Index

_

__call__() (medcat.cat.CAT method) (medcat.config._DefPartial method) (medcat.datasets.data_collator.CollateAndPadNER method) (medcat.linking.context_based_linker.Linker method) (medcat.meta_cat.MetaCAT method) (medcat.ner.transformers_ner.TransformersNER method) (medcat.ner.vocab_based_ner.NER method) (medcat.pipe.Pipe method) (medcat.pipeline.pipe_runner.PipeRunner method) (medcat.preprocessing.taggers._Tagger method) (medcat.preprocessing.tokenizers.TokenizerWrapperBERT method) (medcat.preprocessing.tokenizers.TokenizerWrapperBPE method) (medcat.rel_cat.RelCAT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat.utils.ner.model.NerModel method) (medcat.utils.normalizers.TokenNormalizer method) (medcat.utils.regression.targeting.PhraseChanger method) (medcat.utils.relation_extraction.pad_seq.Pad_Sequence method) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT method) __contains__() (medcat.utils.memory_optimiser.DelegatingDict method) (medcat.utils.memory_optimiser.DelegatingValueSet method) (medcat.utils.normalizers.BasicSpellChecker method) (medcat.vocab.Vocab method) __del__() (medcat.utils.usage_monitoring.UsageMonitor method) __delitem__() (medcat.utils.memory_optimiser.DelegatingDict method) __eq__() (medcat.config._DefPartial method) (medcat.utils.memory_optimiser.DelegatingDict method) (medcat.utils.regression.checking.RegressionCase method) (medcat.utils.regression.checking.RegressionSuite method) __getitem__() (medcat.config.FakeDict method) (medcat.utils.data_utils.MetaAnnotationDS method) (medcat.utils.memory_optimiser.DelegatingDict method) (medcat.utils.relation_extraction.rel_dataset.RelData method) (medcat.vocab.Vocab method) __hash__() (medcat.utils.memory_optimiser.DelegatingDict method) (medcat.utils.regression.checking.RegressionCase method) __init__() (medcat.cat.CAT method) (medcat.cdb.CDB method) (medcat.cdb_maker.CDBMaker method) (medcat.config._DefPartial method) (medcat.config.Config method) (medcat.config.LinkingFilters method) (medcat.config.UseOfOldConfigOptionException method) (medcat.config.ValueExtractor method) (medcat.datasets.data_collator.CollateAndPadNER method) (medcat.linking.context_based_linker.Linker method) (medcat.linking.vector_context_model.ContextModel method) (medcat.meta_cat.MetaCAT method) (medcat.ner.transformers_ner.TransformersNER method) (medcat.ner.vocab_based_ner.NER method) (medcat.pipe.Pipe method) (medcat.pipeline.pipe_runner.PipeRunner method) (medcat.preprocessing.iterators.BaseEmbMimicCSV method) (medcat.preprocessing.iterators.BertEmbMimicCSV method) (medcat.preprocessing.iterators.EmbMimicCSV method) (medcat.preprocessing.iterators.FastEmbMimicCSV method) (medcat.preprocessing.iterators.RawCSV method) (medcat.preprocessing.iterators.SimpleIter method) (medcat.preprocessing.taggers._Tagger method) (medcat.preprocessing.tokenizers.SpacyHFDoc method) (medcat.preprocessing.tokenizers.SpacyHFTok method) (medcat.preprocessing.tokenizers.TokenizerWrapperBERT method) (medcat.preprocessing.tokenizers.TokenizerWrapperBPE method) (medcat.preprocessing.tokenizers.WordpieceTokenizer method) (medcat.rel_cat.RelCAT method) (medcat.stats.kfold.FoldCreator method) (medcat.stats.kfold.PerAnnsFoldCreator method) (medcat.stats.kfold.PerDocsFoldCreator method) (medcat.stats.kfold.SimpleFoldCreator method) (medcat.stats.kfold.WeightedDocumentsCreator method) (medcat.stats.stats.StatsBuilder method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat.tokenizers.transformers_ner.TransformersTokenizerNER method) (medcat.utils.checkpoint.Checkpoint method) (medcat.utils.checkpoint.CheckpointManager method) (medcat.utils.data_utils.MetaAnnotationDS method) (medcat.utils.hasher.Hasher method) (medcat.utils.make_vocab.MakeVocab method) (medcat.utils.memory_optimiser._ItemsView method) (medcat.utils.memory_optimiser._KeysView method) (medcat.utils.memory_optimiser._ValuesView method) (medcat.utils.memory_optimiser.DelegatingDict method) (medcat.utils.memory_optimiser.DelegatingValueSet method) (medcat.utils.meta_cat.data_utils.Doc method) (medcat.utils.meta_cat.data_utils.Empty method) (medcat.utils.meta_cat.data_utils.Span method) (medcat.utils.meta_cat.ml_utils.FocalLoss method) (medcat.utils.meta_cat.models.BertForMetaAnnotation method) (medcat.utils.meta_cat.models.LSTM method) (medcat.utils.ner.deid.DeIdModel method) (medcat.utils.ner.model.NerModel method) (medcat.utils.normalizers.BasicSpellChecker method) (medcat.utils.normalizers.TokenNormalizer method) (medcat.utils.preprocess_snomed.Snomed method) (medcat.utils.preprocess_snomed.UnkownSnomedReleaseException method) (medcat.utils.preprocess_umls.UMLS method) (medcat.utils.regression.checking.MalformedRegressionCaseException method) (medcat.utils.regression.checking.RegressionSuite method) (medcat.utils.regression.results.FindingDeterminer method) (medcat.utils.regression.results.MalformedFinding method) (medcat.utils.regression.targeting.ProblematicOptionSetException method) (medcat.utils.regression.targeting.TranslationLayer method) (medcat.utils.regression.utils.IncompatiblePhraseException method) (medcat.utils.regression.utils.MedCATTrainerExportConverter method) (medcat.utils.relation_extraction.models.BertModel_RelationExtraction method) (medcat.utils.relation_extraction.pad_seq.Pad_Sequence method) (medcat.utils.relation_extraction.rel_dataset.RelData method) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT method) (medcat.utils.saving.coding.CustomDelegatingDecoder method) (medcat.utils.saving.coding.CustomDelegatingEncoder method) (medcat.utils.saving.serializer.CDBSerializer method) (medcat.utils.saving.serializer.JsonSetSerializer method) (medcat.utils.usage_monitoring.UsageMonitor method) (medcat.vocab.Vocab method) __iter__() (medcat.preprocessing.iterators.BaseEmbMimicCSV method) (medcat.preprocessing.iterators.BertEmbMimicCSV method) (medcat.preprocessing.iterators.EmbMimicCSV method) (medcat.preprocessing.iterators.FastEmbMimicCSV method) (medcat.preprocessing.iterators.RawCSV method) (medcat.preprocessing.iterators.SimpleIter method) (medcat.utils.memory_optimiser._ItemsView method) (medcat.utils.memory_optimiser._KeysView method) (medcat.utils.memory_optimiser._ValuesView method) (medcat.utils.memory_optimiser.DelegatingDict method) __len__() (medcat.utils.data_utils.MetaAnnotationDS method) (medcat.utils.memory_optimiser._ItemsView method) (medcat.utils.memory_optimiser._KeysView method) (medcat.utils.memory_optimiser._ValuesView method) (medcat.utils.memory_optimiser.DelegatingDict method) (medcat.utils.relation_extraction.rel_dataset.RelData method) __repr__() (medcat.cat.CAT method) (medcat.meta_cat.MetaCAT method) (medcat.utils.regression.checking.RegressionSuite method) __setattr__() (medcat.config.FakeDict method) __setitem__() (medcat.config.FakeDict method) (medcat.utils.memory_optimiser.DelegatingDict method)

__SPECIALITY_NAMES_CUI (in module medcat.utils.saving.serializer) __SPECIALITY_NAMES_NAME (in module medcat.utils.saving.serializer) __SPECIALITY_NAMES_OTHER (in module medcat.utils.saving.serializer) __str__() (medcat.config.MixingConfig method) (medcat.utils.regression.checking.RegressionSuite method) _add_concept() (medcat.cdb.CDB method) _add_helper() (in module medcat.stats.kfold) _add_nested_ent() (medcat.cat.CAT method) _add_target_ann() (medcat.stats.kfold.PerAnnsFoldCreator method) _add_weighted_helper() (in module medcat.stats.kfold) _attempt_fix_after_load() (in module medcat.utils.memory_optimiser) _batch_generator() (medcat.cat.CAT method) _calc_hash() (medcat.config.MixingConfig method) _check_children() (medcat.utils.regression.results.FindingDeterminer method) _check_medcat_version() (medcat.cdb.CDB class method) _check_parents() (medcat.utils.regression.results.FindingDeterminer method) _check_path_and_release() (medcat.utils.preprocess_snomed.Snomed method) _CITATION (in module medcat.datasets.medcat_annotations) (in module medcat.datasets.patient_concept_stream) (in module medcat.datasets.transformers_ner) _component_lock (medcat.meta_cat.MetaCAT attribute) _count_p_anns_norm() (medcat.stats.stats.StatsBuilder method) _create_annoation() (medcat.stats.stats.StatsBuilder method) _create_annoation_2() (medcat.stats.stats.StatsBuilder method) _create_export_with_documents() (medcat.stats.kfold.FoldCreator method) _create_fold() (medcat.stats.kfold.PerAnnsFoldCreator method) (medcat.stats.kfold.PerDocsFoldCreator method) (medcat.stats.kfold.SimpleFoldCreator method) _create_new_project() (medcat.stats.kfold.FoldCreator method) _create_pipeline() (medcat.cat.CAT method) _create_test_train_datasets() (medcat.rel_cat.RelCAT method) _def_inst (medcat.utils.saving.coding.CustomDelegatingDecoder attribute) _DEFAULT_COLUMNS (in module medcat.utils.preprocess_umls) _DEFAULT_EXTRACTOR (in module medcat.config) _DEFAULT_MRHIER_COLUMNS (in module medcat.utils.preprocess_umls) _DEFAULT_PARTIAL (in module medcat.config) _DEFAULT_SEM_TYPE_COLUMNS (in module medcat.utils.preprocess_umls) _DefPartial (class in medcat.config) _delayed (medcat.pipeline.pipe_runner.PipeRunner attribute) _descr_cui() (medcat.utils.regression.results.FindingDeterminer method) _DESCRIPTION (in module medcat.datasets.medcat_annotations) (in module medcat.datasets.patient_concept_stream) (in module medcat.datasets.transformers_ner) _determine() (medcat.utils.regression.results.FindingDeterminer method) _determine_bundle() (medcat.utils.preprocess_snomed.Snomed class method) _determine_extension() (medcat.utils.preprocess_snomed.Snomed class method) _determine_raw() (medcat.utils.regression.results.FindingDeterminer method) _determine_release() (medcat.utils.preprocess_snomed.Snomed class method) _doc_to_out() (medcat.cat.CAT method) _EMPTY_DICT_2_EMPTY_SET (in module medcat.config) _ensure_serializable() (medcat.pipe.Pipe static method) _execute (medcat.pipeline.pipe_runner.PipeRunner attribute) _find_diff_cui() (medcat.utils.regression.results.FindingDeterminer method) _find_or_add_doc() (medcat.stats.kfold.FoldCreator method) _find_spacy_model_folder() (in module medcat.utils.spacy_compatibility) _fix_waf() (in module medcat.utils.config_utils) _flush_logs() (medcat.utils.usage_monitoring.UsageMonitor method) _format_version() (in module medcat.utils.decorators) _generate_empty_entry() (medcat.utils.memory_optimiser.DelegatingDict method) _generate_examples() (medcat.datasets.medcat_annotations.MedCATAnnotations method) (medcat.datasets.patient_concept_stream.PatientConceptStream method) (medcat.datasets.transformers_ner.TransformersDatasetNER method) _generate_trimmed_texts() (medcat.cat.CAT method) _get_all_combinations() (medcat.utils.regression.targeting.OptionSet method) _get_auto_logs_location() (medcat.utils.usage_monitoring.UsageMonitor method) _get_ckpt_file_paths() (medcat.utils.checkpoint.Checkpoint static method) _get_doc_annotations() (medcat.cat.CAT static method) _get_model() (medcat.rel_cat.RelCAT method) _get_name_and_meta_of_spacy_model_in_medcat_modelpack() (in module medcat.utils.spacy_compatibility) _get_part_report() (medcat.utils.regression.results.MultiDescriptor method) _get_placeholder() (medcat.utils.regression.utils.MedCATTrainerExportConverter method) _get_raw() (medcat.utils.preprocess_snomed.FileFormatDescriptor method) _get_reason_not_deid() (medcat.utils.ner.deid.DeIdModel class method) _get_steps_and_count() (medcat.utils.checkpoint.Checkpoint static method) _get_strict() (medcat.utils.regression.results.FindingDeterminer method) _get_subcases() (medcat.utils.regression.checking.RegressionCase method) _get_training_start() (medcat.cat.CAT static method) _get_trimmed_text() (medcat.cat.CAT method) _get_trimmed_texts() (medcat.cat.CAT method) _IGNORE_TAG (in module medcat.utils.preprocess_snomed) _info() (medcat.datasets.medcat_annotations.MedCATAnnotations method) (medcat.datasets.patient_concept_stream.PatientConceptStream method) (medcat.datasets.transformers_ner.TransformersDatasetNER method) _init_ckpts() (medcat.cat.CAT method) _init_nlp() (medcat.pipe.Pipe method) _init_per_fold() (medcat.stats.kfold.SimpleFoldCreator method) _init_waf_from_config() (medcat.cdb.CDB method) _is_deid_model() (medcat.utils.ner.deid.DeIdModel class method) _is_spacy_model_folder() (in module medcat.utils.spacy_compatibility) _is_spacy_version_within_range() (in module medcat.utils.spacy_compatibility) _ItemsView (class in medcat.utils.memory_optimiser) _iter_anns_backwards() (medcat.utils.regression.utils.MedCATTrainerExportConverter method) _iter_docs() (medcat.utils.regression.utils.MedCATTrainerExportConverter method) _keys_to_ignore_on_load_unexpected (medcat.utils.meta_cat.models.BertForMetaAnnotation attribute) _KeysView (class in medcat.utils.memory_optimiser) _lazy_init_pool() (medcat.pipeline.pipe_runner.PipeRunner method) _map_snomed2refset() (medcat.utils.preprocess_snomed.Snomed method) _merge_examples() (in module medcat.stats.kfold) _mp_cons() (medcat.cat.CAT method) _multiprocessing_batch() (medcat.cat.CAT method) _optimise() (in module medcat.utils.memory_optimiser) _optimise_snames() (in module medcat.utils.memory_optimiser) _pipe_error_handler() (medcat.cat.CAT static method) _prepare_dataset() (medcat.ner.transformers_ner.TransformersNER method) _preprocess_annotations() (medcat.stats.stats.StatsBuilder method) _print_stats() (medcat.cat.CAT method) _process() (medcat.ner.transformers_ner.TransformersNER method) _process_anns_norm() (medcat.stats.stats.StatsBuilder method) _process_p_anns() (medcat.stats.stats.StatsBuilder method) _refset_df2dict() (medcat.utils.preprocess_snomed.Snomed method) _remove_names() (medcat.cdb.CDB method) _reset_stats() (medcat.stats.stats.StatsBuilder method) _run_nn_components() (medcat.cat.CAT method) _run_pipe_on_one() (medcat.pipeline.pipe_runner.PipeRunner static method) _save_docs_to_file() (medcat.cat.CAT method) _separate_nn_components() (medcat.cat.CAT method) _set_extension() (medcat.utils.preprocess_snomed.Snomed method) _set_meta_anns() (medcat.meta_cat.MetaCAT method) _set_value_or_alt() (in module medcat.config) _setup_auto_logs() (medcat.utils.usage_monitoring.UsageMonitor method) _should_log() (medcat.utils.usage_monitoring.UsageMonitor method) _should_recalc_hash() (medcat.cdb.CDB method) _similarity() (medcat.linking.vector_context_model.ContextModel method) _split_generators() (medcat.datasets.medcat_annotations.MedCATAnnotations method) (medcat.datasets.patient_concept_stream.PatientConceptStream method) (medcat.datasets.transformers_ner.TransformersDatasetNER method) _Tagger (class in medcat.preprocessing.taggers) _targets() (medcat.stats.kfold.PerAnnsFoldCreator method) _TEMP_MULTI_PLACEHOLDER (in module medcat.utils.regression.utils) _time_out_in_secs (medcat.pipeline.pipe_runner.PipeRunner attribute) _tok() (medcat.utils.make_vocab.MakeVocab method) _train() (medcat.linking.context_based_linker.Linker method) _unoptimise() (in module medcat.utils.memory_optimiser) _unoptimise_snames() (in module medcat.utils.memory_optimiser) _update_installed_dependencies_recursive() (in module medcat.utils.saving.envsnapshot) _ValuesView (class in medcat.utils.memory_optimiser) _versioning() (medcat.cat.CAT method) _waf_advice (in module medcat.config) _wrapper() (in module medcat.config)

A

adam_epsilon (medcat.config_rel_cat.Train attribute) add() (medcat.stats.kfold.PerCUIMetrics method) add_addl_info() (medcat.cdb.CDB method) add_addl_ner() (medcat.pipe.Pipe method) add_and_train_concept() (medcat.cat.CAT method) add_cui_to_group() (medcat.cat.CAT method) add_default_log_handlers() (in module medcat) add_doc_strings_to_enum() (in module medcat.utils.regression.utils) add_linker() (medcat.pipe.Pipe method) add_meta_cat() (medcat.pipe.Pipe method) add_names() (medcat.cdb.CDB method) add_names_icd10() (in module medcat.utils.helpers) add_names_icd10cm() (in module medcat.utils.helpers) add_ner() (medcat.pipe.Pipe method) add_rel_cat() (medcat.pipe.Pipe method) add_tagger() (medcat.pipe.Pipe method) add_token_normalizer() (medcat.pipe.Pipe method) add_vec() (medcat.vocab.Vocab method) add_vectors() (medcat.utils.make_vocab.MakeVocab method) add_word() (medcat.vocab.Vocab method) add_words() (medcat.vocab.Vocab method)

allow_any_combinations (medcat.utils.regression.targeting.OptionSet attribute) always_calculate_similarity (medcat.config.Linking attribute) annotate_overlapping (medcat.config_meta_cat.General attribute) annotation_output (medcat.config.Config attribute) annotation_schema_tag_ids (medcat.config_rel_cat.General attribute) AnnotationOutput (class in medcat.config) AnnotationOutput.Config (class in medcat.config) ANNOTATIONS (medcat.stats.kfold.SplitType attribute) annotations (medcat.stats.mctexport.MedCATTrainerExportDocument attribute) ANYTHING (medcat.utils.regression.results.Strictness attribute) apply_cdb_state() (in module medcat.utils.cdb_state) arbitrary_types_allowed (medcat.config.Config.Config attribute) are_anns_same() (in module medcat.utils.data_utils) asdict() (medcat.config.MixingConfig method) attempt_fix_after_load() (in module medcat.utils.memory_optimiser) attempt_fix_snames_after_load() (in module medcat.utils.memory_optimiser) attempt_fix_weighted_average_function() (in module medcat.utils.config_utils) attempt_unpack() (medcat.cat.CAT class method) AU (medcat.utils.preprocess_snomed.SupportedExtension attribute) au_ext (medcat.utils.preprocess_snomed.Snomed attribute) auto_save_model (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute)

B

BaseEmbMimicCSV (class in medcat.preprocessing.iterators) basic_clean() (in module medcat.preprocessing.cleaners) BasicSpellChecker (class in medcat.utils.normalizers) batch_generator() (medcat.meta_cat.MetaCAT static method) (medcat.ner.transformers_ner.TransformersNER static method) batch_multi_process() (medcat.pipe.Pipe method) batch_size (medcat.config.UsageMonitor attribute) (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute) batch_size_eval (medcat.config_meta_cat.General attribute) BertEmbMimicCSV (class in medcat.preprocessing.iterators)

BertForMetaAnnotation (class in medcat.utils.meta_cat.models) BertModel_RelationExtraction (class in medcat.utils.relation_extraction.models) BIGGER_SPAN_BOTH (medcat.utils.regression.results.Finding attribute) BIGGER_SPAN_LEFT (medcat.utils.regression.results.Finding attribute) BIGGER_SPAN_RIGHT (medcat.utils.regression.results.Finding attribute) BR (in module medcat.preprocessing.cleaners) BR_U4 (in module medcat.preprocessing.cleaners) build_vocab_from_hf() (in module medcat.utils.ml_utils) BUILDER_CONFIGS (medcat.datasets.medcat_annotations.MedCATAnnotations attribute) (medcat.datasets.patient_concept_stream.PatientConceptStream attribute) (medcat.datasets.transformers_ner.TransformersDatasetNER attribute) BundleDescriptor (class in medcat.utils.preprocess_snomed)

C

calculate_dynamic_threshold (medcat.config.Linking attribute) calculate_hash() (medcat.cdb.CDB method) calculate_label_map() (medcat.tokenizers.transformers_ner.TransformersTokenizerNER method) calculate_report() (medcat.utils.regression.results.MultiDescriptor method) candidates() (medcat.utils.normalizers.BasicSpellChecker method) captured_state_cdb() (in module medcat.utils.cdb_state) CAT (class in medcat.cat) category_name (medcat.config_meta_cat.General attribute) category_undersample (medcat.config_meta_cat.Model attribute) category_value2id (medcat.config_meta_cat.General attribute) CATLike (class in medcat.stats.kfold) CB (in module medcat.preprocessing.cleaners) CB_D (in module medcat.preprocessing.cleaners) CDB (class in medcat.cdb) cdb (medcat.stats.kfold.CATLike property) (medcat.utils.ner.model.NerModel property) cdb_info (medcat.config.VersionInfo attribute) cdb_maker (medcat.config.Config attribute) CDBLike (class in medcat.stats.kfold) CDBMaker (class in medcat.cdb_maker) (class in medcat.config) CDBMaker.Config (class in medcat.config) CDBSerializer (class in medcat.utils.saving.serializer) CDBState (in module medcat.utils.cdb_state) changer (medcat.utils.regression.targeting.TargetedPhraseChanger attribute) check_differences() (in module medcat.utils.data_utils) check_filters() (in module medcat.utils.filters) (medcat.config.LinkingFilters method) check_model() (medcat.utils.regression.checking.RegressionSuite method) check_positive() (in module medcat.utils.decorators) check_specific_for_phrase() (medcat.utils.regression.checking.RegressionCase method) check_upper_case_names (medcat.config.Ner attribute) CheckPoint (class in medcat.config) Checkpoint (class in medcat.utils.checkpoint) checkpoint (medcat.config.General attribute) CheckPoint.Config (class in medcat.config) CheckpointConfig (class in medcat.utils.checkpoint) CheckpointManager (class in medcat.utils.checkpoint) chunking_overlap_window (medcat.config_transformers_ner.General attribute) class_weights (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute) clean_def() (in module medcat.preprocessing.cleaners) clean_drugs_uk() (in module medcat.preprocessing.cleaners) clean_name() (in module medcat.preprocessing.cleaners) clean_snomed_name() (in module medcat.preprocessing.cleaners) clean_snt() (in module medcat.preprocessing.cleaners) clean_text() (in module medcat.preprocessing.cleaners) clean_umls() (in module medcat.preprocessing.cleaners) cntx_left (medcat.config_meta_cat.General attribute) (medcat.config_rel_cat.General attribute) cntx_right (medcat.config_meta_cat.General attribute) (medcat.config_rel_cat.General attribute) CollateAndPadNER (class in medcat.datasets.data_collator) common_prefix (medcat.utils.preprocess_snomed.FileFormatDescriptor attribute) compute_class_weights (medcat.config_meta_cat.Train attribute) concept (medcat.utils.preprocess_snomed.FileFormatDescriptor attribute) (medcat.utils.preprocess_snomed.RefSetFileType attribute)

Config (class in medcat.config) config (medcat.utils.ner.model.NerModel property) Config.Config (class in medcat.config) ConfigMetaCAT (class in medcat.config_meta_cat) ConfigMetaCAT.Config (class in medcat.config_meta_cat) ConfigRelCAT (class in medcat.config_rel_cat) ConfigRelCAT.Config (class in medcat.config_rel_cat) ConfigTransformersNER (class in medcat.config_transformers_ner) ConfigTransformersNER.Config (class in medcat.config_transformers_ner) consolidate_double_annotations() (in module medcat.utils.data_utils) CONTAINS_NUMBER (in module medcat.utils.normalizers) context_ignore_center_tokens (medcat.config.Linking attribute) context_left (medcat.config.AnnotationOutput attribute) context_right (medcat.config.AnnotationOutput attribute) context_vector_sizes (medcat.config.Linking attribute) context_vector_weights (medcat.config.Linking attribute) ContextModel (class in medcat.linking.vector_context_model) convert() (medcat.utils.regression.utils.MedCATTrainerExportConverter method) copy_cdb_state() (in module medcat.utils.cdb_state) copy_of() (medcat.config.LinkingFilters method) count (medcat.utils.checkpoint.Checkpoint property) count() (medcat.vocab.Vocab method) count_all_annotations() (in module medcat.stats.mctexport) count_all_docs() (in module medcat.stats.mctexport) count_annotations() (in module medcat.utils.data_utils) count_annotations_project() (in module medcat.utils.data_utils) create() (medcat.utils.ner.model.NerModel class method) create_base_relations_from_csv() (medcat.utils.relation_extraction.rel_dataset.RelData method) create_base_relations_from_doc() (medcat.utils.relation_extraction.rel_dataset.RelData method) create_batch_piped_data() (in module medcat.utils.meta_cat.ml_utils) create_cdb() (in module medcat.utils.model_creator) create_checkpoint() (medcat.utils.checkpoint.CheckpointManager method) create_eval_pipeline() (medcat.ner.transformers_ner.TransformersNER method) create_folds() (medcat.stats.kfold.FoldCreator method) (medcat.stats.kfold.PerDocsFoldCreator method) (medcat.stats.kfold.SimpleFoldCreator method) (medcat.stats.kfold.WeightedDocumentsCreator method) create_main_ann() (in module medcat.utils.postprocessing) create_model_pack() (medcat.cat.CAT method) create_models() (in module medcat.utils.model_creator) create_relations_from_export() (medcat.utils.relation_extraction.rel_dataset.RelData method) create_tokenizer_pretrain() (in module medcat.utils.relation_extraction.utils) create_vocab() (in module medcat.utils.model_creator) cui (medcat.stats.mctexport.MedCATTrainerExportAnnotation attribute) (medcat.utils.regression.targeting.FinalTarget attribute) (medcat.utils.regression.targeting.TargetedPhraseChanger attribute) cui2tuis() (in module medcat.utils.helpers) CUI_DICT_NAMES_TO_COMBINE (in module medcat.utils.memory_optimiser) cui_filter (medcat.config_meta_cat.Train attribute) cuis (medcat.config.LinkingFilters attribute) (medcat.stats.mctexport.MedCATTrainerExportProject attribute) cuis_exclude (medcat.config.LinkingFilters attribute) CUIS_PART (in module medcat.utils.memory_optimiser) CustomDelegatingDecoder (class in medcat.utils.saving.coding) CustomDelegatingEncoder (class in medcat.utils.saving.coding)

D

data_path (medcat.utils.preprocess_snomed.Snomed attribute) def_inst() (medcat.utils.saving.coding.CustomDelegatingDecoder class method) (medcat.utils.saving.coding.CustomDelegatingEncoder class method) default() (medcat.utils.saving.coding.CustomDelegatingEncoder method) DEFAULT_DECODERS (in module medcat.utils.saving.coding) DEFAULT_ENCODERS (in module medcat.utils.saving.coding) default_hook() (in module medcat.utils.saving.coding) DEFAULT_LOGS_LINUX (in module medcat.utils.usage_monitoring) DEFAULT_LOGS_MACOS (in module medcat.utils.usage_monitoring) DEFAULT_LOGS_WINDOWS (in module medcat.utils.usage_monitoring) DEFAULT_MAX_TO_KEEP (medcat.utils.checkpoint.Checkpoint attribute) DEFAULT_MODEL_PACK_NAME (medcat.cat.CAT attribute) default_postprocessing() (in module medcat.utils.saving.coding) DEFAULT_SPACY_MODEL (in module medcat.pipe) DEFAULT_STEP (medcat.utils.checkpoint.Checkpoint attribute) DEFAULT_TEST_SUITE_PATH (in module medcat.utils.regression.regression_checker) DEFAULT_UNIGRAM_TABLE_SIZE (in module medcat.utils.model_creator) default_weighted_average() (in module medcat.utils.config_utils) deid_multi_texts() (medcat.utils.ner.deid.DeIdModel method) deid_text() (medcat.utils.ner.deid.DeIdModel method) DeIdModel (class in medcat.utils.ner.deid) DELEGATING_DICT_IDENTIFIER (in module medcat.utils.memory_optimiser) DELEGATING_SET_IDENTIFIER (in module medcat.utils.memory_optimiser) DelegatingDict (class in medcat.utils.memory_optimiser) DelegatingDictDecoder (class in medcat.utils.memory_optimiser) DelegatingDictEncoder (class in medcat.utils.memory_optimiser) DelegatingValueSet (class in medcat.utils.memory_optimiser) DelegatingValueSetDecoder (class in medcat.utils.memory_optimiser) DelegatingValueSetEncoder (class in medcat.utils.memory_optimiser) dep_check_scispacy() (in module medcat.utils.helpers) deprecated() (in module medcat.utils.decorators) description (medcat.config.VersionInfo attribute) (medcat.config_meta_cat.General attribute) (medcat.config_transformers_ner.General attribute) (medcat.utils.preprocess_snomed.FileFormatDescriptor attribute) (medcat.utils.preprocess_snomed.RefSetFileType attribute)

deserialize() (medcat.utils.saving.serializer.CDBSerializer method) deserialize_entities() (medcat.pipeline.pipe_runner.PipeRunner static method) destroy() (medcat.pipe.Pipe method) destroy_pipe() (medcat.cat.CAT method) (medcat.cdb_maker.CDBMaker method) (medcat.utils.make_vocab.MakeVocab method) determine() (medcat.utils.regression.results.Finding class method) (medcat.utils.regression.results.FindingDeterminer method) devalue_linked_concepts (medcat.config.Linking attribute) device (medcat.config_meta_cat.General attribute) (medcat.config_rel_cat.General attribute) diacritics (medcat.config.General attribute) dict() (medcat.utils.regression.results.MultiDescriptor method) (medcat.utils.regression.results.ResultDescriptor method) (medcat.utils.regression.results.SingleResultDescriptor method) dir_path (medcat.utils.checkpoint.Checkpoint property) disable_component_lock (medcat.config_meta_cat.General attribute) disamb_length_limit (medcat.config.Linking attribute) disambiguate() (medcat.linking.vector_context_model.ContextModel method) distribution (in module medcat) do_not_normalize (medcat.config.Preprocessing attribute) Doc (class in medcat.utils.meta_cat.data_utils) doc2html() (in module medcat.utils.helpers) doc_extended_info (medcat.config.AnnotationOutput attribute) DOCUMENTS (medcat.stats.kfold.SplitType attribute) documents (medcat.stats.mctexport.MedCATTrainerExportProject attribute) DOCUMENTS_WEIGHTED (medcat.stats.kfold.SplitType attribute) dropout (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Model attribute) dumps() (in module medcat.utils.hasher)

E

edits1() (medcat.utils.normalizers.BasicSpellChecker method) edits2() (medcat.utils.normalizers.BasicSpellChecker method) edits3() (medcat.utils.normalizers.BasicSpellChecker method) emb_grad (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Model attribute) EmbMimicCSV (class in medcat.preprocessing.iterators) Empty (class in medcat.utils.meta_cat.data_utils) empty() (medcat.utils.regression.targeting.PhraseChanger class method) enabled (medcat.config.UsageMonitor attribute) encode() (medcat.preprocessing.tokenizers.SpacyHFTok method) (medcat.tokenizers.transformers_ner.TransformersTokenizerNER method) encode_category_values() (in module medcat.utils.meta_cat.data_utils) encode_examples() (in module medcat.datasets.helpers) EncodeableObject (class in medcat.utils.saving.coding) end (medcat.stats.mctexport.MedCATTrainerExportAnnotation attribute) ensure_backward_compatibility() (in module medcat.utils.config_utils) ensure_spacy_model() (in module medcat.utils.helpers) ensure_tokenizer() (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat.tokenizers.transformers_ner.TransformersTokenizerNER method) ENV_SNAPSHOT_FILE_NAME (in module medcat.utils.saving.envsnapshot) estimate_num_of_diff_subcases() (medcat.utils.regression.checking.RegressionCase method) estimate_num_of_subcases() (medcat.utils.regression.targeting.OptionSet method) estimate_num_variants() (in module medcat.utils.regression.utils) estimate_total_distinct_cases() (medcat.utils.regression.checking.RegressionSuite method) ESTIMATION_MATRIX (in module medcat.utils.regression.utils) eval() (medcat.meta_cat.MetaCAT method) (medcat.ner.transformers_ner.TransformersNER method) eval_model() (in module medcat.utils.meta_cat.ml_utils)

evaluate_() (medcat.rel_cat.RelCAT method) evaluate_results() (medcat.rel_cat.RelCAT method) examples (medcat.utils.regression.results.SingleResultDescriptor attribute) exp_2nd_part_in_folder (medcat.utils.preprocess_snomed.ExtensionDescription attribute) exp_files (medcat.utils.preprocess_snomed.ExtensionDescription attribute) exp_name_in_folder (medcat.utils.preprocess_snomed.ExtensionDescription attribute) ExtensionDescription (class in medcat.utils.preprocess_snomed) extensions (medcat.utils.preprocess_snomed.BundleDescriptor attribute) extra (medcat.config.AnnotationOutput.Config attribute) (medcat.config.CDBMaker.Config attribute) (medcat.config.CheckPoint.Config attribute) (medcat.config.Config.Config attribute) (medcat.config.General.Config attribute) (medcat.config.Linking.Config attribute) (medcat.config.Ner.Config attribute) (medcat.config.Preprocessing.Config attribute) (medcat.config.VersionInfo.Config attribute) (medcat.config_meta_cat.ConfigMetaCAT.Config attribute) (medcat.config_meta_cat.General.Config attribute) (medcat.config_meta_cat.Model.Config attribute) (medcat.config_meta_cat.Train.Config attribute) (medcat.config_rel_cat.ConfigRelCAT.Config attribute) (medcat.config_rel_cat.Model.Config attribute) (medcat.config_rel_cat.Train.Config attribute) (medcat.config_transformers_ner.ConfigTransformersNER.Config attribute) (medcat.config_transformers_ner.General.Config attribute) (medcat.utils.regression.checking.MetaData attribute) extract() (medcat.config.ValueExtractor method)

F

FAIL (medcat.utils.regression.results.Finding attribute) FAIL_AFTER_MULT (in module medcat.utils.regression.utils) FakeDict (class in medcat.config) FAST_SPLIT (in module medcat.preprocessing.iterators) FastEmbMimicCSV (class in medcat.preprocessing.iterators) fields() (medcat.config.MixingConfig method) file_prefix (medcat.config.UsageMonitor attribute) FileFormatDescriptor (class in medcat.utils.preprocess_snomed) filter_before_disamb (medcat.config.Linking attribute) filter_by_cui() (medcat.cdb.CDB method) filter_cdb_by_icd10() (in module medcat.utils.helpers) filter_only_icd10() (in module medcat.utils.helpers) filters (medcat.config.Linking attribute) final_phrase (medcat.utils.regression.targeting.FinalTarget attribute) finalise_report() (medcat.stats.stats.StatsBuilder method) FinalTarget (class in medcat.utils.regression.targeting) Finding (class in medcat.utils.regression.results) FindingDeterminer (class in medcat.utils.regression.results) findings (medcat.utils.regression.results.MultiDescriptor property) (medcat.utils.regression.results.SingleResultDescriptor attribute) fix() (medcat.utils.normalizers.BasicSpellChecker method) fix_np_float64() (in module medcat.utils.regression.checking) fix_waf_lambda() (in module medcat.utils.config_utils) FloatValuedMetric (in module medcat.stats.kfold)

FocalLoss (class in medcat.utils.meta_cat.ml_utils) FoldCreator (class in medcat.stats.kfold) force_remove() (medcat.pipe.Pipe method) forward() (medcat.utils.meta_cat.ml_utils.FocalLoss method) (medcat.utils.meta_cat.models.BertForMetaAnnotation method) (medcat.utils.meta_cat.models.LSTM method) (medcat.utils.relation_extraction.models.BertModel_RelationExtraction method) FOUND_ANY_CHILD (medcat.utils.regression.results.Finding attribute) FOUND_CHILD_PARTIAL (medcat.utils.regression.results.Finding attribute) FOUND_DIR_GRANDPARENT (medcat.utils.regression.results.Finding attribute) FOUND_DIR_PARENT (medcat.utils.regression.results.Finding attribute) FOUND_OTHER (medcat.utils.regression.results.Finding attribute) from_cat() (medcat.stats.stats.StatsBuilder class method) from_CDB() (medcat.utils.regression.targeting.TranslationLayer class method) from_dict() (medcat.config.MixingConfig class method) (medcat.utils.regression.checking.RegressionCase class method) (medcat.utils.regression.checking.RegressionSuite class method) (medcat.utils.regression.targeting.OptionSet class method) from_latest() (medcat.utils.checkpoint.Checkpoint class method) from_mct_export() (medcat.utils.regression.checking.RegressionSuite class method) from_modelcard() (medcat.utils.regression.checking.MetaData class method) from_yaml() (medcat.utils.regression.checking.RegressionSuite class method) full_unlink (medcat.config.General attribute) func_has_kwarg() (in module medcat.ner.transformers_ner)

G

gamma (medcat.config_meta_cat.Train attribute) General (class in medcat.config) (class in medcat.config_meta_cat) (class in medcat.config_rel_cat) (class in medcat.config_transformers_ner) general (medcat.config.Config attribute) (medcat.config_meta_cat.ConfigMetaCAT attribute) (medcat.config_rel_cat.ConfigRelCAT attribute) (medcat.config_transformers_ner.ConfigTransformersNER attribute) General.Config (class in medcat.config) (class in medcat.config_meta_cat) (class in medcat.config_transformers_ner) generate_base_relations() (medcat.utils.relation_extraction.rel_dataset.RelData method) get() (medcat.config.FakeDict method) (medcat.utils.memory_optimiser.DelegatingDict method) get_all_children() (in module medcat.utils.preprocess_snomed) get_all_distinct_cases() (medcat.utils.regression.checking.RegressionSuite method) get_all_edits_n() (in module medcat.utils.normalizers) get_all_from_name() (in module medcat.utils.helpers) get_all_irrelevant_cuis() (in module medcat.utils.filters) get_and_del_weighted_average_from_config() (in module medcat.utils.config_utils) get_ann_from_doc() (in module medcat.utils.data_utils) get_annotation_schema_tag() (medcat.utils.relation_extraction.models.BertModel_RelationExtraction method) get_batch() (in module medcat.utils.ml_utils) get_children_of() (medcat.utils.regression.targeting.TranslationLayer method) get_class_level_docstrings() (in module medcat.utils.regression.utils) get_concept() (medcat.utils.preprocess_snomed.FileFormatDescriptor method) get_context_tokens() (medcat.linking.vector_context_model.ContextModel method) get_context_vectors() (medcat.linking.vector_context_model.ContextModel method) get_description() (medcat.utils.preprocess_snomed.FileFormatDescriptor method) get_direct_children() (medcat.utils.regression.targeting.TranslationLayer method) get_direct_dependencies() (in module medcat.utils.saving.envsnapshot) get_direct_parents() (medcat.utils.regression.targeting.TranslationLayer method) get_direct_refset_mapping() (in module medcat.utils.preprocess_snomed) get_distinct_cases() (medcat.utils.regression.checking.RegressionCase method) get_doc_from_project() (in module medcat.utils.data_utils) get_edits1() (medcat.utils.normalizers.BasicSpellChecker class method) get_entities() (medcat.cat.CAT method) (medcat.utils.ner.model.NerModel method) get_entities_multi_texts() (medcat.cat.CAT method) get_ents() (medcat.meta_cat.MetaCAT method) get_environment_info() (in module medcat.utils.saving.envsnapshot) get_false_positives() (in module medcat.utils.data_utils) get_file_per_type() (medcat.utils.preprocess_snomed.FileFormatDescriptor method) get_first_name() (medcat.utils.regression.targeting.TranslationLayer method) get_fold_creator() (in module medcat.stats.kfold) get_hash() (medcat.cat.CAT method) (medcat.cdb.CDB method) (medcat.config.Config method) (medcat.config.MixingConfig method) (medcat.meta_cat.MetaCAT method) (medcat.ner.transformers_ner.TransformersNER method)

get_important_config_parameters() (in module medcat.utils.helpers) get_installed_model_version() (in module medcat.utils.spacy_compatibility) get_installed_packages() (in module medcat.utils.saving.envsnapshot) get_installed_spacy_version() (in module medcat.utils.spacy_compatibility) get_json() (medcat.cat.CAT method) get_k_fold_stats() (in module medcat.stats.kfold) get_labels() (medcat.utils.relation_extraction.rel_dataset.RelData class method) get_latest_checkpoint() (medcat.utils.checkpoint.CheckpointManager method) get_latest_training_dir() (medcat.utils.checkpoint.CheckpointManager class method) get_lr_linking() (in module medcat.utils.ml_utils) get_mean() (medcat.stats.kfold.PerCUIMetrics method) get_metrics_mean() (in module medcat.stats.kfold) get_model() (medcat.meta_cat.MetaCAT method) get_model_card() (medcat.cat.CAT method) (medcat.meta_cat.MetaCAT method) get_name() (medcat.cdb.CDB method) get_name_and_version_of_spacy_model_in_medcat_modelpack() (in module medcat.utils.spacy_compatibility) get_names_of() (medcat.utils.regression.targeting.TranslationLayer method) get_negative_samples() (medcat.vocab.Vocab method) get_nr_of_annotations() (in module medcat.stats.mctexport) get_ontology_and_version() (in module medcat.utils.regression.checking) get_pad_id() (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT method) get_per_fold_metrics() (in module medcat.stats.kfold) get_preferred_name() (medcat.utils.regression.targeting.TranslationLayer method) get_preprocessors_and_targets() (medcat.utils.regression.targeting.OptionSet method) get_project_filters() (in module medcat.utils.filters) get_pt2ch() (medcat.utils.preprocess_umls.UMLS method) get_refset() (medcat.utils.preprocess_snomed.FileFormatDescriptor method) get_relationship() (medcat.utils.preprocess_snomed.FileFormatDescriptor method) get_report() (medcat.utils.regression.results.MultiDescriptor method) (medcat.utils.regression.results.ResultDescriptor method) (medcat.utils.regression.results.SingleResultDescriptor method) get_rng() (in module medcat.utils.regression.utils) get_same_anns() (in module medcat.utils.data_utils) get_size() (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT method) get_stats() (in module medcat.stats.stats) get_std() (medcat.stats.kfold.PerCUIMetrics method) get_transitive_deps() (in module medcat.utils.saving.envsnapshot) gradient_acc_steps (medcat.config_rel_cat.Train attribute)

H

has_correct_cui() (medcat.utils.regression.results.Finding method) has_invalid() (medcat.utils.preprocess_snomed.BundleDescriptor method) HAS_NEW_SPACY (in module medcat.cat) has_new_spacy() (in module medcat.utils.helpers) has_spacy_model() (in module medcat.utils.helpers) hash (medcat.config.Config attribute)

Hasher (class in medcat.utils.hasher) hexdigest() (medcat.utils.hasher.Hasher method) hidden_layers (medcat.config_rel_cat.Model attribute) hidden_size (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Model attribute) history (medcat.config.VersionInfo attribute)

I

id (medcat.config.VersionInfo attribute) (medcat.stats.mctexport.MedCATTrainerExportDocument attribute) (medcat.stats.mctexport.MedCATTrainerExportProject attribute) IDENTICAL (medcat.utils.regression.results.Finding attribute) idx2labels (medcat.config_rel_cat.General attribute) ignore_all() (medcat.utils.preprocess_snomed.FileFormatDescriptor class method) ignore_cpos (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Model attribute) ignores (medcat.utils.preprocess_snomed.BundleDescriptor attribute) import_training() (medcat.cdb.CDB method) in_memory_state_capture() (in module medcat.utils.cdb_state) inc_or_add() (medcat.vocab.Vocab method) inc_wc() (medcat.vocab.Vocab method) include_text_in_output (medcat.config.AnnotationOutput attribute) IncompatiblePhraseException input_size (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Model attribute)

INSTALL_REQUIRES_FILE_PATH (in module medcat.utils.saving.envsnapshot) INSTALL_REQUIRES_FILE_PATH_PIP (in module medcat.utils.saving.envsnapshot) INTERNATIONAL (medcat.utils.preprocess_snomed.SupportedExtension attribute) intersect_nonempty_set() (in module medcat.utils.matutils) IntValuedMetric (in module medcat.stats.kfold) is_old_type_config_dict() (in module medcat.utils.config_utils) is_older_spacy_version() (in module medcat.utils.spacy_compatibility) item() (medcat.vocab.Vocab method) items() (medcat.utils.memory_optimiser.DelegatingDict method) iter_anns() (in module medcat.stats.mctexport) iter_docs() (in module medcat.stats.mctexport) iter_examples() (medcat.utils.regression.results.MultiDescriptor method) (medcat.utils.regression.results.ResultDescriptor method) iter_projects() (in module medcat.stats.mctexport) iter_subcases() (medcat.utils.regression.checking.RegressionSuite method)

J

json() (medcat.utils.regression.results.SingleResultDescriptor method) json2html() (in module medcat.utils.helpers)

json_to_fake_spacy() (in module medcat.utils.meta_cat.data_utils) JsonSetSerializer (class in medcat.utils.saving.serializer)

K

keep_punct (medcat.config.Preprocessing attribute)

keys() (medcat.utils.memory_optimiser.DelegatingDict method) known() (medcat.utils.normalizers.BasicSpellChecker method)

L

labels2idx (medcat.config_rel_cat.General attribute) LabelStyle (class in medcat.utils.postprocessing) last_modified (medcat.config.VersionInfo attribute) (medcat.stats.mctexport.MedCATTrainerExportDocument attribute) last_train_on (medcat.config_meta_cat.Train attribute) (medcat.config_transformers_ner.General attribute) LENIENT (medcat.utils.regression.results.Strictness attribute) limit_str_len() (in module medcat.utils.regression.utils) Linker (class in medcat.linking.context_based_linker) Linking (class in medcat.config) linking (medcat.config.Config attribute) Linking.Config (class in medcat.config) LinkingFilters (class in medcat.config) list_all_relationships() (medcat.utils.preprocess_snomed.Snomed method) load() (medcat.cdb.CDB class method) (medcat.config.MixingConfig class method) (medcat.meta_cat.MetaCAT class method) (medcat.ner.transformers_ner.TransformersNER class method) (medcat.preprocessing.tokenizers.TokenizerWrapperBERT class method) (medcat.preprocessing.tokenizers.TokenizerWrapperBPE class method) (medcat.rel_cat.RelCAT class method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase class method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT class method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE class method) (medcat.tokenizers.transformers_ner.TransformersTokenizerNER class method) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT class method) (medcat.vocab.Vocab class method) load_and_apply_cdb_state() (in module medcat.utils.cdb_state) load_bin_file() (in module medcat.utils.relation_extraction.utils) load_cdb() (medcat.cat.CAT class method) load_config() (medcat.cdb.CDB method) load_data() (in module medcat.utils.data_utils) load_hf_tokenizer() (in module medcat.utils.ml_utils) load_meta_cats() (medcat.cat.CAT class method) load_model_pack() (medcat.cat.CAT class method) (medcat.utils.ner.deid.DeIdModel class method) (medcat.utils.ner.model.NerModel class method) load_results() (in module medcat.utils.relation_extraction.utils) load_state() (in module medcat.utils.relation_extraction.utils) LOADING_POSTPROCESSORS (in module medcat.utils.saving.coding) location (medcat.config.VersionInfo attribute) log (medcat.rel_cat.RelCAT attribute) (medcat.utils.relation_extraction.models.BertModel_RelationExtraction attribute) (medcat.utils.relation_extraction.rel_dataset.RelData attribute) log_file (medcat.utils.usage_monitoring.UsageMonitor property) log_folder (medcat.config.UsageMonitor attribute) log_format (medcat.config.General attribute) log_inference() (medcat.utils.usage_monitoring.UsageMonitor method)

log_level (medcat.config.General attribute) (medcat.config_rel_cat.General attribute) log_path (medcat.config.General attribute) logger (in module medcat) (in module medcat.cat) (in module medcat.cdb) (in module medcat.cdb_maker) (in module medcat.config) (in module medcat.linking.context_based_linker) (in module medcat.linking.vector_context_model) (in module medcat.meta_cat) (in module medcat.ner.transformers_ner) (in module medcat.ner.vocab_based_annotator) (in module medcat.ner.vocab_based_ner) (in module medcat.pipe) (in module medcat.pipeline.pipe_runner) (in module medcat.tokenizers.transformers_ner) (in module medcat.utils.cdb_state) (in module medcat.utils.cdb_utils) (in module medcat.utils.checkpoint) (in module medcat.utils.config_utils) (in module medcat.utils.data_utils) (in module medcat.utils.helpers) (in module medcat.utils.make_vocab) (in module medcat.utils.meta_cat.data_utils) (in module medcat.utils.meta_cat.ml_utils) (in module medcat.utils.meta_cat.models) (in module medcat.utils.model_creator) (in module medcat.utils.ner.deid) (in module medcat.utils.ner.metrics) (in module medcat.utils.regression) (in module medcat.utils.regression.checking) (in module medcat.utils.regression.regression_checker) (in module medcat.utils.regression.targeting), [1] (in module medcat.utils.saving) (in module medcat.utils.saving.converter) (in module medcat.utils.saving.envsnapshot) (in module medcat.utils.saving.serializer) (in module medcat.utils.usage_monitoring) LOGS_ENV (in module medcat.utils.usage_monitoring) LOGS_LOC_ENV (in module medcat.utils.usage_monitoring) long (medcat.utils.postprocessing.LabelStyle attribute) loss_funct (medcat.config_meta_cat.Train attribute) lowercase (medcat.config_meta_cat.General attribute) (medcat.config_rel_cat.General attribute) lowercase_context (medcat.config.AnnotationOutput attribute) lr (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute) LSTM (class in medcat.utils.meta_cat.models)

M

main() (in module medcat.utils.model_creator) (in module medcat.utils.regression.regression_checker) (in module medcat.utils.saving.converter) make() (medcat.utils.make_vocab.MakeVocab method) make_mc_train_test() (in module medcat.utils.data_utils) make_or_update_cdb() (in module medcat.utils.ner) (in module medcat.utils.ner.helpers) make_pretty_labels (medcat.config.General attribute) make_pretty_labels() (in module medcat.utils.postprocessing) make_stats() (medcat.cdb.CDB method) make_unigram_table() (medcat.vocab.Vocab method) MakeVocab (class in medcat.utils.make_vocab) MalformedFinding MalformedRegressionCaseException map_cui_to_group (medcat.config.General attribute) map_ents_to_groups() (in module medcat.utils.postprocessing) map_snomed2icd10() (medcat.utils.preprocess_snomed.Snomed method) map_snomed2opcs4() (medcat.utils.preprocess_snomed.Snomed method) map_to_many() (in module medcat.utils.memory_optimiser) map_umls2icd10() (medcat.utils.preprocess_umls.UMLS method) map_umls2snomed() (medcat.utils.preprocess_umls.UMLS method) map_umls2source() (medcat.utils.preprocess_umls.UMLS method) match_partials_with_folders() (in module medcat.utils.preprocess_snomed) max_document_length (medcat.config.Preprocessing attribute) max_grad_norm (medcat.config_rel_cat.Train attribute) max_seq_length (medcat.config_rel_cat.General attribute) max_skip_tokens (medcat.config.Ner attribute) max_to_keep (medcat.config.CheckPoint attribute) (medcat.utils.checkpoint.Checkpoint property) (medcat.utils.checkpoint.CheckpointConfig attribute) maybe_annotate_name() (in module medcat.ner.vocab_based_annotator) mct_export_create_addl_rels (medcat.config_rel_cat.General attribute) mct_export_max_non_rel_sample_size (medcat.config_rel_cat.General attribute) medcat module medcat.cat module medcat.cdb module medcat.cdb_maker module medcat.config module medcat.config_meta_cat module medcat.config_rel_cat module medcat.config_transformers_ner module medcat.datasets module medcat.datasets.data_collator module medcat.datasets.helpers module medcat.datasets.medcat_annotations module medcat.datasets.patient_concept_stream module medcat.datasets.transformers_ner module medcat.linking module medcat.linking.context_based_linker module medcat.linking.vector_context_model module medcat.meta_cat module medcat.ner module medcat.ner.transformers_ner module medcat.ner.vocab_based_annotator module medcat.ner.vocab_based_ner module medcat.pipe module medcat.pipeline module medcat.pipeline.pipe_runner module medcat.preprocessing module medcat.preprocessing.cleaners module medcat.preprocessing.iterators module medcat.preprocessing.taggers module medcat.preprocessing.tokenizers module medcat.rel_cat module medcat.stats module medcat.stats.kfold module medcat.stats.mctexport module medcat.stats.stats module medcat.tokenizers module medcat.tokenizers.meta_cat_tokenizers module medcat.tokenizers.transformers_ner module medcat.utils module medcat.utils.cdb_state module medcat.utils.cdb_utils module medcat.utils.checkpoint module medcat.utils.config_utils module medcat.utils.data_utils module medcat.utils.decorators module medcat.utils.filters module medcat.utils.hasher module medcat.utils.helpers module medcat.utils.make_vocab module medcat.utils.matutils module medcat.utils.medmentions module medcat.utils.memory_optimiser module medcat.utils.meta_cat module medcat.utils.meta_cat.data_utils module medcat.utils.meta_cat.ml_utils module medcat.utils.meta_cat.models module medcat.utils.ml_utils module medcat.utils.model_creator module medcat.utils.ner module medcat.utils.ner.deid module medcat.utils.ner.helpers module medcat.utils.ner.metrics module medcat.utils.ner.model module medcat.utils.normalizers module medcat.utils.other module medcat.utils.postprocessing module medcat.utils.preprocess_snomed module medcat.utils.preprocess_umls module medcat.utils.regression module medcat.utils.regression.checking module

medcat.utils.regression.regression_checker module medcat.utils.regression.results module medcat.utils.regression.targeting module medcat.utils.regression.utils module medcat.utils.relation_extraction module medcat.utils.relation_extraction.models module medcat.utils.relation_extraction.pad_seq module medcat.utils.relation_extraction.rel_dataset module medcat.utils.relation_extraction.tokenizer module medcat.utils.relation_extraction.utils module medcat.utils.saving module medcat.utils.saving.coding module medcat.utils.saving.converter module medcat.utils.saving.envsnapshot module medcat.utils.saving.serializer module medcat.utils.spacy_compatibility module medcat.utils.usage_monitoring module medcat.vocab module medcat_csv_mapper (in module medcat.utils.preprocess_umls) medcat_model_pack_has_compatible_spacy_model() (in module medcat.utils.spacy_compatibility) medcat_model_pack_has_semi_compatible_spacy_model() (in module medcat.utils.spacy_compatibility) medcat_version (medcat.config.VersionInfo attribute) MedCATAnnotations (class in medcat.datasets.medcat_annotations) MedCATAnnotationsConfig (class in medcat.datasets.medcat_annotations) (class in medcat.datasets.transformers_ner) MedCATTrainerExport (class in medcat.stats.mctexport) MedCATTrainerExportAnnotation (class in medcat.stats.mctexport) MedCATTrainerExportConverter (class in medcat.utils.regression.utils) MedCATTrainerExportDocument (class in medcat.stats.mctexport) MedCATTrainerExportProject (class in medcat.stats.mctexport) MedCATTrainerExportProjectInfo (in module medcat.stats.mctexport) merge_cdb() (in module medcat.utils.cdb_utils) merge_config() (medcat.config.MixingConfig method) merge_with() (medcat.config.LinkingFilters method) meta_ann_from_ann() (in module medcat.utils.data_utils) meta_cats (medcat.config.VersionInfo attribute) MetaAnnotationDS (class in medcat.utils.data_utils) MetaCAT (class in medcat.meta_cat) MetaData (class in medcat.utils.regression.checking) metric (medcat.config_meta_cat.Train attribute) metrics() (in module medcat.utils.ner) (in module medcat.utils.ner.metrics) MIN_GEN_LEN_FOR_WARN (in module medcat.cat) min_len_normalize (medcat.config.Preprocessing attribute) min_letters_required (medcat.config.CDBMaker attribute) min_name_len (medcat.config.Ner attribute) MixingConfig (class in medcat.config) Model (class in medcat.config_meta_cat) (class in medcat.config_rel_cat) model (medcat.config_meta_cat.ConfigMetaCAT attribute) (medcat.config_rel_cat.ConfigRelCAT attribute) Model.Config (class in medcat.config_meta_cat) (class in medcat.config_rel_cat) model_architecture_config (medcat.config_meta_cat.Model attribute) model_freeze_layers (medcat.config_meta_cat.Model attribute) model_name (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.General attribute) (medcat.config_transformers_ner.General attribute) model_size (medcat.config_rel_cat.Model attribute) model_variant (medcat.config_meta_cat.Model attribute) module medcat medcat.cat medcat.cdb medcat.cdb_maker medcat.config medcat.config_meta_cat medcat.config_rel_cat medcat.config_transformers_ner medcat.datasets medcat.datasets.data_collator medcat.datasets.helpers medcat.datasets.medcat_annotations medcat.datasets.patient_concept_stream medcat.datasets.transformers_ner medcat.linking medcat.linking.context_based_linker medcat.linking.vector_context_model medcat.meta_cat medcat.ner medcat.ner.transformers_ner medcat.ner.vocab_based_annotator medcat.ner.vocab_based_ner medcat.pipe medcat.pipeline medcat.pipeline.pipe_runner medcat.preprocessing medcat.preprocessing.cleaners medcat.preprocessing.iterators medcat.preprocessing.taggers medcat.preprocessing.tokenizers medcat.rel_cat medcat.stats medcat.stats.kfold medcat.stats.mctexport medcat.stats.stats medcat.tokenizers medcat.tokenizers.meta_cat_tokenizers medcat.tokenizers.transformers_ner medcat.utils medcat.utils.cdb_state medcat.utils.cdb_utils medcat.utils.checkpoint medcat.utils.config_utils medcat.utils.data_utils medcat.utils.decorators medcat.utils.filters medcat.utils.hasher medcat.utils.helpers medcat.utils.make_vocab medcat.utils.matutils medcat.utils.medmentions medcat.utils.memory_optimiser medcat.utils.meta_cat medcat.utils.meta_cat.data_utils medcat.utils.meta_cat.ml_utils medcat.utils.meta_cat.models medcat.utils.ml_utils medcat.utils.model_creator medcat.utils.ner medcat.utils.ner.deid medcat.utils.ner.helpers medcat.utils.ner.metrics medcat.utils.ner.model medcat.utils.normalizers medcat.utils.other medcat.utils.postprocessing medcat.utils.preprocess_snomed medcat.utils.preprocess_umls medcat.utils.regression medcat.utils.regression.checking medcat.utils.regression.regression_checker medcat.utils.regression.results medcat.utils.regression.targeting medcat.utils.regression.utils medcat.utils.relation_extraction medcat.utils.relation_extraction.models medcat.utils.relation_extraction.pad_seq medcat.utils.relation_extraction.rel_dataset medcat.utils.relation_extraction.tokenizer medcat.utils.relation_extraction.utils medcat.utils.saving medcat.utils.saving.coding medcat.utils.saving.converter medcat.utils.saving.envsnapshot medcat.utils.saving.serializer medcat.utils.spacy_compatibility medcat.utils.usage_monitoring medcat.vocab most_similar() (medcat.cdb.CDB method) multi_separator (medcat.config.CDBMaker attribute) MultiDescriptor (class in medcat.utils.regression.results) multiprocessing_batch_char_size() (medcat.cat.CAT method) multiprocessing_batch_docs_size() (medcat.cat.CAT method) multistep_lr_gamma (medcat.config_rel_cat.Train attribute) multistep_milestones (medcat.config_rel_cat.Train attribute)

N

name (in module medcat) (medcat.config_transformers_ner.General attribute) (medcat.linking.context_based_linker.Linker attribute) (medcat.meta_cat.MetaCAT attribute) (medcat.ner.transformers_ner.TransformersNER attribute) (medcat.ner.vocab_based_ner.NER attribute) (medcat.rel_cat.RelCAT attribute) (medcat.stats.mctexport.MedCATTrainerExportDocument attribute) (medcat.stats.mctexport.MedCATTrainerExportProject attribute) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase attribute) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT attribute) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE attribute) (medcat.utils.normalizers.TokenNormalizer attribute) (medcat.utils.regression.checking.RegressionCase attribute) (medcat.utils.regression.results.MultiDescriptor attribute) (medcat.utils.regression.results.SingleResultDescriptor attribute) (medcat.utils.regression.targeting.FinalTarget attribute) (medcat.utils.relation_extraction.models.BertModel_RelationExtraction attribute) (medcat.utils.relation_extraction.rel_dataset.RelData attribute) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT attribute) NAME2MANY (in module medcat.utils.memory_optimiser)

NAME_DICT_NAMES_TO_COMBINE (in module medcat.utils.memory_optimiser) name_versions (medcat.config.CDBMaker attribute) NAMES_PART (in module medcat.utils.memory_optimiser) nclasses (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Train attribute) negative_ignore_punct_and_num (medcat.config.Linking attribute) negative_probability (medcat.config.Linking attribute) nepochs (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute) Ner (class in medcat.config) NER (class in medcat.ner.vocab_based_ner) ner (medcat.config.Config attribute) Ner.Config (class in medcat.config) ner_aggregation_strategy (medcat.config_transformers_ner.General attribute) NerModel (class in medcat.utils.ner.model) NO_VERSION_DETECTED (medcat.utils.preprocess_snomed.Snomed attribute) NORMAL (medcat.utils.regression.results.Strictness attribute) NUM (in module medcat.preprocessing.iterators) num_directions (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Model attribute) num_layers (medcat.config_meta_cat.Model attribute)

O

object_hook() (medcat.utils.saving.coding.CustomDelegatingDecoder method) on_disk_memory_capture() (in module medcat.utils.cdb_state) ONE2MANY (in module medcat.utils.memory_optimiser) (in module medcat.utils.saving.serializer) onlyprefnames (medcat.utils.regression.targeting.TargetedPhraseChanger attribute) (medcat.utils.regression.targeting.TargetPlaceholder attribute) ontology (medcat.config.VersionInfo attribute) (medcat.utils.regression.checking.MetaData attribute) ontology_version (medcat.utils.regression.checking.MetaData attribute)

optim (medcat.config.Linking attribute) options (medcat.utils.regression.checking.RegressionCase attribute) (medcat.utils.regression.targeting.OptionSet attribute) OptionSet (class in medcat.utils.regression.targeting) original2concept_csv() (in module medcat.utils.medmentions) original2json() (in module medcat.utils.medmentions) original2pure_text() (in module medcat.utils.medmentions) output2logits() (medcat.utils.relation_extraction.models.BertModel_RelationExtraction method) output_dir (medcat.config.CheckPoint attribute) (medcat.utils.checkpoint.CheckpointConfig attribute)

P

P() (medcat.utils.normalizers.BasicSpellChecker method) Pad_Sequence (class in medcat.utils.relation_extraction.pad_seq) padding_idx (medcat.config_meta_cat.Model attribute) (medcat.config_rel_cat.Model attribute) parse_config_file() (medcat.config.MixingConfig method) parse_file() (in module medcat.utils.preprocess_snomed) parser (in module medcat.utils.model_creator) (in module medcat.utils.regression.regression_checker) PartDecoder (class in medcat.utils.saving.coding) PartEncoder (class in medcat.utils.saving.coding) PARTIAL_OVERLAP (medcat.utils.regression.results.Finding attribute) partial_substitute() (in module medcat.utils.regression.utils) parts (medcat.utils.regression.results.MultiDescriptor attribute) PatientConceptStream (class in medcat.datasets.patient_concept_stream) PatientConceptStreamConfig (class in medcat.datasets.patient_concept_stream) PATTERN_IDENTIFIER (in module medcat.utils.saving.coding) PatternDecoder (class in medcat.utils.saving.coding) PatternEncoder (class in medcat.utils.saving.coding) PER_FILE_TYPE_PATHS (in module medcat.utils.preprocess_snomed) per_phrase_results (medcat.utils.regression.results.ResultDescriptor attribute) PerAnnsFoldCreator (class in medcat.stats.kfold) PerCUIMetrics (class in medcat.stats.kfold) PerDocsFoldCreator (class in medcat.stats.kfold) perform_optimisation() (in module medcat.utils.memory_optimiser) performance (medcat.config.VersionInfo attribute) PH_REMOVE (in module medcat.cdb_maker) PH_RM (in module medcat.preprocessing.cleaners) phase_number (medcat.config_meta_cat.Model attribute) PhraseChanger (class in medcat.utils.regression.targeting) phrases (medcat.utils.regression.checking.RegressionCase attribute) pick_random_edits() (in module medcat.utils.regression.utils) pin_memory (medcat.config_rel_cat.General attribute) Pipe (class in medcat.pipe) pipe() (medcat.meta_cat.MetaCAT method) (medcat.ner.transformers_ner.TransformersNER method) (medcat.pipeline.pipe_runner.PipeRunner method) (medcat.rel_cat.RelCAT method)

pipe_batch_size_in_chars (medcat.config_meta_cat.General attribute) (medcat.config_transformers_ner.General attribute) PipeRunner (class in medcat.pipeline.pipe_runner) placeholder (medcat.utils.regression.targeting.FinalTarget attribute) (medcat.utils.regression.targeting.TargetedPhraseChanger attribute) (medcat.utils.regression.targeting.TargetPlaceholder attribute) pop() (medcat.utils.memory_optimiser.DelegatingDict method) populate_cui2snames() (medcat.cdb.CDB method) PostProcessor (in module medcat.utils.saving.coding) predict() (in module medcat.utils.meta_cat.ml_utils) prefer_frequent_concepts (medcat.config.Linking attribute) prefer_primary_name (medcat.config.Linking attribute) prepare_csvs() (medcat.cdb_maker.CDBMaker method) prepare_document() (medcat.meta_cat.MetaCAT method) prepare_for_oversampled_data() (in module medcat.utils.meta_cat.data_utils) prepare_from_json() (in module medcat.utils.meta_cat.data_utils) prepare_from_json_chars() (in module medcat.utils.data_utils) prepare_from_json_hf() (in module medcat.utils.data_utils) prepare_name() (in module medcat.preprocessing.cleaners) (in module medcat.utils.helpers) preprocess_placeholders (medcat.utils.regression.targeting.PhraseChanger attribute) Preprocessing (class in medcat.config) preprocessing (medcat.config.Config attribute) Preprocessing.Config (class in medcat.config) prerequisites (medcat.config_meta_cat.Train attribute) print_consolid_stats() (in module medcat.utils.data_utils) print_report() (in module medcat.utils.meta_cat.ml_utils) print_stats() (medcat.cdb.CDB method) ProblematicOptionSetException process_document() (medcat.stats.stats.StatsBuilder method) process_project() (medcat.stats.stats.StatsBuilder method) projects (medcat.stats.mctexport.MedCATTrainerExport attribute) punct_checker (medcat.config.Config attribute) put_blanks() (in module medcat.utils.relation_extraction.utils)

R

random_replacement_unsupervised (medcat.config.Linking attribute) RawCSV (class in medcat.preprocessing.iterators) read() (medcat.utils.saving.serializer.JsonSetSerializer method) rebuild_re() (medcat.config.Config method) (medcat.config.MixingConfig method) refset (medcat.utils.preprocess_snomed.FileFormatDescriptor attribute) (medcat.utils.preprocess_snomed.RefSetFileType attribute) RefSetFileType (class in medcat.utils.preprocess_snomed) register_encoder_decoder() (in module medcat.utils.saving.coding) regr_suite_creation_date (medcat.utils.regression.checking.MetaData attribute) RegressionCase (class in medcat.utils.regression.checking) RegressionSuite (class in medcat.utils.regression.checking) relation_type_filter_pairs (medcat.config_rel_cat.General attribute) relationship (medcat.utils.preprocess_snomed.FileFormatDescriptor attribute) (medcat.utils.preprocess_snomed.RefSetFileType attribute) relationship2json() (medcat.utils.preprocess_snomed.Snomed method) RelCAT (class in medcat.rel_cat) RelData (class in medcat.utils.relation_extraction.rel_dataset) release (medcat.utils.preprocess_snomed.Snomed attribute)

remove_all_vectors() (medcat.vocab.Vocab method) remove_cui() (medcat.cdb.CDB method) remove_icd10_ranges() (in module medcat.utils.helpers) remove_parenthesis (medcat.config.CDBMaker attribute) remove_words_below_cnt() (medcat.vocab.Vocab method) replace_center (medcat.config_meta_cat.General attribute) replace_entities_in_text() (in module medcat.utils.ner.helpers) report (medcat.utils.regression.checking.RegressionCase attribute) report() (medcat.utils.regression.results.ResultDescriptor method) report_success() (medcat.utils.regression.results.SingleResultDescriptor method) reset_cdb() (medcat.cdb_maker.CDBMaker method) reset_concept_similarity() (medcat.cdb.CDB method) reset_counts() (medcat.vocab.Vocab method) reset_cui_count() (medcat.cdb.CDB method) reset_error_handler() (medcat.pipe.Pipe method) reset_training() (medcat.cdb.CDB method) restore_latest_cdb() (medcat.utils.checkpoint.Checkpoint method) ResultDescriptor (class in medcat.utils.regression.results) run_conversion() (in module medcat.utils.saving.converter) run_cv() (in module medcat.utils.helpers)

S

save() (medcat.cdb.CDB method) (medcat.config.MixingConfig method) (medcat.meta_cat.MetaCAT method) (medcat.ner.transformers_ner.TransformersNER method) (medcat.preprocessing.tokenizers.TokenizerWrapperBERT method) (medcat.preprocessing.tokenizers.TokenizerWrapperBPE method) (medcat.rel_cat.RelCAT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat.tokenizers.transformers_ner.TransformersTokenizerNER method) (medcat.utils.checkpoint.Checkpoint method) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT method) (medcat.vocab.Vocab method) save_and_reuse_tokens (medcat.config_meta_cat.General attribute) save_async() (medcat.cdb.CDB method) save_bin_file() (in module medcat.utils.relation_extraction.utils) save_cdb_state() (in module medcat.utils.cdb_state) save_results() (in module medcat.utils.relation_extraction.utils) save_state() (in module medcat.utils.relation_extraction.utils) score_average (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute) seed (medcat.config_meta_cat.General attribute) (medcat.config_rel_cat.General attribute) (medcat.config_transformers_ner.General attribute) separator (medcat.config.General attribute) serialize() (medcat.utils.saving.serializer.CDBSerializer method) serialize_entities() (medcat.pipeline.pipe_runner.PipeRunner static method) set_all_seeds() (in module medcat.utils.data_utils) (in module medcat.utils.meta_cat.ml_utils) set_error_handler() (medcat.pipe.Pipe method) SET_IDENTIFIER (in module medcat.utils.saving.coding) set_project_filters() (in module medcat.utils.filters) SetDecoder (class in medcat.utils.saving.coding) SetEncoder (class in medcat.utils.saving.coding) short (medcat.utils.postprocessing.LabelStyle attribute) show_description() (in module medcat.utils.regression.regression_checker) show_nested_entities (medcat.config.General attribute) shuffle_data (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute) sigmoid() (in module medcat.utils.matutils) similarity() (medcat.linking.vector_context_model.ContextModel method) similarity_threshold (medcat.config.Linking attribute)

similarity_threshold_type (medcat.config.Linking attribute) simple_hash (medcat.config.General attribute) SimpleFoldCreator (class in medcat.stats.kfold) SimpleIter (class in medcat.preprocessing.iterators) SingleResultDescriptor (class in medcat.utils.regression.results) SKIP_CHARS (in module medcat.preprocessing.cleaners) skip_stopwords (medcat.config.Preprocessing attribute) SMALLER_SPAN (medcat.utils.regression.results.Finding attribute) SNAMES_PART (in module medcat.utils.memory_optimiser) Snomed (class in medcat.utils.preprocess_snomed) SNOMED_FOLDER_NAME_PATTERN (in module medcat.utils.preprocess_snomed) snomed_to_desc() (in module medcat.utils.helpers) snomed_to_icd10() (in module medcat.utils.helpers) snomed_to_umls() (in module medcat.utils.helpers) spacy_disabled_components (medcat.config.General attribute) spacy_extended() (in module medcat.preprocessing.tokenizers) spacy_model (medcat.config.General attribute) SPACY_MODEL_REGEX (in module medcat.utils.spacy_compatibility) spacy_nlp (medcat.pipe.Pipe property) spacy_split_all() (in module medcat.preprocessing.tokenizers) SpacyHFDoc (class in medcat.preprocessing.tokenizers) SpacyHFTok (class in medcat.preprocessing.tokenizers) Span (class in medcat.utils.meta_cat.data_utils) span_group (medcat.config_meta_cat.General attribute) SPECIALITY_NAMES (in module medcat.utils.saving.serializer) spell_check (medcat.config.General attribute) spell_check_deep (medcat.config.General attribute) spell_check_len_limit (medcat.config.General attribute) split_list_train_test() (in module medcat.utils.meta_cat.ml_utils) split_list_train_test_by_class() (in module medcat.utils.relation_extraction.utils) SplitType (class in medcat.stats.kfold) start (medcat.stats.mctexport.MedCATTrainerExportAnnotation attribute) StatsBuilder (class in medcat.stats.stats) steps (medcat.config.CheckPoint attribute) (medcat.utils.checkpoint.Checkpoint property) (medcat.utils.checkpoint.CheckpointConfig attribute) stopwords (medcat.config.Preprocessing attribute) STRICT (medcat.utils.regression.results.Strictness attribute) STRICTEST (medcat.utils.regression.results.Strictness attribute) Strictness (class in medcat.utils.regression.results) STRICTNESS_MATRIX (in module medcat.utils.regression.results) subsample_after (medcat.config.Linking attribute) SupportedBundles (class in medcat.utils.preprocess_snomed) SupportedExtension (class in medcat.utils.preprocess_snomed)

T

T (in module medcat.utils.checkpoint) tag_skip_and_punct() (in module medcat.preprocessing.taggers) target_cuis (medcat.utils.regression.targeting.TargetPlaceholder attribute) TargetedPhraseChanger (class in medcat.utils.regression.targeting) TargetPlaceholder (class in medcat.utils.regression.targeting) task (medcat.config_rel_cat.General attribute) TEMP_PLACEHOLDER (medcat.utils.regression.utils.MedCATTrainerExportConverter attribute) test_size (medcat.config_meta_cat.Train attribute) (medcat.config_rel_cat.Train attribute) (medcat.config_transformers_ner.General attribute) text (medcat.stats.mctexport.MedCATTrainerExportDocument attribute) tkn_inds_from_doc() (in module medcat.utils.helpers) tkns_from_doc() (in module medcat.utils.helpers) to_concept_df() (medcat.utils.preprocess_snomed.Snomed method) (medcat.utils.preprocess_umls.UMLS method) to_dict() (medcat.utils.memory_optimiser.DelegatingDict method) (medcat.utils.memory_optimiser.DelegatingValueSet method) (medcat.utils.regression.checking.RegressionCase method) (medcat.utils.regression.checking.RegressionSuite method) (medcat.utils.regression.targeting.OptionSet method) (medcat.utils.saving.coding.EncodeableObject method) to_json_simple() (in module medcat.utils.helpers) to_json_sumithra() (in module medcat.utils.helpers) to_yaml() (medcat.utils.regression.checking.RegressionSuite method) token_to_id() (medcat.preprocessing.tokenizers.SpacyHFTok method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBERT method) (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBPE method) (medcat.utils.relation_extraction.tokenizer.TokenizerWrapperBERT method) tokenize() (in module medcat.utils.relation_extraction.utils) (medcat.preprocessing.tokenizers.WordpieceTokenizer method) tokenizer_name (medcat.config_meta_cat.General attribute) (medcat.config_rel_cat.General attribute) tokenizer_special_tokens (medcat.config_rel_cat.General attribute) TokenizerWrapperBase (class in medcat.tokenizers.meta_cat_tokenizers) TokenizerWrapperBERT (class in medcat.preprocessing.tokenizers) (class in medcat.tokenizers.meta_cat_tokenizers) (class in medcat.utils.relation_extraction.tokenizer) TokenizerWrapperBPE (class in medcat.preprocessing.tokenizers) (class in medcat.tokenizers.meta_cat_tokenizers) TokenNormalizer (class in medcat.utils.normalizers)

TPL_ENT (in module medcat.utils.other) TPL_ENTS (in module medcat.utils.other) Train (class in medcat.config_meta_cat) (class in medcat.config_rel_cat) train (medcat.config.Linking attribute) (medcat.config_meta_cat.ConfigMetaCAT attribute) (medcat.config_rel_cat.ConfigRelCAT attribute) train() (medcat.cat.CAT method) (medcat.linking.vector_context_model.ContextModel method) (medcat.ner.transformers_ner.TransformersNER method) (medcat.rel_cat.RelCAT method) (medcat.utils.ner.deid.DeIdModel method) (medcat.utils.ner.model.NerModel method) Train.Config (class in medcat.config_meta_cat) (class in medcat.config_rel_cat) train_count_threshold (medcat.config.Linking attribute) train_from_json() (medcat.meta_cat.MetaCAT method) train_model() (in module medcat.utils.meta_cat.ml_utils) train_raw() (medcat.meta_cat.MetaCAT method) train_supervised_from_json() (medcat.cat.CAT method) train_supervised_raw() (medcat.cat.CAT method) (medcat.stats.kfold.CATLike method) train_unsupervised() (in module medcat.utils.model_creator) train_using_negative_sampling() (medcat.linking.vector_context_model.ContextModel method) TransformersDatasetNER (class in medcat.datasets.transformers_ner) TransformersNER (class in medcat.ner.transformers_ner) TransformersTokenizerNER (class in medcat.tokenizers.transformers_ner) TranslationLayer (class in medcat.utils.regression.targeting) try_decode() (medcat.utils.memory_optimiser.DelegatingDictDecoder method) (medcat.utils.memory_optimiser.DelegatingValueSetDecoder method) (medcat.utils.saving.coding.PartDecoder method) (medcat.utils.saving.coding.PatternDecoder method) (medcat.utils.saving.coding.SetDecoder method) try_encode() (medcat.utils.memory_optimiser.DelegatingDictEncoder method) (medcat.utils.memory_optimiser.DelegatingValueSetEncoder method) (medcat.utils.saving.coding.PartEncoder method) (medcat.utils.saving.coding.PatternEncoder method) (medcat.utils.saving.coding.SetEncoder method) try_reverse_word_order (medcat.config.Ner attribute) tui2name() (in module medcat.utils.helpers) tuis (medcat.stats.mctexport.MedCATTrainerExportProject attribute) tuple3_parser() (in module medcat.utils.regression.regression_checker)

U

UK_CLIN (medcat.utils.preprocess_snomed.SupportedBundles attribute) UK_CLINICAL (medcat.utils.preprocess_snomed.SupportedExtension attribute) UK_CLINICAL_REFSET (medcat.utils.preprocess_snomed.SupportedExtension attribute) UK_DRUG (medcat.utils.preprocess_snomed.SupportedExtension attribute) uk_drug_ext (medcat.utils.preprocess_snomed.Snomed attribute) UK_DRUG_EXT (medcat.utils.preprocess_snomed.SupportedBundles attribute) UK_EDITION (medcat.utils.preprocess_snomed.SupportedExtension attribute) uk_ext (medcat.utils.preprocess_snomed.Snomed attribute) UMLS (class in medcat.utils.preprocess_umls) umls (in module medcat.utils.preprocess_umls) umls_to_icd10() (in module medcat.utils.helpers) umls_to_icd10_ext() (in module medcat.utils.helpers) umls_to_icd10_over_snomed() (in module medcat.utils.helpers) umls_to_icd10cm() (in module medcat.utils.helpers) umls_to_snomed() (in module medcat.utils.helpers) unitvec() (in module medcat.utils.matutils) unknown() (medcat.utils.regression.checking.MetaData class method)

UNKNOWN_METADATA (in module medcat.utils.regression.checking) UnkownSnomedReleaseException unlink_concept_name() (medcat.cat.CAT method) unoptimise_cdb() (in module medcat.utils.memory_optimiser) UnsuitableObject unwrap() (medcat.stats.stats.StatsBuilder method) update() (medcat.utils.hasher.Hasher method) (medcat.utils.memory_optimiser.DelegatingValueSet method) update_bytes() (medcat.utils.hasher.Hasher method) update_context_vector() (medcat.cdb.CDB method) update_counts() (medcat.vocab.Vocab method) update_cui2average_confidence() (medcat.cdb.CDB method) upper_case_limit_len (medcat.config.Ner attribute) usage_monitor (medcat.config.General attribute) UsageMonitor (class in medcat.config) (class in medcat.utils.usage_monitoring) UseOfOldConfigOptionException

V

validate_assignment (medcat.config.AnnotationOutput.Config attribute) (medcat.config.CDBMaker.Config attribute) (medcat.config.CheckPoint.Config attribute) (medcat.config.Config.Config attribute) (medcat.config.General.Config attribute) (medcat.config.Linking.Config attribute) (medcat.config.Ner.Config attribute) (medcat.config.Preprocessing.Config attribute) (medcat.config.VersionInfo.Config attribute) (medcat.config_meta_cat.ConfigMetaCAT.Config attribute) (medcat.config_meta_cat.General.Config attribute) (medcat.config_meta_cat.Model.Config attribute) (medcat.config_meta_cat.Train.Config attribute) (medcat.config_rel_cat.ConfigRelCAT.Config attribute) (medcat.config_rel_cat.Model.Config attribute) (medcat.config_rel_cat.Train.Config attribute) (medcat.config_transformers_ner.ConfigTransformersNER.Config attribute) (medcat.config_transformers_ner.General.Config attribute)

validate_ner_data() (in module medcat.utils.data_utils) vals (medcat.stats.kfold.PerCUIMetrics attribute) value (medcat.stats.mctexport.MedCATTrainerExportAnnotation attribute) ValueExtractor (class in medcat.config) values() (medcat.utils.memory_optimiser.DelegatingDict method) vec() (medcat.vocab.Vocab method) verbose_metrics (medcat.config_transformers_ner.General attribute) version (medcat.config.Config attribute) VersionInfo (class in medcat.config) VersionInfo.Config (class in medcat.config) Vocab (class in medcat.vocab) vocab_size (medcat.config_meta_cat.General attribute) (medcat.config_rel_cat.General attribute)

W

WAFCarrier (class in medcat.utils.config_utils) weighted_average() (in module medcat.utils.config_utils) weighted_average_function (medcat.utils.config_utils.WAFCarrier property) WeightedDocumentsCreator (class in medcat.stats.kfold) weights (medcat.stats.kfold.PerCUIMetrics attribute) window_size (medcat.config_rel_cat.General attribute)

word_skipper (medcat.config.Config attribute) WordpieceTokenizer (class in medcat.preprocessing.tokenizers) words_to_skip (medcat.config.Preprocessing attribute) workers (medcat.config.General attribute) workers() (in module medcat.config) write() (medcat.utils.saving.serializer.JsonSetSerializer method)