medcat2.components.addons.meta_cat.ml_utils) (class in medcat2.utils.legacy.convert_meta_cat) TokenizerWrapperBERT (class in medcat2.components.addons.meta_cat.meta_cat_tokenizers) (class in medcat2.utils.legacy.convert_meta_cat) TokenizerWrapperBPE (class in medcat2.components.addons.meta_cat.meta_cat_tokenizers) (class in medcat2.utils.legacy.convert_meta_cat) TokenNormalizer (class in medcat2.components.normalizing.normalizer) tokens (medcat2.cat.Entities attribute) (medcat2.cat.OnlyCUIEntities attribute) (medcat2.cdb.cdb.NameDescriptor attribute) (medcat2.components.ner.trf.model.Entities attribute) (medcat2.components.ner.trf.model.OnlyCUIEntities attribute) (medcat2.components.ner.trf.transformers_ner.NameDescriptor attribute) (medcat2.data.entities.Entities attribute) (medcat2.data.entities.OnlyCUIEntities attribute) (medcat2.preprocessors.cleaners.NameDescriptor attribute) (medcat2.trainer.NameDescriptor attribute) total (medcat2.stats.kfold.PerAnnsFoldCreator attribute) (medcat2.stats.kfold.SimpleFoldCreator attribute) Train (class in medcat2.config.config_meta_cat) train (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT attribute) (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT attribute) train() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.context_based_linker.Linker method) (medcat2.components.linking.vector_context_model.ContextModel method) (medcat2.components.ner.trf.deid.DeIdModel method) (medcat2.components.ner.trf.deid.NerModel method) (medcat2.components.ner.trf.model.NerModel method) (medcat2.components.ner.trf.transformers_ner.TransformersNERComponent method) (medcat2.components.types.TrainableComponent method) (medcat2.trainer.TrainableComponent method) Train.Config (class in medcat2.config.config_meta_cat) train_count_threshold (medcat2.components.linking.vector_context_model.Linking attribute) (medcat2.config.config.Linking attribute) train_counter (medcat2.components.linking.context_based_linker.Linker attribute) train_from_json() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) train_model() (in module medcat2.components.addons.meta_cat.meta_cat) (in module medcat2.components.addons.meta_cat.ml_utils) train_raw() (medcat2.components.addons.meta_cat.meta_cat.MetaCAT method) (medcat2.utils.legacy.convert_meta_cat.MetaCAT method) train_supervised_raw() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) train_time_end (medcat2.config.config.TrainingDescriptor attribute) train_time_start (medcat2.config.config.TrainingDescriptor attribute) train_unsupervised() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) train_using_negative_sampling() (medcat2.components.linking.context_based_linker.ContextModel method) (medcat2.components.linking.vector_context_model.ContextModel method) TrainableComponent (class in medcat2.components.types) (class in medcat2.trainer) Trainer (class in medcat2.cat) (class in medcat2.trainer) trainer (medcat2.cat.CAT property) (medcat2.components.ner.trf.deid.CAT property) (medcat2.components.ner.trf.model.CAT property) (medcat2.stats.kfold.CAT property) (medcat2.stats.stats.CAT property) (medcat2.utils.legacy.conversion_all.CAT property) training (medcat2.components.addons.meta_cat.ml_utils.FocalLoss attribute) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation attribute) (medcat2.components.addons.meta_cat.models.LSTM attribute) TrainingDescriptor (class in medcat2.config.config) TransformersDatasetNER (class in medcat2.utils.ner.transformers_ner) TransformersNER (class in medcat2.components.ner.trf.deid) (class in medcat2.components.ner.trf.model) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.utils.legacy.convert_deid) TransformersNERComponent (class in medcat2.components.ner.trf.transformers_ner) TransformersTokenizer (class in medcat2.components.ner.trf.tokenizer) (class in medcat2.components.ner.trf.transformers_ner) transitive_deps (medcat2.config.config.Environment attribute) (medcat2.utils.envsnapshot.Environment attribute) TrCBCreator (in module medcat2.components.ner.trf.transformers_ner) trf_ner (medcat2.components.ner.trf.deid.DeIdModel property) (medcat2.components.ner.trf.deid.NerModel property) (medcat2.components.ner.trf.model.NerModel property) try_reverse_word_order (medcat2.config.config.Ner attribute) tuis (medcat2.data.mctexport.MedCATTrainerExportProject attribute) (medcat2.stats.kfold.MedCATTrainerExportProject attribute) (medcat2.stats.stats.MedCATTrainerExportProject attribute) (medcat2.trainer.MedCATTrainerExportProject attribute) (medcat2.utils.data_utils.MedCATTrainerExportProject attribute) (medcat2.utils.filters.MedCATTrainerExportProject attribute) type() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method) type_id (medcat2.cdb.cdb.TypeInfo attribute) (medcat2.cdb.concepts.TypeInfo attribute) (medcat2.utils.legacy.convert_cdb.TypeInfo attribute) type_id2info (medcat2.cat.CDB attribute) (medcat2.cdb.CDB attribute) (medcat2.cdb.cdb.CDB attribute) (medcat2.components.addons.meta_cat.meta_cat.CDB attribute) (medcat2.components.linking.context_based_linker.CDB attribute) (medcat2.components.linking.no_action_linker.CDB attribute) (medcat2.components.ner.dict_based_ner.CDB attribute) (medcat2.components.ner.trf.deid.CDB attribute) (medcat2.components.ner.trf.helpers.CDB attribute) (medcat2.components.ner.trf.model.CDB attribute) (medcat2.components.ner.trf.transformers_ner.CDB attribute) (medcat2.components.ner.vocab_based_annotator.CDB attribute) (medcat2.components.ner.vocab_based_ner.CDB attribute) (medcat2.components.normalizing.normalizer.CDB attribute) (medcat2.components.tagging.tagger.CDB attribute) (medcat2.components.types.CDB attribute) (medcat2.model_creation.cdb_maker.CDB attribute) (medcat2.pipeline.pipeline.CDB attribute) (medcat2.trainer.CDB attribute) (medcat2.utils.data_utils.CDB attribute) (medcat2.utils.default_args.CDB attribute) (medcat2.utils.legacy.convert_cdb.CDB attribute) (medcat2.utils.legacy.convert_deid.CDB attribute) (medcat2.utils.vocab_utils.CDB attribute) type_ids (medcat2.cat.Entity attribute) (medcat2.cdb.cdb.CUIInfo attribute) (medcat2.cdb.concepts.CUIInfo attribute) (medcat2.components.linking.vector_context_model.CUIInfo attribute) (medcat2.data.entities.Entity attribute) (medcat2.stats.stats.CUIInfo attribute) (medcat2.utils.cdb_state.CUIInfo attribute) TypeInfo (class in medcat2.cdb.cdb) (class in medcat2.cdb.concepts) (class in medcat2.utils.legacy.convert_cdb)

U

unitvec() (in module medcat2.components.linking.vector_context_model) (in module medcat2.utils.matutils) UnknownTokenVersion UnknownTokenVersion.__cause__ (class in medcat2.preprocessors.cleaners) UnknownTokenVersion.__context__ (class in medcat2.preprocessors.cleaners) UnknownTokenVersion.__suppress_context__ (class in medcat2.preprocessors.cleaners) UnknownTokenVersion.__traceback__ (class in medcat2.preprocessors.cleaners) UnknownTokenVersion.args (class in medcat2.preprocessors.cleaners) UnkownAddonConfig UnkownAddonConfig.__cause__ (class in medcat2.pipeline.pipeline) UnkownAddonConfig.__context__ (class in medcat2.pipeline.pipeline) UnkownAddonConfig.__suppress_context__ (class in medcat2.pipeline.pipeline) UnkownAddonConfig.__traceback__ (class in medcat2.pipeline.pipeline) UnkownAddonConfig.args (class in medcat2.pipeline.pipeline) unlink_concept_name() (medcat2.cat.Trainer method) (medcat2.trainer.Trainer method) unpack() (in module medcat2.utils.legacy.conversion_all) unregister_all_components() (medcat2.components.addons.addons.Registry method) (medcat2.components.types.Registry method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.utils.registry.Registry method) unregister_component() (medcat2.components.addons.addons.Registry method) (medcat2.components.types.Registry method) (medcat2.tokenizing.tokenizers.Registry method) (medcat2.utils.registry.Registry method) UnregisteredDataPathException, [1], [2] UnregisteredDataPathException.__cause__ (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) UnregisteredDataPathException.__context__ (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) UnregisteredDataPathException.__suppress_context__ (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) UnregisteredDataPathException.__traceback__ (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) UnregisteredDataPathException.args (class in medcat2.tokenizing.regex_impl.tokenizer) (class in medcat2.tokenizing.spacy_impl.tokens) (class in medcat2.tokenizing.tokens) unsup_trained (medcat2.config.config.ModelMeta attribute) (medcat2.utils.cdb_state.ModelMeta attribute) unwrap() (medcat2.stats.stats.StatsBuilder method) update() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.Hasher method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.Hasher method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.Hasher method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.components.ner.trf.transformers_ner.Hasher method) (medcat2.config.config_transformers_ner.Hasher method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.hasher.Hasher method) (medcat2.utils.import_utils.KeyDefaultDict method)

update_bytes() (medcat2.cat.Hasher method) (medcat2.cdb.cdb.Hasher method) (medcat2.components.addons.meta_cat.meta_cat.Hasher method) (medcat2.components.ner.trf.transformers_ner.Hasher method) (medcat2.config.config_transformers_ner.Hasher method) (medcat2.utils.hasher.Hasher method) update_context_vectors() (in module medcat2.components.linking.vector_context_model) update_counts() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) update_forward_refs() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) update_names() (in module medcat2.utils.legacy.convert_cdb) upper_case_limit_len (medcat2.config.config.Ner attribute) use_overlaps (medcat2.stats.stats.StatsBuilder attribute) use_project_filters (medcat2.stats.stats.StatsBuilder attribute)

V

validate() (medcat2.cat.Config class method) (medcat2.cdb.cdb.Config class method) (medcat2.components.addons.addons.ComponentConfig class method) (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT class method) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT class method) (medcat2.components.linking.context_based_linker.Config class method) (medcat2.components.linking.vector_context_model.Linking class method) (medcat2.components.ner.trf.deid.ConfigTransformersNER class method) (medcat2.components.ner.trf.helpers.Config class method) (medcat2.components.ner.trf.model.Config class method) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER class method) (medcat2.components.ner.vocab_based_annotator.Config class method) (medcat2.components.normalizing.normalizer.Config class method) (medcat2.components.tagging.tagger.Preprocessing class method) (medcat2.config.Config class method) (medcat2.config.config.AnnotationOutput class method) (medcat2.config.config.CDBMaker class method) (medcat2.config.config.ComponentConfig class method) (medcat2.config.config.Components class method) (medcat2.config.config.Config class method) (medcat2.config.config.Environment class method) (medcat2.config.config.General class method) (medcat2.config.config.Linking class method) (medcat2.config.config.LinkingFilters class method) (medcat2.config.config.ModelMeta class method) (medcat2.config.config.Ner class method) (medcat2.config.config.NLPConfig class method) (medcat2.config.config.Preprocessing class method) (medcat2.config.config.SerialisableBaseModel class method) (medcat2.config.config.TrainingDescriptor class method) (medcat2.config.config_meta_cat.ComponentConfig class method) (medcat2.config.config_meta_cat.ConfigMetaCAT class method) (medcat2.config.config_meta_cat.General class method) (medcat2.config.config_meta_cat.Model class method) (medcat2.config.config_meta_cat.SerialisableBaseModel class method) (medcat2.config.config_meta_cat.Train class method) (medcat2.config.config_transformers_ner.ConfigTransformersNER class method) (medcat2.config.config_transformers_ner.General class method) (medcat2.config.config_transformers_ner.SerialisableBaseModel class method) (medcat2.model_creation.cdb_maker.Config class method) (medcat2.pipeline.pipeline.ComponentConfig class method) (medcat2.pipeline.pipeline.Config class method) (medcat2.pipeline.pipeline.ConfigMetaCAT class method) (medcat2.stats.kfold.PerCUIMetrics class method) (medcat2.stats.stats.LinkingFilters class method) (medcat2.tokenizing.regex_impl.tokenizer.Config class method) (medcat2.tokenizing.spacy_impl.tokenizers.Config class method) (medcat2.tokenizing.tokenizers.Config class method) (medcat2.trainer.CDBMaker class method) (medcat2.trainer.General class method) (medcat2.trainer.Preprocessing class method) (medcat2.utils.cdb_state.ModelMeta class method) (medcat2.utils.default_args.ComponentConfig class method) (medcat2.utils.default_args.Config class method) (medcat2.utils.envsnapshot.Environment class method) (medcat2.utils.filters.LinkingFilters class method) (medcat2.utils.legacy.convert_cdb.Config class method) (medcat2.utils.legacy.convert_config.Config class method) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER class method) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT class method) validate_assignment (medcat2.components.addons.meta_cat.meta_cat.ConfigMetaCAT.Config attribute) (medcat2.components.addons.meta_cat.ml_utils.ConfigMetaCAT.Config attribute) (medcat2.components.addons.meta_cat.models.ConfigMetaCAT.Config attribute) (medcat2.components.ner.trf.deid.ConfigTransformersNER.Config attribute) (medcat2.components.ner.trf.transformers_ner.ConfigTransformersNER.Config attribute) (medcat2.config.config.NLPConfig.Config attribute) (medcat2.config.config_meta_cat.ConfigMetaCAT.Config attribute) (medcat2.config.config_meta_cat.General.Config attribute) (medcat2.config.config_meta_cat.Model.Config attribute) (medcat2.config.config_meta_cat.Train.Config attribute) (medcat2.config.config_transformers_ner.ConfigTransformersNER.Config attribute) (medcat2.config.config_transformers_ner.General.Config attribute) (medcat2.pipeline.pipeline.ConfigMetaCAT.Config attribute) (medcat2.utils.legacy.convert_deid.ConfigTransformersNER.Config attribute) (medcat2.utils.legacy.convert_meta_cat.ConfigMetaCAT.Config attribute) vals (medcat2.stats.kfold.PerCUIMetrics attribute) value (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument attribute) (medcat2.data.entities.MetaAnnotation attribute) (medcat2.data.mctexport.MedCATTrainerExportAnnotation attribute) (medcat2.stats.kfold.MedCATTrainerExportAnnotation attribute) (medcat2.stats.stats.MedCATTrainerExportAnnotation attribute) value() (medcat2.cat.AvailableSerialisers method) (medcat2.components.addons.meta_cat.meta_cat.SerialisingStrategy method) (medcat2.components.linking.context_based_linker.CoreComponentType method) (medcat2.components.linking.no_action_linker.CoreComponentType method) (medcat2.components.ner.dict_based_ner.CoreComponentType method) (medcat2.components.ner.trf.deid.CoreComponentType method) (medcat2.components.ner.trf.model.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers method) (medcat2.components.ner.trf.transformers_ner.CoreComponentType method) (medcat2.components.ner.trf.transformers_ner.SerialisingStrategy method) (medcat2.components.ner.vocab_based_ner.CoreComponentType method) (medcat2.components.normalizing.normalizer.CoreComponentType method) (medcat2.components.tagging.tagger.CoreComponentType method) (medcat2.components.types.CoreComponentType method) (medcat2.config.config.SerialisingStrategy method) (medcat2.config.config_meta_cat.AvailableSerialisers method) (medcat2.pipeline.pipeline.AvailableSerialisers method) (medcat2.pipeline.pipeline.CoreComponentType method) (medcat2.stats.kfold.SplitType method) (medcat2.storage.serialisables.SerialisingStrategy method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.trainer.CoreComponentType method) (medcat2.utils.default_args.CoreComponentType method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.CoreComponentType method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method) values() (medcat2.cat.Entities method) (medcat2.cat.Entity method) (medcat2.cat.OnlyCUIEntities method) (medcat2.cdb.cdb.CUIInfo method) (medcat2.cdb.cdb.NameInfo method) (medcat2.cdb.concepts.CUIInfo method) (medcat2.cdb.concepts.NameInfo method) (medcat2.components.addons.meta_cat.meta_cat.MedCATTrainerExportDocument method) (medcat2.components.linking.context_based_linker.PerDocumentTokenCache method) (medcat2.components.linking.vector_context_model.CUIInfo method) (medcat2.components.linking.vector_context_model.NameInfo method) (medcat2.components.linking.vector_context_model.PerDocumentTokenCache method) (medcat2.components.ner.trf.model.Entities method) (medcat2.components.ner.trf.model.OnlyCUIEntities method) (medcat2.data.entities.Entities method) (medcat2.data.entities.Entity method) (medcat2.data.entities.MetaAnnotation method) (medcat2.data.entities.OnlyCUIEntities method) (medcat2.data.mctexport.MedCATTrainerExport method) (medcat2.data.mctexport.MedCATTrainerExportAnnotation method) (medcat2.data.mctexport.MedCATTrainerExportDocument method) (medcat2.data.mctexport.MedCATTrainerExportProject method) (medcat2.stats.kfold.MedCATTrainerExport method) (medcat2.stats.kfold.MedCATTrainerExportAnnotation method) (medcat2.stats.kfold.MedCATTrainerExportDocument method) (medcat2.stats.kfold.MedCATTrainerExportProject method) (medcat2.stats.stats.CUIInfo method) (medcat2.stats.stats.MedCATTrainerExport method) (medcat2.stats.stats.MedCATTrainerExportAnnotation method) (medcat2.stats.stats.MedCATTrainerExportDocument method) (medcat2.stats.stats.MedCATTrainerExportProject method) (medcat2.trainer.MedCATTrainerExport method) (medcat2.trainer.MedCATTrainerExportDocument method) (medcat2.trainer.MedCATTrainerExportProject method) (medcat2.utils.cdb_state.CUIInfo method) (medcat2.utils.cdb_state.NameInfo method) (medcat2.utils.data_utils.MedCATTrainerExport method) (medcat2.utils.data_utils.MedCATTrainerExportDocument method) (medcat2.utils.data_utils.MedCATTrainerExportProject method) (medcat2.utils.filters.MedCATTrainerExportProject method) (medcat2.utils.import_utils.KeyDefaultDict method)

vec() (medcat2.cat.Vocab method) (medcat2.components.addons.meta_cat.meta_cat.Vocab method) (medcat2.components.linking.context_based_linker.Vocab method) (medcat2.components.linking.no_action_linker.Vocab method) (medcat2.components.linking.vector_context_model.Vocab method) (medcat2.components.ner.dict_based_ner.Vocab method) (medcat2.components.ner.trf.transformers_ner.Vocab method) (medcat2.components.ner.vocab_based_ner.Vocab method) (medcat2.components.normalizing.normalizer.Vocab method) (medcat2.components.tagging.tagger.Vocab method) (medcat2.components.types.Vocab method) (medcat2.pipeline.pipeline.Vocab method) (medcat2.utils.default_args.Vocab method) (medcat2.utils.legacy.convert_vocab.Vocab method) (medcat2.utils.vocab_utils.Vocab method) (medcat2.vocab.Vocab method) vec_index2word (medcat2.cat.Vocab attribute) (medcat2.components.addons.meta_cat.meta_cat.Vocab attribute) (medcat2.components.linking.context_based_linker.Vocab attribute) (medcat2.components.linking.no_action_linker.Vocab attribute) (medcat2.components.linking.vector_context_model.Vocab attribute) (medcat2.components.ner.dict_based_ner.Vocab attribute) (medcat2.components.ner.trf.transformers_ner.Vocab attribute) (medcat2.components.ner.vocab_based_ner.Vocab attribute) (medcat2.components.normalizing.normalizer.Vocab attribute) (medcat2.components.tagging.tagger.Vocab attribute) (medcat2.components.types.Vocab attribute) (medcat2.pipeline.pipeline.Vocab attribute) (medcat2.utils.default_args.Vocab attribute) (medcat2.utils.legacy.convert_vocab.Vocab attribute) (medcat2.utils.vocab_utils.Vocab attribute) (medcat2.vocab.Vocab attribute) verbose_metrics (medcat2.config.config_transformers_ner.General attribute) Vocab (class in medcat2.cat) (class in medcat2.components.addons.meta_cat.meta_cat) (class in medcat2.components.linking.context_based_linker) (class in medcat2.components.linking.no_action_linker) (class in medcat2.components.linking.vector_context_model) (class in medcat2.components.ner.dict_based_ner) (class in medcat2.components.ner.trf.transformers_ner) (class in medcat2.components.ner.vocab_based_ner) (class in medcat2.components.normalizing.normalizer) (class in medcat2.components.tagging.tagger) (class in medcat2.components.types) (class in medcat2.pipeline.pipeline) (class in medcat2.utils.default_args) (class in medcat2.utils.legacy.convert_vocab) (class in medcat2.utils.vocab_utils) (class in medcat2.vocab) vocab (medcat2.cat.CAT attribute) (medcat2.cat.Vocab attribute) (medcat2.components.addons.meta_cat.meta_cat.Vocab attribute) (medcat2.components.linking.context_based_linker.ContextModel attribute) (medcat2.components.linking.context_based_linker.Linker attribute) (medcat2.components.linking.context_based_linker.Vocab attribute) (medcat2.components.linking.no_action_linker.Vocab attribute) (medcat2.components.linking.vector_context_model.ContextModel attribute) (medcat2.components.linking.vector_context_model.Vocab attribute) (medcat2.components.ner.dict_based_ner.Vocab attribute) (medcat2.components.ner.trf.deid.CAT attribute) (medcat2.components.ner.trf.model.CAT attribute) (medcat2.components.ner.trf.transformers_ner.Vocab attribute) (medcat2.components.ner.vocab_based_ner.Vocab attribute) (medcat2.components.normalizing.normalizer.BasicSpellChecker attribute) (medcat2.components.normalizing.normalizer.Vocab attribute) (medcat2.components.tagging.tagger.Vocab attribute) (medcat2.components.types.Vocab attribute) (medcat2.pipeline.pipeline.Vocab attribute) (medcat2.stats.kfold.CAT attribute) (medcat2.stats.stats.CAT attribute) (medcat2.utils.default_args.Vocab attribute) (medcat2.utils.legacy.conversion_all.CAT attribute) (medcat2.utils.legacy.convert_vocab.Vocab attribute) (medcat2.utils.vocab_utils.Vocab attribute) (medcat2.vocab.Vocab attribute) vocab_name (medcat2.utils.legacy.conversion_all.Converter attribute) (medcat2.utils.legacy.legacy_converter.Converter attribute) vocab_size (medcat2.config.config_meta_cat.General attribute)

W

weighted_average_function (medcat2.components.linking.context_based_linker.ContextModel attribute) (medcat2.components.linking.vector_context_model.ContextModel attribute) weighted_average_function() (medcat2.cat.CDB method) (medcat2.cdb.CDB method) (medcat2.cdb.cdb.CDB method) (medcat2.components.addons.meta_cat.meta_cat.CDB method) (medcat2.components.linking.context_based_linker.CDB method) (medcat2.components.linking.no_action_linker.CDB method) (medcat2.components.ner.dict_based_ner.CDB method) (medcat2.components.ner.trf.deid.CDB method) (medcat2.components.ner.trf.helpers.CDB method) (medcat2.components.ner.trf.model.CDB method) (medcat2.components.ner.trf.transformers_ner.CDB method) (medcat2.components.ner.vocab_based_annotator.CDB method) (medcat2.components.ner.vocab_based_ner.CDB method) (medcat2.components.normalizing.normalizer.CDB method) (medcat2.components.tagging.tagger.CDB method) (medcat2.components.types.CDB method) (medcat2.model_creation.cdb_maker.CDB method) (medcat2.pipeline.pipeline.CDB method) (medcat2.trainer.CDB method) (medcat2.utils.data_utils.CDB method) (medcat2.utils.default_args.CDB method) (medcat2.utils.legacy.convert_cdb.CDB method) (medcat2.utils.legacy.convert_deid.CDB method) (medcat2.utils.vocab_utils.CDB method) WeightedDocumentsCreator (class in medcat2.stats.kfold) weights (medcat2.stats.kfold.PerCUIMetrics attribute) with_traceback() (medcat2.components.addons.meta_cat.meta_cat.MisconfiguredMetaCATException method) (medcat2.config.config.IncorrectConfigValues method) (medcat2.pipeline.pipeline.IncorrectAddonLoaded method) (medcat2.pipeline.pipeline.IncorrectArgumentsForComponent method) (medcat2.pipeline.pipeline.IncorrectArgumentsForTokenizer method) (medcat2.pipeline.pipeline.IncorrectCoreComponent method) (medcat2.pipeline.pipeline.IncorrectFolderUponLoad method) (medcat2.pipeline.pipeline.UnkownAddonConfig method) (medcat2.preprocessors.cleaners.UnknownTokenVersion method) (medcat2.storage.schema.IllegalSchemaException method) (medcat2.storage.serialisers.IllegalSchemaException method) (medcat2.tokenizing.regex_impl.tokenizer.UnregisteredDataPathException method) (medcat2.tokenizing.spacy_impl.tokens.UnregisteredDataPathException method) (medcat2.tokenizing.tokens.UnregisteredDataPathException method) (medcat2.utils.config_utils.IllegalConfigPathException method) (medcat2.utils.default_args.OptionalPartNotInstalledException method) (medcat2.utils.import_utils.IncorrectExtraComponent method) (medcat2.utils.import_utils.MissingDependenciesError method) (medcat2.utils.registry.MedCATRegistryException method)

word_skipper (medcat2.components.tagging.tagger.TagAndSkipTagger attribute) WordDescriptor (in module medcat2.vocab) words_to_skip (medcat2.components.tagging.tagger.Preprocessing attribute) (medcat2.config.config.Preprocessing attribute) (medcat2.trainer.Preprocessing attribute) workers (medcat2.config.config.General attribute) (medcat2.trainer.General attribute) workers() (in module medcat2.config.config) (in module medcat2.utils.defaults) write_to() (medcat2.cat.AvailableSerialisers method) (medcat2.components.ner.trf.transformers_ner.AvailableSerialisers method) (medcat2.config.config_meta_cat.AvailableSerialisers method) (medcat2.pipeline.pipeline.AvailableSerialisers method) (medcat2.storage.serialisers.AvailableSerialisers method) (medcat2.utils.legacy.conversion_all.AvailableSerialisers method) (medcat2.utils.legacy.legacy_converter.AvailableSerialisers method)

X

xpu() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method)

Z

zero_grad() (medcat2.components.addons.meta_cat.ml_utils.FocalLoss method) (medcat2.components.addons.meta_cat.models.BertForMetaAnnotation method) (medcat2.components.addons.meta_cat.models.LSTM method)