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Contents:
Medical
oncept Annotation Tool
API Reference
MedCAT
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_
__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.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)
__delitem__() (medcat.utils.memory_optimiser.DelegatingDict method)
__eq__() (medcat.config._DefPartial method)
(medcat.utils.memory_optimiser.DelegatingDict method)
(medcat.utils.regression.category_separation.AllPartsCategory method)
(medcat.utils.regression.category_separation.AnyPartOfCategory method)
(medcat.utils.regression.category_separation.CategoryDescription method)
(medcat.utils.regression.checking.RegressionCase method)
(medcat.utils.regression.checking.RegressionChecker 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.category_separation.AllPartsCategory method)
(medcat.utils.regression.category_separation.AnyPartOfCategory method)
(medcat.utils.regression.category_separation.CategoryDescription 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.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.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.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_umls.UMLS method)
(medcat.utils.regression.category_separation.AllPartsCategory method)
(medcat.utils.regression.category_separation.AnyPartOfCategory method)
(medcat.utils.regression.category_separation.Category method)
(medcat.utils.regression.category_separation.SeparationObserver method)
(medcat.utils.regression.category_separation.SeparatorStrategy method)
(medcat.utils.regression.checking.RegressionChecker method)
(medcat.utils.regression.converting.PerWordContextSelector method)
(medcat.utils.regression.converting.UniqueNamePreserver method)
(medcat.utils.regression.targeting.TranslationLayer 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.versioning.ConfigUpgrader 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.category_separation.AllPartsCategory method)
(medcat.utils.regression.category_separation.AnyPartOfCategory method)
(medcat.utils.regression.checking.RegressionChecker 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.category_separation.AllPartsCategory method)
(medcat.utils.regression.category_separation.AnyPartOfCategory method)
(medcat.utils.regression.checking.RegressionChecker method)
_add_concept() (medcat.cdb.CDB method)
_add_nested_ent() (medcat.cat.CAT method)
_attempt_category_for() (medcat.utils.regression.category_separation.RegressionCheckerSeparator method)
_attempt_fix_after_load() (in module medcat.utils.memory_optimiser)
_batch_generator() (medcat.cat.CAT method)
_calc_hash() (medcat.config.MixingConfig method)
_check_existance() (medcat.utils.versioning.ConfigUpgrader method)
_check_medcat_version() (medcat.cdb.CDB class 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)
_copy_files() (medcat.utils.versioning.ConfigUpgrader method)
_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_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)
_deid_text() (in module medcat.utils.ner.helpers)
_delayed (medcat.pipeline.pipe_runner.PipeRunner attribute)
_DESCRIPTION (in module medcat.datasets.medcat_annotations)
(in module medcat.datasets.patient_concept_stream)
(in module medcat.datasets.transformers_ner)
_doc_to_out() (medcat.cat.CAT method)
_EMPTY_DICT_2_EMPTY_SET (in module medcat.config)
_ensure_backward_compatibility() (medcat.cdb.CDB static method)
_ensure_serializable() (medcat.pipe.Pipe static method)
_execute (medcat.pipeline.pipe_runner.PipeRunner attribute)
_find_spacy_model_folder() (in module medcat.utils.spacy_compatibility)
_fix_cdb() (medcat.utils.versioning.ConfigUpgrader method)
_fix_waf() (in module medcat.utils.config_utils)
_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_cuis_names_types() (medcat.utils.regression.checking.RegressionCase 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_reason_not_deid() (medcat.utils.ner.deid.DeIdModel class method)
_get_relevant_files() (medcat.utils.versioning.ConfigUpgrader method)
_get_required_filter() (medcat.utils.regression.category_separation.CategoryDescription method)
_get_specific_cui_and_name() (medcat.utils.regression.checking.RegressionCase method)
_get_steps_and_count() (medcat.utils.checkpoint.Checkpoint static method)
_get_training_start() (medcat.cat.CAT static method)
_get_trimmed_text() (medcat.cat.CAT method)
_get_trimmed_texts() (medcat.cat.CAT method)
_has_specific_from() (medcat.utils.regression.category_separation.CategoryDescription method)
_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)
_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)
_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)
_make_archive() (medcat.utils.versioning.ConfigUpgrader method)
_map_snomed2refset() (medcat.utils.preprocess_snomed.Snomed method)
_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_args() (in module medcat.utils.regression.category_separator)
_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)
_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_meta_anns() (medcat.meta_cat.MetaCAT method)
_set_value_or_alt() (in module medcat.config)
_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)
_splitter() (medcat.utils.regression.converting.ContextSelector method)
_Tagger (class in medcat.preprocessing.taggers)
_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)
_ValuesView (class in medcat.utils.memory_optimiser)
_versioning() (medcat.cat.CAT method)
A
adam_epsilon (medcat.config_rel_cat.Train attribute)
add_addl_info() (medcat.cdb.CDB method)
add_addl_ner() (medcat.pipe.Pipe method)
add_and_train_concept() (medcat.cat.CAT method)
add_concept() (medcat.cdb.CDB method)
add_cui_to_group() (medcat.cat.CAT method)
add_default_log_handlers() (in module medcat)
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)
ALL (medcat.utils.regression.category_separation.StrategyType attribute)
(medcat.utils.regression.targeting.FilterStrategy attribute)
all_targets() (medcat.utils.regression.targeting.TranslationLayer method)
allow_everything (medcat.utils.regression.category_separation.CategoryDescription attribute)
AllPartsCategory (class in medcat.utils.regression.category_separation)
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)
ANY (medcat.utils.regression.targeting.FilterStrategy attribute)
AnyPartOfCategory (class in medcat.utils.regression.category_separation)
anything_goes() (medcat.utils.regression.category_separation.CategoryDescription class method)
arbitrary_types_allowed (medcat.config.Config.Config attribute)
(medcat.utils.regression.category_separation.RegressionCheckerSeparator.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_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_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)
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)
C
calculate_dynamic_threshold (medcat.config.Linking attribute)
calculate_hash() (medcat.cdb.CDB method)
calculate_label_map() (medcat.tokenizers.transformers_ner.TransformersTokenizerNER method)
can_separate() (medcat.utils.regression.category_separation.SeparateToAll method)
(medcat.utils.regression.category_separation.SeparateToFirst method)
(medcat.utils.regression.category_separation.SeparatorStrategy method)
candidates() (medcat.utils.normalizers.BasicSpellChecker method)
CAT (class in medcat.cat)
categories (medcat.utils.regression.category_separation.RegressionCheckerSeparator attribute)
Category (class in medcat.utils.regression.category_separation)
category_name (medcat.config_meta_cat.General attribute)
category_value2id (medcat.config_meta_cat.General attribute)
CategoryDescription (class in medcat.utils.regression.category_separation)
CB (in module medcat.preprocessing.cleaners)
CB_D (in module medcat.preprocessing.cleaners)
CDB (class in medcat.cdb)
cdb (medcat.utils.ner.model.NerModel property)
CDB_FILE_NAME (in module medcat.utils.versioning)
cdb_info (medcat.config.VersionInfo attribute)
cdb_maker (medcat.config.Config attribute)
CDBMaker (class in medcat.cdb_maker)
(class in medcat.config)
CDBMaker.Config (class in medcat.config)
CDBSerializer (class in medcat.utils.saving.serializer)
check_case() (medcat.utils.regression.checking.RegressionCase method)
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.RegressionChecker 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)
combine_contents() (in module medcat.utils.regression.editing)
combine_dicts() (in module medcat.utils.regression.editing)
combine_yamls() (in module medcat.utils.regression.editing)
CONCEPT_NOT_ANNOTATED (medcat.utils.regression.results.FailReason 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)
ConfigUpgrader (class in medcat.utils.versioning)
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)
ContextSelector (class in medcat.utils.regression.converting)
copy_of() (medcat.config.LinkingFilters method)
count (medcat.utils.checkpoint.Checkpoint property)
count() (medcat.vocab.Vocab method)
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_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.utils.regression.results.FailDescriptor attribute)
CUI (medcat.utils.regression.targeting.FilterType attribute)
cui2tuis() (in module medcat.utils.helpers)
CUI_AND_CHILDREN (medcat.utils.regression.targeting.FilterType attribute)
CUI_CHILD_FOUND (medcat.utils.regression.results.FailReason attribute)
CUI_DICT_NAMES_TO_COMBINE (in module medcat.utils.memory_optimiser)
cui_filter (medcat.config_meta_cat.Train attribute)
CUI_NOT_FOUND (medcat.utils.regression.results.FailReason attribute)
CUI_PARENT_FOUND (medcat.utils.regression.results.FailReason attribute)
cuis (medcat.config.LinkingFilters attribute)
cuis_exclude (medcat.config.LinkingFilters attribute)
CUIS_PART (in module medcat.utils.memory_optimiser)
CUIWithChildFilter (class in medcat.utils.regression.targeting)
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_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_UNIGRAM_TABLE_SIZE (in module medcat.utils.model_creator)
deid_multi_texts() (medcat.utils.ner.deid.DeIdModel method)
deid_text() (in module medcat.utils.ner)
(in module medcat.utils.ner.helpers)
(medcat.utils.ner.deid.DeIdModel method)
DeIdModel (class in medcat.utils.ner.deid)
delegate (medcat.utils.regression.targeting.CUIWithChildFilter attribute)
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)
depth (medcat.utils.regression.targeting.CUIWithChildFilter attribute)
description (medcat.config.VersionInfo attribute)
(medcat.config_meta_cat.General attribute)
(medcat.config_transformers_ner.General 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)
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)
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)
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)
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)
ensure_spacy_model() (in module medcat.utils.helpers)
ensure_tokenizer() (medcat.tokenizers.meta_cat_tokenizers.TokenizerWrapperBase method)
(medcat.tokenizers.transformers_ner.TransformersTokenizerNER method)
ENUM (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)
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)
(medcat.utils.regression.results.FailDescriptor attribute)
extract() (medcat.config.ValueExtractor method)
F
fail (medcat.utils.regression.results.MultiDescriptor property)
(medcat.utils.regression.results.SingleResultDescriptor attribute)
FailDescriptor (class in medcat.utils.regression.results)
FailReason (class in medcat.utils.regression.results)
failures (medcat.utils.regression.results.SingleResultDescriptor attribute)
FakeDict (class in medcat.config)
FAST_SPLIT (in module medcat.preprocessing.iterators)
FastEmbMimicCSV (class in medcat.preprocessing.iterators)
fields() (medcat.config.MixingConfig method)
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)
FilterOptions (class in medcat.utils.regression.targeting)
filters (medcat.config.Linking attribute)
(medcat.utils.regression.checking.RegressionCase attribute)
FilterStrategy (class in medcat.utils.regression.targeting)
FilterType (class in medcat.utils.regression.targeting)
finalise_report() (medcat.stats.stats.StatsBuilder method)
find_categories_for() (medcat.utils.regression.category_separation.RegressionCheckerSeparator method)
FIRST (medcat.utils.regression.category_separation.StrategyType attribute)
fits() (medcat.utils.regression.category_separation.AllPartsCategory method)
(medcat.utils.regression.category_separation.AnyPartOfCategory method)
(medcat.utils.regression.category_separation.Category method)
fix() (medcat.utils.normalizers.BasicSpellChecker method)
fix_config() (in module medcat.utils.versioning)
fix_np_float64() (in module medcat.utils.regression.checking)
force_remove() (medcat.pipe.Pipe method)
forward() (medcat.utils.meta_cat.models.BertForMetaAnnotation method)
(medcat.utils.meta_cat.models.LSTM method)
(medcat.utils.relation_extraction.models.BertModel_RelationExtraction method)
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.RegressionChecker class method)
(medcat.utils.regression.targeting.FilterOptions class method)
(medcat.utils.regression.targeting.TypedFilter class method)
from_latest() (medcat.utils.checkpoint.Checkpoint class method)
from_modelcard() (medcat.utils.regression.checking.MetaData class method)
from_yaml() (medcat.utils.regression.checking.RegressionChecker class method)
full_unlink (medcat.config.General attribute)
G
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_from_name() (in module medcat.utils.helpers)
get_all_irrelevant_cuis() (in module medcat.utils.filters)
get_all_subcases() (medcat.utils.regression.checking.RegressionCase method)
(medcat.utils.regression.checking.RegressionChecker method)
get_all_targets() (medcat.utils.regression.checking.RegressionCase method)
get_ann_from_doc() (in module medcat.utils.data_utils)
get_annotation_schema_tag() (medcat.utils.relation_extraction.models.BertModel_RelationExtraction method)
get_applicable_targets() (medcat.utils.regression.targeting.CUIWithChildFilter method)
(medcat.utils.regression.targeting.TypedFilter method)
get_batch() (in module medcat.utils.ml_utils)
get_category() (in module medcat.utils.regression.category_separation)
get_children_of() (medcat.utils.regression.targeting.CUIWithChildFilter method)
(medcat.utils.regression.targeting.TranslationLayer method)
get_context() (medcat.utils.regression.converting.ContextSelector method)
(medcat.utils.regression.converting.PerSentenceSelector method)
(medcat.utils.regression.converting.PerWordContextSelector method)
get_context_tokens() (medcat.linking.vector_context_model.ContextModel method)
get_context_vectors() (medcat.linking.vector_context_model.ContextModel method)
get_description() (in module medcat.utils.regression.category_separation)
get_direct_refset_mapping() (in module medcat.utils.preprocess_snomed)
get_doc_from_project() (in module medcat.utils.data_utils)
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_false_positives() (in module medcat.utils.data_utils)
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_spacy_version() (in module medcat.utils.spacy_compatibility)
get_json() (medcat.cat.CAT method)
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_matching_case() (in module medcat.utils.regression.converting)
get_model() (medcat.meta_cat.MetaCAT method)
get_model_card() (medcat.cat.CAT method)
(medcat.meta_cat.MetaCAT method)
get_model_card_from_file() (in module medcat.utils.regression.mct_converter)
get_model_card_from_model() (in module medcat.utils.regression.mct_converter)
get_name() (medcat.cdb.CDB method)
get_name_and_version_of_spacy_model_in_medcat_modelpack() (in module medcat.utils.spacy_compatibility)
get_negative_samples() (medcat.vocab.Vocab method)
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_parents_of() (medcat.utils.regression.targeting.TranslationLayer method)
get_project_filters() (in module medcat.utils.filters)
get_pt2ch() (medcat.utils.preprocess_umls.UMLS method)
get_random_str() (in module medcat.utils.regression.category_separation)
get_reason_for() (medcat.utils.regression.results.FailDescriptor class method)
get_report() (medcat.utils.regression.results.MultiDescriptor method)
(medcat.utils.regression.results.ResultDescriptor method)
(medcat.utils.regression.results.SingleResultDescriptor method)
get_same_anns() (in module medcat.utils.data_utils)
get_semantic_version() (in module medcat.utils.versioning)
get_semantic_version_from_model() (in module medcat.utils.versioning)
get_separator() (in module medcat.utils.regression.category_separation)
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_spacy_nlp() (medcat.cat.CAT method)
get_stats() (in module medcat.stats.stats)
get_strategy() (in module medcat.utils.regression.category_separation)
get_unique_name() (medcat.utils.regression.converting.UniqueNamePreserver method)
get_version_from_cdb_dump() (in module medcat.utils.versioning)
get_version_from_modelcard() (in module medcat.utils.versioning)
get_version_from_modelpack_zip() (in module medcat.utils.versioning)
gradient_acc_steps (medcat.config_rel_cat.Train attribute)
H
has_cui_from() (medcat.utils.regression.category_separation.CategoryDescription method)
has_name_from() (medcat.utils.regression.category_separation.CategoryDescription method)
HAS_NEW_SPACY (in module medcat.cat)
has_new_spacy() (in module medcat.utils.helpers)
has_observed() (medcat.utils.regression.category_separation.SeparationObserver method)
has_spacy_model() (in module medcat.utils.helpers)
has_tui_from() (medcat.utils.regression.category_separation.CategoryDescription method)
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)
idx2labels (medcat.config_rel_cat.General attribute)
ignore_cpos (medcat.config_meta_cat.Model attribute)
(medcat.config_rel_cat.Model attribute)
import_training() (medcat.cdb.CDB method)
inc_or_add() (medcat.vocab.Vocab method)
inc_wc() (medcat.vocab.Vocab method)
include_text_in_output (medcat.config.AnnotationOutput attribute)
INCORRECT_CUI_FOUND (medcat.utils.regression.results.FailReason attribute)
INCORRECT_SPAN_BIG (medcat.utils.regression.results.FailReason attribute)
INCORRECT_SPAN_SMALL (medcat.utils.regression.results.FailReason attribute)
input_size (medcat.config_meta_cat.Model attribute)
(medcat.config_rel_cat.Model attribute)
intersect_nonempty_set() (in module medcat.utils.matutils)
is_older_spacy_version() (in module medcat.utils.spacy_compatibility)
item() (medcat.vocab.Vocab method)
items() (medcat.utils.memory_optimiser.DelegatingDict method)
J
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)
last_train_on (medcat.config_meta_cat.Train attribute)
(medcat.config_transformers_ner.General attribute)
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)
list_to_dict() (medcat.utils.regression.targeting.TypedFilter static method)
list_to_dicts() (medcat.utils.regression.targeting.TypedFilter static 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_bin_file() (in module medcat.utils.relation_extraction.utils)
load_config() (medcat.cdb.CDB method)
load_data() (in module medcat.utils.data_utils)
load_hf_tokenizer() (in module medcat.utils.ml_utils)
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_format (medcat.config.General attribute)
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.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.ml_utils)
(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.category_separation)
(in module medcat.utils.regression.category_separator)
(in module medcat.utils.regression.checking)
(in module medcat.utils.regression.converting)
(in module medcat.utils.regression.editing)
(in module medcat.utils.regression.mct_converter)
(in module medcat.utils.regression.regression_checker)
(in module medcat.utils.regression.suite_editor)
(in module medcat.utils.regression.targeting)
,
[1]
(in module medcat.utils.saving)
(in module medcat.utils.saving.converter)
(in module medcat.utils.saving.serializer)
(in module medcat.utils.versioning)
long (medcat.utils.postprocessing.LabelStyle attribute)
loosely_match_enum() (in module medcat.utils.regression.utils)
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.category_separator)
(in module medcat.utils.regression.mct_converter)
(in module medcat.utils.regression.regression_checker)
(in module medcat.utils.regression.suite_editor)
(in module medcat.utils.saving.converter)
(in module medcat.utils.versioning)
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_replace_safe() (medcat.utils.regression.converting.ContextSelector method)
make_stats() (medcat.cdb.CDB method)
make_unigram_table() (medcat.vocab.Vocab method)
MakeVocab (class in medcat.utils.make_vocab)
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_str() (medcat.utils.regression.targeting.FilterStrategy class method)
(medcat.utils.regression.targeting.FilterType class method)
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.stats
module
medcat.tokenizers
module
medcat.tokenizers.meta_cat_tokenizers
module
medcat.tokenizers.transformers_ner
module
medcat.utils
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.category_separation
module
medcat.utils.regression.category_separator
module
medcat.utils.regression.checking
module
medcat.utils.regression.converting
module
medcat.utils.regression.editing
module
medcat.utils.regression.mct_converter
module
medcat.utils.regression.regression_checker
module
medcat.utils.regression.results
module
medcat.utils.regression.suite_editor
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.serializer
module
medcat.utils.spacy_compatibility
module
medcat.utils.versioning
module
medcat.vocab
module
medcat_csv_mapper (in module medcat.utils.preprocess_umls)
medcat_export_json_to_regression_yml() (in module medcat.utils.regression.converting)
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)
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_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_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)
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.stats
medcat.tokenizers
medcat.tokenizers.meta_cat_tokenizers
medcat.tokenizers.transformers_ner
medcat.utils
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.category_separation
medcat.utils.regression.category_separator
medcat.utils.regression.checking
medcat.utils.regression.converting
medcat.utils.regression.editing
medcat.utils.regression.mct_converter
medcat.utils.regression.regression_checker
medcat.utils.regression.results
medcat.utils.regression.suite_editor
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.serializer
medcat.utils.spacy_compatibility
medcat.utils.versioning
medcat.vocab
most_similar() (medcat.cdb.CDB method)
multi_separator (medcat.config.CDBMaker attribute)
MultiDescriptor (class in medcat.utils.regression.results)
multiprocessing() (medcat.cat.CAT method)
multiprocessing_batch_char_size() (medcat.cat.CAT method)
multiprocessing_batch_docs_size() (medcat.cat.CAT method)
multiprocessing_pipe() (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.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.FailDescriptor attribute)
(medcat.utils.regression.results.MultiDescriptor attribute)
(medcat.utils.regression.results.SingleResultDescriptor attribute)
NAME (medcat.utils.regression.targeting.FilterType attribute)
name (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)
name2nrgen() (medcat.utils.regression.converting.UniqueNamePreserver method)
NAME_DICT_NAMES_TO_COMBINE (in module medcat.utils.memory_optimiser)
NAME_NOT_FOUND (medcat.utils.regression.results.FailReason attribute)
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)
needs_upgrade() (medcat.utils.versioning.ConfigUpgrader method)
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)
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)
observe() (medcat.utils.regression.category_separation.SeparationObserver method)
ONE2MANY (in module medcat.utils.memory_optimiser)
(in module medcat.utils.saving.serializer)
one_from_input() (medcat.utils.regression.targeting.TypedFilter class method)
onlyprefnames (medcat.utils.regression.targeting.FilterOptions 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)
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)
overflow_category (medcat.utils.regression.category_separation.RegressionCheckerSeparator 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_args() (in module medcat.utils.versioning)
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.mct_converter)
(in module medcat.utils.regression.regression_checker)
(in module medcat.utils.regression.suite_editor)
PartDecoder (class in medcat.utils.saving.coding)
PartEncoder (class in medcat.utils.saving.coding)
parts (medcat.utils.regression.results.MultiDescriptor attribute)
PatientConceptStream (class in medcat.datasets.patient_concept_stream)
PatientConceptStreamConfig (class in medcat.datasets.patient_concept_stream)
per_phrase_results (medcat.utils.regression.results.ResultDescriptor attribute)
perform_optimisation() (in module medcat.utils.memory_optimiser)
performance (medcat.config.VersionInfo attribute)
PerSentenceSelector (class in medcat.utils.regression.converting)
PerWordContextSelector (class in medcat.utils.regression.converting)
PH_REMOVE (in module medcat.cdb_maker)
PH_RM (in module medcat.preprocessing.cleaners)
phrases (medcat.utils.regression.checking.RegressionCase attribute)
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)
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_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)
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)
process_document() (medcat.stats.stats.StatsBuilder method)
process_project() (medcat.stats.stats.StatsBuilder method)
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)
read_categories() (in module medcat.utils.regression.category_separation)
reason (medcat.utils.regression.results.FailDescriptor attribute)
rebuild_re() (medcat.config.Config method)
(medcat.config.MixingConfig method)
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)
RegressionChecker (class in medcat.utils.regression.checking)
RegressionCheckerSeparator (class in medcat.utils.regression.category_separation)
RegressionCheckerSeparator.Config (class in medcat.utils.regression.category_separation)
relation_type_filter_pairs (medcat.config_rel_cat.General 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_names() (medcat.cdb.CDB method)
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() (medcat.utils.regression.category_separation.SeparationObserver method)
(medcat.utils.regression.category_separation.SeparatorStrategy 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.regression.category_separation.RegressionCheckerSeparator 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_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)
SEMANTIC_VERSION_PATTERN (in module medcat.utils.versioning)
SEMANTIC_VERSION_REGEX (in module medcat.utils.versioning)
SemanticVersion (in module medcat.utils.versioning)
separate() (medcat.utils.regression.category_separation.RegressionCheckerSeparator method)
(medcat.utils.regression.category_separation.SeparateToAll method)
(medcat.utils.regression.category_separation.SeparateToFirst method)
(medcat.utils.regression.category_separation.SeparatorStrategy method)
separate_categories() (in module medcat.utils.regression.category_separation)
SeparateToAll (class in medcat.utils.regression.category_separation)
SeparateToFirst (class in medcat.utils.regression.category_separation)
SeparationObserver (class in medcat.utils.regression.category_separation)
separator (medcat.config.General attribute)
SeparatorStrategy (class in medcat.utils.regression.category_separation)
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)
setup_logging() (in module medcat.utils.versioning)
short (medcat.utils.postprocessing.LabelStyle attribute)
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)
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)
SNAMES_PART (in module medcat.utils.memory_optimiser)
Snomed (class in 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)
StatsBuilder (class in medcat.stats.stats)
steps (medcat.config.CheckPoint attribute)
(medcat.utils.checkpoint.Checkpoint property)
(medcat.utils.checkpoint.CheckpointConfig attribute)
stoppers (medcat.utils.regression.converting.PerSentenceSelector attribute)
stopwords (medcat.config.Preprocessing attribute)
strategy (medcat.utils.regression.category_separation.RegressionCheckerSeparator attribute)
(medcat.utils.regression.targeting.FilterOptions attribute)
StrategyType (class in medcat.utils.regression.category_separation)
subsample_after (medcat.config.Linking attribute)
success (medcat.utils.regression.results.MultiDescriptor property)
(medcat.utils.regression.results.SingleResultDescriptor attribute)
T
T (in module medcat.utils.checkpoint)
tag_skip_and_punct() (in module medcat.preprocessing.taggers)
target_cuis (medcat.utils.regression.category_separation.CategoryDescription attribute)
target_names (medcat.utils.regression.category_separation.CategoryDescription attribute)
target_tuis (medcat.utils.regression.category_separation.CategoryDescription attribute)
targets_for() (medcat.utils.regression.targeting.TranslationLayer method)
task (medcat.config_rel_cat.General attribute)
test_size (medcat.config_meta_cat.Train attribute)
(medcat.config_rel_cat.Train attribute)
(medcat.config_transformers_ner.General 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.RegressionChecker method)
(medcat.utils.regression.targeting.CUIWithChildFilter method)
(medcat.utils.regression.targeting.FilterOptions method)
(medcat.utils.regression.targeting.TypedFilter 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.RegressionChecker 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.meta_cat.MetaCAT 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() (medcat.cat.CAT method)
train_supervised_from_json() (medcat.cat.CAT method)
train_supervised_raw() (medcat.cat.CAT 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.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.SetEncoder method)
try_reverse_word_order (medcat.config.Ner attribute)
tui2name() (in module medcat.utils.helpers)
type (medcat.utils.regression.targeting.TypedFilter attribute)
TYPE_ID (medcat.utils.regression.targeting.FilterType attribute)
TypedFilter (class in medcat.utils.regression.targeting)
U
uk_drug_ext (medcat.utils.preprocess_snomed.Snomed 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)
UniqueNamePreserver (class in medcat.utils.regression.converting)
unitvec() (in module medcat.utils.matutils)
UNKNOWN (medcat.utils.regression.results.FailReason attribute)
unknown() (medcat.utils.regression.checking.MetaData class method)
UNKNOWN_METADATA (in module medcat.utils.regression.checking)
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)
UPDATE_VERSION (in module medcat.utils.versioning)
upgrade() (medcat.utils.versioning.ConfigUpgrader method)
upper_case_limit_len (medcat.config.Ner attribute)
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)
ValueExtractor (class in medcat.config)
values (medcat.utils.regression.targeting.CUIWithChildFilter attribute)
(medcat.utils.regression.targeting.TypedFilter attribute)
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
weighted_average() (in module medcat.utils.config_utils)
weighted_average_function (medcat.config.Linking 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)
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