Index

A

add() (AnnotationContainer method), [1] (AttributeContainer method), [1] (AudioAnnotationContainer method), [1] (EntityAttributeContainer method), [1] (TextAnnotationContainer method), [1] add_class_name_to_data_dict() (in module medkit.core.dict_conv) add_install() (QuickUMLSMatcher class method) add_prov() (ProvTracer method), [1] add_prov_from_sub_tracer() (ProvTracer method), [1] ADICAPNormAttribute (class in medkit.text.ner) (class in medkit.text.ner.adicap_norm_attribute) align_and_map_tokens_with_tags() (in module medkit.text.ner.hf_tokenization_utils) ALL_CHAR_RULES (in module medkit.text.preprocessing.char_rules) all_docs (Collection property), [1] Annotation (class in medkit.core.annotation) AnnotationContainer (class in medkit.core) (class in medkit.core.annotation_container)

AnnotationType (in module medkit.core.annotation) AnySpan (class in medkit.core.text) (class in medkit.core.text.span) Attribute (class in medkit.core) (class in medkit.core.attribute) AttributeContainer (class in medkit.core) (class in medkit.core.attribute_container) AttributeDuplicator (class in medkit.text.postprocessing) (class in medkit.text.postprocessing.attribute_duplicator) AudioAnnotationContainer (class in medkit.core.audio) (class in medkit.core.audio.annotation_container) AudioBuffer (class in medkit.core.audio) (class in medkit.core.audio.audio_buffer) AudioDocument (class in medkit.core.audio) (class in medkit.core.audio.document) augment_full_text_for_next_segment() (DocTranscriber method), [1]

B

batch_iter() (in module medkit.core.utils) batch_list() (in module medkit.core.utils) BatchData (class in medkit.training) (class in medkit.training.utils) BratInputConverter (class in medkit.io) (class in medkit.io.brat) BratOutputConverter (class in medkit.io) (class in medkit.io.brat)

build_adicap_attribute() (in module medkit.text.spacy.edsnlp) build_date_attribute() (in module medkit.text.spacy.edsnlp) build_duration_attribute() (in module medkit.text.spacy.edsnlp) build_measurement_attribute() (in module medkit.text.spacy.edsnlp) build_spacy_doc_from_medkit_doc() (in module medkit.text.spacy.spacy_utils) build_spacy_doc_from_medkit_segment() (in module medkit.text.spacy.spacy_utils) build_tnm_attribute() (in module medkit.text.spacy.edsnlp)

C

CharReplacer (class in medkit.text.preprocessing) (class in medkit.text.preprocessing.char_replacer) check_model_for_task_HF() (in module medkit.tools.hf_utils) check_rules_sanity() (FamilyDetector static method), [1] (HypothesisDetector static method), [1] (NegationDetector static method), [1] (RegexpMatcher static method), [1] clean_multiple_whitespaces_in_sentence() (in module medkit.core.text.utils) clean_newline_character() (in module medkit.core.text.utils) clean_parentheses_eds() (in module medkit.core.text.utils) clean_up_gaps_in_normalized_spans() (in module medkit.core.text.span_utils) clear() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method) clear_installs() (QuickUMLSMatcher class method) CLINENTITY_LABEL (in module medkit.tools.e3c_corpus) collate() (TrainableComponent method), [1] Collection (class in medkit.core) (class in medkit.core.collection) compute() (DiarizationEvaluator method) (MetricsComputer method), [1] (SeqEvalEvaluator method) (SeqEvalMetricsComputer method) (TranscriptionEvaluator method) compute_classification_report() (TextClassificationEvaluator method) compute_cohen_kappa() (TextClassificationEvaluator method) compute_krippendorff_alpha() (TextClassificationEvaluator method) compute_nested_segments() (in module medkit.text.postprocessing) (in module medkit.text.postprocessing.alignment_utils)

concatenate() (in module medkit.core.text.span_utils) configure_optimizer() (TrainableComponent method), [1] ContextOperation (class in medkit.core.text) (class in medkit.core.text.operation) convert() (SpacyOutputConverter method) convert_data_annotation_to_medkit() (in module medkit.tools.e3c_corpus) convert_data_collection_to_medkit() (in module medkit.tools.e3c_corpus) convert_labels_to_tags() (in module medkit.text.ner.hf_tokenization_utils) convert_mtsamples_to_medkit() (in module medkit.tools.mtsamples) copy() (ADICAPNormAttribute method), [1] (Attribute method), [1] (BatchData method) (DateAttribute method), [1] (DuplicationAttribute method), [1] (DurationAttribute method), [1] (EntityNormAttribute method), [1] (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method) (RelativeDateAttribute method), [1] (TNMAttribute method) (UMLSNormAttribute method), [1] count() (Span method), [1] CREATE_ONE_TO_N (CustomTextOpType attribute), [1] create_text_operation() (in module medkit.core.text) (in module medkit.core.text.operation) CustomTextOpType (class in medkit.core.text) (class in medkit.core.text.operation)

D

DateAttribute (class in medkit.text.ner) (class in medkit.text.ner.date_attribute) DEFAULT_ATTRIBUTE_FACTORIES (in module medkit.text.spacy.edsnlp) DefaultPrinterCallback (class in medkit.training) (class in medkit.training.callbacks) del_store() (GlobalStore class method), [1] DescribableOperation (class in medkit.core) (class in medkit.core.pipeline) description (AttributeDuplicator property), [1] (CharReplacer property), [1] (ContextOperation property), [1] (DoccanoInputConverter property), [1] (DocOperation property), [1] (DocPipeline property), [1] (DocTranscriber property), [1] (DocumentSplitter property), [1] (Downmixer property), [1] (DucklingMatcher property), [1] (DuplicateFinder property), [1] (EDSCleaner property), [1] (EDSNLPDateMatcher property) (EDSNLPDocPipeline property) (EDSNLPPipeline property) (EDSNLPTNMMatcher property) (FamilyDetector property), [1] (HFEntityMatcher property) (HFTranscriber property) (HFTranslator property) (HypothesisDetector property), [1] (IAMSystemMatcher property), [1] (NegationDetector property), [1] (NEROperation property), [1] (Operation property), [1] (PASpeakerDetector property) (PowerNormalizer property), [1] (PreprocessingOperation property), [1] (QuickUMLSMatcher property) (RegexpMatcher property), [1] (RegexpReplacer property), [1] (Resampler property) (RTTMInputConverter property), [1] (RushSentenceTokenizer property) (SBTranscriber property) (SectionTokenizer property), [1] (SegmentationOperation property), [1], [2], [3] (SentenceTokenizer property), [1] (SimstringMatcher property), [1] (SpacyDocPipeline property), [1] (SpacyPipeline property), [1] (SRTInputConverter property), [1] (SyntacticRelationExtractor property) (SyntagmaTokenizer property), [1] (UMLSCoderNormalizer property) (UMLSMatcher property), [1] (WebRTCVoiceDetector property)

DiarizationEvaluator (class in medkit.audio.metrics.diarization) DiarizationEvaluatorResult (class in medkit.audio.metrics.diarization) DictConvertible (class in medkit.core.dict_conv) DoccanoClientConfig (class in medkit.io) (class in medkit.io.doccano) DoccanoInputConverter (class in medkit.io) (class in medkit.io.doccano) DoccanoOutputConverter (class in medkit.io) (class in medkit.io.doccano) DoccanoTask (class in medkit.io) (class in medkit.io.doccano) DocOperation (class in medkit.core) (class in medkit.core.operation) DocPipeline (class in medkit.core) (class in medkit.core.doc_pipeline) DocTranscriber (class in medkit.audio.transcription) (class in medkit.audio.transcription.doc_transcriber) Document (class in medkit.core) (class in medkit.core.document) DocumentSplitter (class in medkit.text.postprocessing) (class in medkit.text.postprocessing.document_splitter) DOT_RULES (in module medkit.text.preprocessing.char_rules) Downmixer (class in medkit.audio.preprocessing) (class in medkit.audio.preprocessing.downmixer) DucklingMatcher (class in medkit.text.ner) (class in medkit.text.ner.duckling_matcher) DuplicateFinder (class in medkit.text.preprocessing) (class in medkit.text.preprocessing.duplicate_finder) DuplicationAttribute (class in medkit.text.preprocessing) (class in medkit.text.preprocessing.duplicate_finder) duration (AudioBuffer property), [1] (FileAudioBuffer property), [1] (MemoryAudioBuffer property), [1] (PlaceholderAudioBuffer property) DurationAttribute (class in medkit.text.ner) (class in medkit.text.ner.date_attribute)

E

EDSCleaner (class in medkit.text.preprocessing) (class in medkit.text.preprocessing.eds_cleaner) EDSNLPDateMatcher (class in medkit.text.ner.edsnlp_date_matcher) EDSNLPDocPipeline (class in medkit.text.spacy.edsnlp) EDSNLPPipeline (class in medkit.text.spacy.edsnlp) EDSNLPTNMMatcher (class in medkit.text.ner.edsnlp_tnm_matcher) end (Span attribute), [1] entities (TextAnnotationContainer property), [1] entities_to_displacy() (in module medkit.text.spacy.displacy_utils)

Entity (class in medkit.core.text) (class in medkit.core.text.annotation) EntityAttributeContainer (class in medkit.core.text) (class in medkit.core.text.entity_attribute_container) EntityNormAttribute (class in medkit.core.text) (class in medkit.core.text.entity_norm_attribute) evaluation_epoch() (Trainer method), [1] extract() (in module medkit.core.text.span_utils) extract_anns_and_attrs_from_spacy_doc() (in module medkit.text.spacy.spacy_utils) EXTRACT_ONE_TO_N (CustomTextOpType attribute), [1]

F

FamilyDetector (class in medkit.text.context) (class in medkit.text.context.family_detector) FamilyDetectorRule (class in medkit.text.context) (class in medkit.text.context.family_detector) FamilyMetadata (class in medkit.text.context) (class in medkit.text.context.family_detector) FileAudioBuffer (class in medkit.core.audio) (class in medkit.core.audio.audio_buffer) FILTER (CustomTextOpType attribute), [1] filter_overlapping_entities() (in module medkit.text.postprocessing) (in module medkit.text.postprocessing.overlapping) forward() (TrainableComponent method), [1] FRACTION_RULES (in module medkit.text.preprocessing.char_rules) from_dict() (ADICAPNormAttribute class method), [1] (Attribute class method), [1] (DateAttribute class method), [1] (DictConvertible class method) (DuplicationAttribute class method), [1] (DurationAttribute class method), [1] (Entity class method), [1] (EntityNormAttribute class method), [1] (ModifiedSpan class method), [1] (Relation class method), [1] (RelativeDateAttribute class method), [1] (Segment class method), [1] (SimstringMatcherNormalization static method), [1] (SimstringMatcherRule static method), [1] (Span class method), [1] (TextDocument class method), [1] (TNMAttribute class method) (TranscribedTextDocument class method), [1] (UMLSNormAttribute class method), [1]

from_dir() (AudioDocument class method), [1] (TextDocument class method), [1] (TranscribedTextDocument class method), [1] from_file() (AudioDocument class method), [1] (TextDocument class method), [1] (TranscribedTextDocument class method), [1] fromkeys() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method)

G

generate_deterministic_id() (in module medkit.core) (in module medkit.core.id) get() (AnnotationContainer method), [1] (AttributeContainer method), [1] (AudioAnnotationContainer method), [1] (BatchData method) (EntityAttributeContainer method), [1] (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method) (TextAnnotationContainer method), [1] get_ascii_from_unicode() (in module medkit.text.utils.decoding) get_by_id() (AnnotationContainer method), [1] (AttributeContainer method), [1] (AudioAnnotationContainer method), [1] (EntityAttributeContainer method), [1] (TextAnnotationContainer method), [1] get_class_name_from_data_dict() (in module medkit.core.dict_conv) get_containing_audio_spans() (TranscribedTextDocument method), [1] get_dataloader() (Trainer method), [1] get_entities() (TextAnnotationContainer method), [1] get_example() (HypothesisDetector class method), [1] get_ids() (AnnotationContainer method), [1] (AudioAnnotationContainer method), [1] (TextAnnotationContainer method), [1] get_norms() (EntityAttributeContainer method), [1] get_prov() (ProvTracer method), [1] get_provs() (ProvTracer method), [1] get_relations() (TextAnnotationContainer method), [1] get_segments() (TextAnnotationContainer method), [1]

get_snippet() (TextDocument method), [1] (TranscribedTextDocument method), [1] get_store() (GlobalStore class method), [1] get_sub_prov_tracer() (ProvTracer method), [1] get_sub_prov_tracers() (ProvTracer method), [1] get_subclass_for_data_dict() (ADICAPNormAttribute class method), [1] (AnySpan class method), [1] (Attribute class method), [1] (AudioBuffer class method), [1] (AudioDocument class method), [1] (DateAttribute class method), [1] (DuplicationAttribute class method), [1] (DurationAttribute class method), [1] (Entity class method), [1] (EntityNormAttribute class method), [1] (FileAudioBuffer class method), [1] (MemoryAudioBuffer class method), [1] (ModifiedSpan class method), [1] (PlaceholderAudioBuffer class method) (Relation class method), [1] (RelativeDateAttribute class method), [1] (Segment class method), [1], [2], [3] (Span class method), [1] (SubclassMapping class method) (TextAnnotation class method), [1] (TextDocument class method), [1] (TNMAttribute class method) (TranscribedTextDocument class method), [1] (UMLSNormAttribute class method), [1] GlobalStore (class in medkit.core) (class in medkit.core.store) guess_umls_version() (in module medkit.text.ner.umls_utils)

H

has_prov() (ProvTracer method), [1] has_sub_prov_tracer() (ProvTracer method), [1] HFEntityMatcher (class in medkit.text.ner.hf_entity_matcher) HFEntityMatcherTrainable (class in medkit.text.ner.hf_entity_matcher_trainable) HFTranscriber (class in medkit.audio.transcription.hf_transcriber) HFTranslator (class in medkit.text.translation.hf_translator) HypothesisDetector (class in medkit.text.context) (class in medkit.text.context.hypothesis_detector)

HypothesisDetectorRule (class in medkit.text.context) (class in medkit.text.context.hypothesis_detector) HypothesisRuleMetadata (class in medkit.text.context) (class in medkit.text.context.hypothesis_detector) HypothesisVerbMetadata (class in medkit.text.context) (class in medkit.text.context.hypothesis_detector)

I

IAMSystemMatcher (class in medkit.text.ner) (class in medkit.text.ner.iamsystem_matcher) IdentifiableDataItem (class in medkit.core) (class in medkit.core.data_item) IdentifiableDataItemWithAttrs (class in medkit.core) (class in medkit.core.data_item) index() (Span method), [1] init_store() (GlobalStore class method), [1]

InputConverter (class in medkit.core) (class in medkit.core.conversion) insert() (in module medkit.core.text.span_utils) items() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method)

K

keys() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method)

krippendorff_alpha() (in module medkit.text.metrics.irr_utils)

L

LABEL (DuplicationAttribute attribute), [1] (EntityNormAttribute attribute), [1] (TNMAttribute attribute) length (Span property), [1] LIGATURE_RULES (in module medkit.text.preprocessing.char_rules) load() (BratInputConverter method), [1] (RTTMInputConverter method), [1] (SpacyInputConverter method) (SRTInputConverter method), [1] (TrainableComponent method), [1] load_annotated_document() (in module medkit.tools.e3c_corpus) load_annotations() (BratInputConverter method), [1] load_audio_anns() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.audio) load_audio_document() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.audio) load_audio_documents() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.audio) load_data_annotation() (in module medkit.tools.e3c_corpus) load_data_collection() (in module medkit.tools.e3c_corpus) load_doc() (BratInputConverter method), [1] (RTTMInputConverter method), [1] (SRTInputConverter method), [1]

load_document() (in module medkit.tools.e3c_corpus) load_from_directory_zip() (DoccanoInputConverter method), [1] load_from_file() (DoccanoInputConverter method), [1] load_from_zip() (DoccanoInputConverter method), [1] load_mtsamples() (in module medkit.tools.mtsamples) load_rules() (FamilyDetector static method), [1] (HypothesisDetector static method), [1] (NegationDetector static method), [1] (RegexpMatcher static method), [1] (SimstringMatcher static method), [1] load_section_definition() (SectionTokenizer static method), [1] load_segments() (SRTInputConverter method), [1] load_syntagma_definition() (SyntagmaTokenizer static method), [1] load_text_anns() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.text) load_text_document() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.text) load_text_documents() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.text) load_turns() (RTTMInputConverter method), [1] load_umls_entries() (in module medkit.text.ner.umls_utils) load_verbs() (HypothesisDetector static method), [1] lstrip() (in module medkit.core.text.utils)

M

make_forward_pass() (Trainer method), [1] make_trainable() (HFEntityMatcher static method) medkit.audio module medkit.audio.metrics module medkit.audio.metrics.diarization module medkit.audio.metrics.transcription module medkit.audio.preprocessing module medkit.audio.preprocessing.downmixer module medkit.audio.preprocessing.power_normalizer module medkit.audio.preprocessing.resampler module medkit.audio.segmentation module medkit.audio.segmentation.pa_speaker_detector module medkit.audio.segmentation.webrtc_voice_detector module medkit.audio.transcription module medkit.audio.transcription.doc_transcriber module medkit.audio.transcription.hf_transcriber module medkit.audio.transcription.sb_transcriber module medkit.audio.transcription.transcribed_text_document module medkit.core module medkit.core.annotation module medkit.core.annotation_container module medkit.core.attribute module medkit.core.attribute_container module medkit.core.audio module medkit.core.audio.annotation module medkit.core.audio.annotation_container module medkit.core.audio.audio_buffer module medkit.core.audio.document module medkit.core.audio.operation module medkit.core.audio.span module medkit.core.collection module medkit.core.conversion module medkit.core.data_item module medkit.core.dict_conv module medkit.core.doc_pipeline module medkit.core.document module medkit.core.id module medkit.core.operation module medkit.core.operation_desc module medkit.core.pipeline module medkit.core.prov_store module medkit.core.prov_tracer module medkit.core.store module medkit.core.text module medkit.core.text.annotation module medkit.core.text.annotation_container module medkit.core.text.document module medkit.core.text.entity_attribute_container module medkit.core.text.entity_norm_attribute module medkit.core.text.operation module medkit.core.text.span module medkit.core.text.span_utils module medkit.core.text.umls_norm_attribute module medkit.core.text.utils module medkit.core.utils module medkit.io module medkit.io.brat module medkit.io.doccano module medkit.io.medkit_json module medkit.io.medkit_json.audio module medkit.io.medkit_json.text module medkit.io.rttm module medkit.io.spacy module medkit.io.srt module medkit.text module medkit.text.context module medkit.text.context.family_detector module medkit.text.context.hypothesis_detector module medkit.text.context.negation_detector module medkit.text.metrics module medkit.text.metrics.classification module medkit.text.metrics.irr_utils module medkit.text.metrics.ner module medkit.text.ner module medkit.text.ner.adicap_norm_attribute module medkit.text.ner.date_attribute module medkit.text.ner.duckling_matcher module medkit.text.ner.edsnlp_date_matcher module medkit.text.ner.edsnlp_tnm_matcher module medkit.text.ner.hf_entity_matcher module medkit.text.ner.hf_entity_matcher_trainable module medkit.text.ner.hf_tokenization_utils module medkit.text.ner.iamsystem_matcher module medkit.text.ner.quick_umls_matcher module medkit.text.ner.regexp_matcher module medkit.text.ner.simstring_matcher module medkit.text.ner.tnm_attribute module medkit.text.ner.umls_coder_normalizer module medkit.text.ner.umls_matcher module medkit.text.ner.umls_utils module medkit.text.postprocessing module medkit.text.postprocessing.alignment_utils module medkit.text.postprocessing.attribute_duplicator module medkit.text.postprocessing.document_splitter module medkit.text.postprocessing.overlapping module medkit.text.preprocessing module medkit.text.preprocessing.char_replacer module medkit.text.preprocessing.char_rules module medkit.text.preprocessing.duplicate_finder module

medkit.text.preprocessing.eds_cleaner module medkit.text.preprocessing.regexp_replacer module medkit.text.relations module medkit.text.relations.syntactic_relation_extractor module medkit.text.segmentation module medkit.text.segmentation.rush_sentence_tokenizer module medkit.text.segmentation.section_tokenizer module medkit.text.segmentation.sentence_tokenizer module medkit.text.segmentation.syntagma_tokenizer module medkit.text.spacy module medkit.text.spacy.displacy_utils module medkit.text.spacy.doc_pipeline module medkit.text.spacy.edsnlp module medkit.text.spacy.pipeline module medkit.text.spacy.spacy_utils module medkit.text.translation module medkit.text.translation.hf_translator module medkit.text.utils module medkit.text.utils.decoding module medkit.tools module medkit.tools.e3c_corpus module medkit.tools.hf_utils module medkit.tools.mtsamples module medkit.training module medkit.training.callbacks module medkit.training.trainable_component module medkit.training.trainer module medkit.training.trainer_config module medkit.training.utils module medkit_doc_to_displacy() (in module medkit.text.spacy.displacy_utils) MedkitKeyword (class in medkit.text.ner) (class in medkit.text.ner.iamsystem_matcher) MemoryAudioBuffer (class in medkit.core.audio) (class in medkit.core.audio.audio_buffer) MetricsComputer (class in medkit.training) (class in medkit.training.utils) ModifiedSpan (class in medkit.core.text) (class in medkit.core.text.span) module medkit.audio medkit.audio.metrics medkit.audio.metrics.diarization medkit.audio.metrics.transcription medkit.audio.preprocessing medkit.audio.preprocessing.downmixer medkit.audio.preprocessing.power_normalizer medkit.audio.preprocessing.resampler medkit.audio.segmentation medkit.audio.segmentation.pa_speaker_detector medkit.audio.segmentation.webrtc_voice_detector medkit.audio.transcription medkit.audio.transcription.doc_transcriber medkit.audio.transcription.hf_transcriber medkit.audio.transcription.sb_transcriber medkit.audio.transcription.transcribed_text_document medkit.core medkit.core.annotation medkit.core.annotation_container medkit.core.attribute medkit.core.attribute_container medkit.core.audio medkit.core.audio.annotation medkit.core.audio.annotation_container medkit.core.audio.audio_buffer medkit.core.audio.document medkit.core.audio.operation medkit.core.audio.span medkit.core.collection medkit.core.conversion medkit.core.data_item medkit.core.dict_conv medkit.core.doc_pipeline medkit.core.document medkit.core.id medkit.core.operation medkit.core.operation_desc medkit.core.pipeline medkit.core.prov_store medkit.core.prov_tracer medkit.core.store medkit.core.text medkit.core.text.annotation medkit.core.text.annotation_container medkit.core.text.document medkit.core.text.entity_attribute_container medkit.core.text.entity_norm_attribute medkit.core.text.operation medkit.core.text.span medkit.core.text.span_utils medkit.core.text.umls_norm_attribute medkit.core.text.utils medkit.core.utils medkit.io medkit.io.brat medkit.io.doccano medkit.io.medkit_json medkit.io.medkit_json.audio medkit.io.medkit_json.text medkit.io.rttm medkit.io.spacy medkit.io.srt medkit.text medkit.text.context medkit.text.context.family_detector medkit.text.context.hypothesis_detector medkit.text.context.negation_detector medkit.text.metrics medkit.text.metrics.classification medkit.text.metrics.irr_utils medkit.text.metrics.ner medkit.text.ner medkit.text.ner.adicap_norm_attribute medkit.text.ner.date_attribute medkit.text.ner.duckling_matcher medkit.text.ner.edsnlp_date_matcher medkit.text.ner.edsnlp_tnm_matcher medkit.text.ner.hf_entity_matcher medkit.text.ner.hf_entity_matcher_trainable medkit.text.ner.hf_tokenization_utils medkit.text.ner.iamsystem_matcher medkit.text.ner.quick_umls_matcher medkit.text.ner.regexp_matcher medkit.text.ner.simstring_matcher medkit.text.ner.tnm_attribute medkit.text.ner.umls_coder_normalizer medkit.text.ner.umls_matcher medkit.text.ner.umls_utils medkit.text.postprocessing medkit.text.postprocessing.alignment_utils medkit.text.postprocessing.attribute_duplicator medkit.text.postprocessing.document_splitter medkit.text.postprocessing.overlapping medkit.text.preprocessing medkit.text.preprocessing.char_replacer medkit.text.preprocessing.char_rules medkit.text.preprocessing.duplicate_finder medkit.text.preprocessing.eds_cleaner medkit.text.preprocessing.regexp_replacer medkit.text.relations medkit.text.relations.syntactic_relation_extractor medkit.text.segmentation medkit.text.segmentation.rush_sentence_tokenizer medkit.text.segmentation.section_tokenizer medkit.text.segmentation.sentence_tokenizer medkit.text.segmentation.syntagma_tokenizer medkit.text.spacy medkit.text.spacy.displacy_utils medkit.text.spacy.doc_pipeline medkit.text.spacy.edsnlp medkit.text.spacy.pipeline medkit.text.spacy.spacy_utils medkit.text.translation medkit.text.translation.hf_translator medkit.text.utils medkit.text.utils.decoding medkit.tools medkit.tools.e3c_corpus medkit.tools.hf_utils medkit.tools.mtsamples medkit.training medkit.training.callbacks medkit.training.trainable_component medkit.training.trainer medkit.training.trainer_config medkit.training.utils move() (in module medkit.core.text.span_utils)

N

NegationDetector (class in medkit.text.context) (class in medkit.text.context.negation_detector) NegationDetectorRule (class in medkit.text.context) (class in medkit.text.context.negation_detector) NegationMetadata (class in medkit.text.context) (class in medkit.text.context.negation_detector)

NEROperation (class in medkit.core.text) (class in medkit.core.text.operation) normalize_spans() (in module medkit.core.text.span_utils) norms (EntityAttributeContainer property), [1]

O

on_epoch_begin() (DefaultPrinterCallback method), [1] (TrainerCallback method), [1] on_epoch_end() (DefaultPrinterCallback method), [1] (TrainerCallback method), [1] on_save() (DefaultPrinterCallback method), [1] (TrainerCallback method), [1] on_step_begin() (DefaultPrinterCallback method), [1] (TrainerCallback method), [1] on_step_end() (DefaultPrinterCallback method), [1] (TrainerCallback method), [1] on_train_begin() (DefaultPrinterCallback method), [1] (TrainerCallback method), [1]

on_train_end() (DefaultPrinterCallback method), [1] (TrainerCallback method), [1] Operation (class in medkit.core) (class in medkit.core.operation) OperationDescription (class in medkit.core) (class in medkit.core.operation_desc) output_label (TranscriptionOperation attribute), [1] OutputConverter (class in medkit.core) (class in medkit.core.conversion) overlaps() (Span method), [1]

P

PASpeakerDetector (class in medkit.audio.segmentation.pa_speaker_detector) Pipeline (class in medkit.core) (class in medkit.core.pipeline) PipelineCompatibleOperation (class in medkit.core) (class in medkit.core.pipeline) PipelineStep (class in medkit.core) (class in medkit.core.pipeline) PlaceholderAudioBuffer (class in medkit.core.audio.audio_buffer) pop() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method) popitem() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method)

PowerNormalizer (class in medkit.audio.preprocessing) (class in medkit.audio.preprocessing.power_normalizer) prepare_batch() (MetricsComputer method), [1] (SeqEvalMetricsComputer method) preprocess() (TrainableComponent method), [1] preprocess_acronym() (in module medkit.text.ner.umls_utils) preprocess_term_to_match() (in module medkit.text.ner.umls_utils) PreprocessingOperation (class in medkit.core.audio) (class in medkit.core.audio.operation) Prov (class in medkit.core) (class in medkit.core.prov_tracer) ProvCompatibleOperation (class in medkit.core) (class in medkit.core.pipeline) ProvStore (class in medkit.core) (class in medkit.core.prov_store) ProvTracer (class in medkit.core) (class in medkit.core.prov_tracer)

Q

QuickUMLSMatcher (class in medkit.text.ner.quick_umls_matcher)

QUOTATION_RULES (in module medkit.text.preprocessing.char_rules)

R

RAW_LABEL (AudioDocument attribute), [1] read() (AudioBuffer method), [1] (FileAudioBuffer method), [1] (MemoryAudioBuffer method), [1] (PlaceholderAudioBuffer method) RegexpMatcher (class in medkit.text.ner) (class in medkit.text.ner.regexp_matcher) RegexpMatcherNormalization (class in medkit.text.ner) (class in medkit.text.ner.regexp_matcher) RegexpMatcherRule (class in medkit.text.ner) (class in medkit.text.ner.regexp_matcher) RegexpMetadata (class in medkit.text.ner) (class in medkit.text.ner.regexp_matcher) RegexpReplacer (class in medkit.text.preprocessing) (class in medkit.text.preprocessing.regexp_replacer) Relation (class in medkit.core.text) (class in medkit.core.text.annotation) relations (TextAnnotationContainer property), [1] RelativeDateAttribute (class in medkit.text.ner) (class in medkit.text.ner.date_attribute) RelativeDateDirection (class in medkit.text.ner) (class in medkit.text.ner.date_attribute) remove() (in module medkit.core.text.span_utils) replace() (in module medkit.core.text.span_utils) replace_multiple_newline_after_sentence() (in module medkit.core.text.utils) replace_newline_inside_sentence() (in module medkit.core.text.utils) replace_point_after_keywords() (in module medkit.core.text.utils) replace_point_before_keywords() (in module medkit.core.text.utils) replace_point_in_numbers() (in module medkit.core.text.utils) replace_point_in_uppercase() (in module medkit.core.text.utils) Resampler (class in medkit.audio.preprocessing.resampler) rstrip() (in module medkit.core.text.utils) RTTMInputConverter (class in medkit.io) (class in medkit.io.rttm) RTTMOutputConverter (class in medkit.io) (class in medkit.io.rttm) run() (AttributeDuplicator method), [1] (CharReplacer method), [1] (DocPipeline method), [1] (DocTranscriber method), [1] (DocumentSplitter method), [1] (Downmixer method), [1] (DucklingMatcher method), [1] (DuplicateFinder method), [1] (EDSCleaner method), [1] (EDSNLPDateMatcher method) (EDSNLPDocPipeline method) (EDSNLPPipeline method) (EDSNLPTNMMatcher method) (FamilyDetector method), [1] (HFEntityMatcher method) (HFTranscriber method) (HFTranslator method) (HypothesisDetector method), [1] (NegationDetector method), [1] (PASpeakerDetector method) (Pipeline method), [1] (PipelineCompatibleOperation method), [1] (PowerNormalizer method), [1] (QuickUMLSMatcher method) (RegexpMatcher method), [1] (RegexpReplacer method), [1] (Resampler method) (RushSentenceTokenizer method) (SBTranscriber method) (SectionTokenizer method), [1] (SentenceTokenizer method), [1] (SimstringMatcher method), [1] (SpacyDocPipeline method), [1] (SpacyPipeline method), [1] (SyntacticRelationExtractor method) (SyntagmaTokenizer method), [1] (TranscriptionOperation method), [1] (UMLSCoderNormalizer method) (UMLSMatcher method), [1] (WebRTCVoiceDetector method)

RushSentenceTokenizer (class in medkit.text.segmentation.rush_sentence_tokenizer)

S

save() (BratOutputConverter method), [1] (DoccanoOutputConverter method), [1] (RTTMOutputConverter method), [1] (SRTOutputConverter method), [1] (TrainableComponent method), [1] (Trainer method), [1] save_audio_anns() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.audio) save_audio_document() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.audio) save_audio_documents() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.audio) save_doc() (RTTMOutputConverter method), [1] (SRTOutputConverter method), [1] save_prov_to_dot() (in module medkit.tools) save_rules() (FamilyDetector static method), [1] (HypothesisDetector static method), [1] (NegationDetector static method), [1] (RegexpMatcher static method), [1] (SimstringMatcher static method), [1] save_section_definition() (SectionTokenizer static method), [1] save_segments() (SRTOutputConverter method), [1] save_syntagma_definition() (SyntagmaTokenizer static method), [1] save_text_anns() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.text) save_text_document() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.text) save_text_documents() (in module medkit.io.medkit_json) (in module medkit.io.medkit_json.text) save_turn_segments() (RTTMOutputConverter method), [1] SBTranscriber (class in medkit.audio.transcription.sb_transcriber) SectionModificationRule (class in medkit.text.segmentation) (class in medkit.text.segmentation.section_tokenizer) SectionTokenizer (class in medkit.text.segmentation) (class in medkit.text.segmentation.section_tokenizer) Segment (class in medkit.core.audio) (class in medkit.core.audio.annotation) (class in medkit.core.text) (class in medkit.core.text.annotation) SegmentationOperation (class in medkit.core.audio) (class in medkit.core.audio.operation) (class in medkit.core.text) (class in medkit.core.text.operation) segments (TextAnnotationContainer property), [1] SEMGROUP_LABELS (in module medkit.text.ner.umls_utils) SEMGROUPS (in module medkit.text.ner.umls_utils) SENTENCE_LABEL (in module medkit.tools.e3c_corpus) SentenceTokenizer (class in medkit.text.segmentation) (class in medkit.text.segmentation.sentence_tokenizer) SeqEvalEvaluator (class in medkit.text.metrics.ner) SeqEvalMetricsComputer (class in medkit.text.metrics.ner) set_prov_tracer() (AttributeDuplicator method), [1] (CharReplacer method), [1] (ContextOperation method), [1] (DoccanoInputConverter method), [1] (DocOperation method), [1] (DocPipeline method), [1] (DocTranscriber method), [1] (DocumentSplitter method), [1] (Downmixer method), [1] (DucklingMatcher method), [1] (DuplicateFinder method), [1] (EDSCleaner method), [1] (EDSNLPDateMatcher method) (EDSNLPDocPipeline method) (EDSNLPPipeline method) (EDSNLPTNMMatcher method) (FamilyDetector method), [1] (HFEntityMatcher method) (HFTranscriber method) (HFTranslator method) (HypothesisDetector method), [1] (IAMSystemMatcher method), [1] (NegationDetector method), [1] (NEROperation method), [1] (Operation method), [1] (PASpeakerDetector method) (PowerNormalizer method), [1] (PreprocessingOperation method), [1] (QuickUMLSMatcher method) (RegexpMatcher method), [1] (RegexpReplacer method), [1] (Resampler method) (RTTMInputConverter method), [1] (RushSentenceTokenizer method) (SBTranscriber method) (SectionTokenizer method), [1] (SegmentationOperation method), [1], [2], [3] (SentenceTokenizer method), [1] (SimstringMatcher method), [1] (SpacyDocPipeline method), [1] (SpacyPipeline method), [1] (SRTInputConverter method), [1] (SyntacticRelationExtractor method) (SyntagmaTokenizer method), [1] (UMLSCoderNormalizer method) (UMLSMatcher method), [1] (WebRTCVoiceDetector method)

setdefault() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method) SIGN_RULES (in module medkit.text.preprocessing.char_rules) SimstringMatcher (class in medkit.text.ner) (class in medkit.text.ner.simstring_matcher) SimstringMatcherNormalization (class in medkit.text.ner) (class in medkit.text.ner.simstring_matcher) SimstringMatcherRule (class in medkit.text.ner) (class in medkit.text.ner.simstring_matcher) SPACE_RULES (in module medkit.text.preprocessing.char_rules) SpacyDocPipeline (class in medkit.text.spacy) (class in medkit.text.spacy.doc_pipeline) SpacyInputConverter (class in medkit.io.spacy) SpacyOutputConverter (class in medkit.io.spacy) SpacyPipeline (class in medkit.text.spacy) (class in medkit.text.spacy.pipeline) Span (class in medkit.core.audio) (class in medkit.core.audio.span) (class in medkit.core.text) (class in medkit.core.text.span) SRTInputConverter (class in medkit.io) (class in medkit.io.srt) SRTOutputConverter (class in medkit.io) (class in medkit.io.srt) start (Span attribute), [1] Store (class in medkit.core) (class in medkit.core.store) strip() (in module medkit.core.text.utils) SubclassMapping (class in medkit.core.dict_conv) SyntacticRelationExtractor (class in medkit.text.relations.syntactic_relation_extractor) SyntagmaTokenizer (class in medkit.text.segmentation) (class in medkit.text.segmentation.syntagma_tokenizer)

T

TextAnnotation (class in medkit.core.text) (class in medkit.core.text.annotation) TextAnnotationContainer (class in medkit.core.text) (class in medkit.core.text.annotation_container) TextClassificationEvaluator (class in medkit.text.metrics.classification) TextDocument (class in medkit.core.text) (class in medkit.core.text.document) TNMAttribute (class in medkit.text.ner.tnm_attribute) to_attribute() (SimstringMatcherNormalization method), [1] to_brat() (ADICAPNormAttribute method), [1] (Attribute method), [1] (DateAttribute method), [1] (DuplicationAttribute method), [1] (DurationAttribute method), [1] (EntityNormAttribute method), [1] (RelativeDateAttribute method), [1] (TNMAttribute method) (UMLSNormAttribute method), [1] to_device() (BatchData method), [1] to_dict() (DictConvertible method) to_spacy() (ADICAPNormAttribute method), [1] (Attribute method), [1] (DateAttribute method), [1] (DuplicationAttribute method), [1] (DurationAttribute method), [1] (EntityNormAttribute method), [1] (RelativeDateAttribute method), [1] (TNMAttribute method) (UMLSNormAttribute method), [1]

train() (Trainer method), [1] TrainableComponent (class in medkit.training) (class in medkit.training.trainable_component) Trainer (class in medkit.training) (class in medkit.training.trainer) TrainerCallback (class in medkit.training) (class in medkit.training.callbacks) TrainerConfig (class in medkit.training) (class in medkit.training.trainer_config) training_epoch() (Trainer method), [1] TranscribedTextDocument (class in medkit.audio.transcription) (class in medkit.audio.transcription.transcribed_text_document) TranscriptionEvaluator (class in medkit.audio.metrics.transcription) TranscriptionEvaluatorResult (class in medkit.audio.metrics.transcription) TranscriptionOperation (class in medkit.audio.transcription) (class in medkit.audio.transcription.doc_transcriber) transform_entities_to_tags() (in module medkit.text.ner.hf_tokenization_utils) trim() (AudioBuffer method), [1] (FileAudioBuffer method), [1] (MemoryAudioBuffer method), [1] (PlaceholderAudioBuffer method) trim_duration() (AudioBuffer method), [1] (FileAudioBuffer method), [1] (MemoryAudioBuffer method), [1] (PlaceholderAudioBuffer method)

U

UMLSCoderNormalizer (class in medkit.text.ner.umls_coder_normalizer) UMLSEntry (class in medkit.text.ner.umls_utils) UMLSMatcher (class in medkit.text.ner) (class in medkit.text.ner.umls_matcher) UMLSNormAttribute (class in medkit.core.text) (class in medkit.core.text.umls_norm_attribute)

update() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method) update_learning_rate() (Trainer method), [1]

V

values() (BatchData method) (FamilyMetadata method) (HypothesisRuleMetadata method) (HypothesisVerbMetadata method) (NegationMetadata method) (RegexpMetadata method)

W

WebRTCVoiceDetector (class in medkit.audio.segmentation.webrtc_voice_detector)