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Functions614 in github.com/allenai/SciREX

↓ 1 callersMethoddecode
Take the output and convert it into a list of dicts. Each entry is a sentence. Each key is a pair of span indices for that sentence,
dygiepp/dygie/models/events.py:304
↓ 1 callersMethoddecode
Take the output and convert it into a list of dicts. Each entry is a sentence. Each key is a pair of span indices for that sentence,
dygiepp/dygie/models/relation.py:202
↓ 1 callersMethoddecode
(self, output_dict: Dict[str, torch.Tensor])
scirex/models/doctaet.py:84
↓ 1 callersFunctiondecode_arguments
(output, decoded_trig, vocab)
dygiepp/dygie/commands/predict_from_ensemble.py:57
↓ 1 callersFunctiondecode_arguments
(output, decoded_trig, vocab)
dygiepp/dygie/commands/predict_from_pair.py:28
↓ 1 callersMethoddecode_relations
(self, batch)
scirex/models/scirex_model.py:367
↓ 1 callersMethoddecode_saliency
(self, batch, saliency_threshold)
scirex/models/scirex_model.py:347
↓ 1 callersFunctiondecode_trigger
(outputs, trigger_vocabs)
dygiepp/dygie/commands/predict_from_ensemble.py:37
↓ 1 callersFunctiondecode_trigger
(output, vocab)
dygiepp/dygie/commands/predict_from_pair.py:18
↓ 1 callersFunctiondecoding
(f1, f2)
scirex_utilities/decoding.py:33
↓ 1 callersFunctiondoc_to_json
A list of sentences (a document) to json.
dygiepp/scripts/data/genia/convert_to_json.py:69
↓ 1 callersFunctiondump_sciERC_to_file
(input_dir, output_dir)
scirex/data/utils/scierc_to_scirex_format.py:37
↓ 1 callersFunctiondump_scores
(doc, pred, score_dir)
dygiepp/dygie/commands/predict_dygie.py:130
↓ 1 callersMethodequals
(self, span2)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:71
↓ 1 callersFunctionevaluate
(predicted_data, gold_data)
dygiepp/scripts/dygie_results_in_scirex_format.py:43
↓ 1 callersFunctionextract_references_from_paragraph_text
Parameters ---------- tag: `bs4.element.Tag` The <div/> element of a xml document produced by Grobid. Returns ------
scirex_utilities/preprocessing/grobid_util.py:58
↓ 1 callersFunctionextract_sentence_features
(sentences, words, entities)
scirex/data/utils/section_feature_extraction.py:32
↓ 1 callersMethodextract_span_embeddings
(self, contextualized_embeddings, spans)
scirex/models/scirex_model.py:330
↓ 1 callersFunctionfilter_to_doctaet
(json_dict)
scirex/data/utils/section_feature_extraction.py:50
↓ 1 callersMethodfind_spans
Given an entity from the lex attribute of cons, and the list of possible constituents (with their character spans), return the list of character spans
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:313
↓ 1 callersFunctionfix_fold
(fold)
dygiepp/scripts/data/genia/resolve_differences.py:49
↓ 1 callersFunctionformat_fold
Take data SUTD-formatted documents and convert to our JSON format.
dygiepp/scripts/data/genia/convert_to_json.py:99
↓ 1 callersFunctionformat_label_fields
Format the label fields, making the following changes: 1. Span indices should be with respect to sentence, not document. 2. Return dicts
dygiepp/dygie/data/dataset_readers/ie_json.py:69
↓ 1 callersFunctionformat_tag
(tag, offset)
dygiepp/scripts/data/genia/convert_to_json.py:32
↓ 1 callersFunctiongenerate_folders_for_documents
(pwc_grouped, BRAT_ANNO_FOLDER)
scirex_utilities/convert_pwc_to_brat.py:19
↓ 1 callersFunctiongenerate_folders_for_documents
(documents, BRAT_ANNO_FOLDER)
scirex_utilities/convert_predictions_to_brat.py:21
↓ 1 callersFunctiongenerate_matrix_for_document
(document, span_field, matrix_field)
scirex/models/clustering/clustering.py:8
↓ 1 callersMethodgenerate_pairs
(self, file_path)
scirex/data/dataset_readers/coreference_eval_reader.py:39
↓ 1 callersMethodgenerate_pairs
(file_path)
scirex/data/dataset_readers/coreference_train_reader.py:48
↓ 1 callersMethodgenerate_product
( self, type_to_clusters_map: Dict[str, List[int]], n_true_clusters: int, rela
scirex/models/relations/entity_relation.py:68
↓ 1 callersFunctiongenerate_relations_in_pwc_df
(pwc_df)
scirex_utilities/convert_brat_annotations_to_json.py:367
↓ 1 callersFunctiongenerate_token_and_indices
(sentence)
scirex_utilities/convert_brat_annotations_to_json.py:321
↓ 1 callersFunctionget_aggregated_field
(pwc_df, field)
scirex_utilities/analyse_pwc_entity_results.py:85
↓ 1 callersFunctionget_all_document_annotations
(brat_folder: str)
scirex_utilities/convert_brat_annotations_to_json.py:70
↓ 1 callersMethodget_annotations
Extracts annotations from a sentence annotation
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:180
↓ 1 callersFunctionget_clusters
Add coref to json, filtering to only keep coref roots and `coref_types`.
dygiepp/scripts/data/genia/merge_coref.py:228
↓ 1 callersFunctionget_coref_info
(name)
dygiepp/scripts/data/genia/align_articles.py:49
↓ 1 callersMethodget_doc_key
(article_xml)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:389
↓ 1 callersFunctionget_excluded
Get list of files that had random off-by-1-errors and will be excluded.
dygiepp/scripts/data/genia/merge_coref.py:200
↓ 1 callersFunctionget_gold_data
(test_file)
dygiepp/dygie/commands/predict_from_ensemble.py:125
↓ 1 callersFunctionget_gold_data
(test_file)
dygiepp/dygie/commands/predict_from_pair.py:94
↓ 1 callersFunctionget_json_sentences
(input_file, output_file)
scirex_utilities/preprocessing/process_pwc_to_sentences.py:43
↓ 1 callersFunctionget_matching_sentences
(sentences_article, sutd)
dygiepp/scripts/data/genia/resolve_differences.py:41
↓ 1 callersFunctionget_ner_info
(article)
dygiepp/scripts/data/genia/align_articles.py:37
↓ 1 callersMethodget_padding_lengths
(self)
scirex/data/dataset_readers/multi_label_field.py:118
↓ 1 callersMethodget_raw_data
(self)
dygiepp/dygie/tests/scripts/m2.py:23
↓ 1 callersMethodget_raw_data
(self)
dygiepp/dygie/tests/models/coref_test.py:22
↓ 1 callersMethodget_relation_scores
(self, relation_embeddings)
scirex/models/relations/entity_relation.py:172
↓ 1 callersMethodget_relation_scores
(self, spans, top_span_embeddings)
scirex/models/relations/mention_binary_relation.py:94
↓ 1 callersFunctionget_scores
(arxiv_id: str, clusters: List[List[str]])
scirex_utilities/result_from_pwc_table.py:15
↓ 1 callersFunctionget_sentence_of_span
Return the index of the sentence that the span is part of.
dygiepp/dygie/data/dataset_readers/data_structures.py:6
↓ 1 callersMethodget_sentences
(article_xml)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:381
↓ 1 callersMethodget_span_one_hot_labels
(self, label_namespace, span_labels, spans)
scirex/models/scirex_model.py:300
↓ 1 callersMethodget_span_position
(metadata, span_offset)
scirex/models/scirex_model.py:316
↓ 1 callersFunctionget_spans
(taglist, wordlist)
scirex_utilities/analyse_pwc_entity_results.py:13
↓ 1 callersMethodget_tokens
Returns the list of tokens from a sentence This method oversplits the tokens, so that, as much as possible, all entities can be composed by j
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:136
↓ 1 callersFunctionget_unique_ner_labels
Get unique NER labels.
dygiepp/scripts/data/genia/convert_to_json.py:90
↓ 1 callersFunctionin_between
(ix, pair)
dygiepp/scripts/data/ace-event/parse_ace_event.py:30
↓ 1 callersFunctionintersect_predicted_clusters_to_gold
( predicted_clusters: Dict[str, List[Tuple[int, int]]], gold_clusters: Dict[str, List[Tuple[int, int]]] )
scirex/predictors/utils.py:27
↓ 1 callersMethodis_real
(self)
dygiepp/scripts/data/ace-event/parse_ace_event.py:195
↓ 1 callersFunctionis_reference_tag
(tag: bs4.element.Tag)
scirex_utilities/preprocessing/grobid_util.py:55
↓ 1 callersFunctionjaccard_similarity
(list1, list2)
scirex_utilities/entity_matching_algorithms.py:12
↓ 1 callersFunctionload_json
(test_file)
dygiepp/dygie/commands/predict_dygie_whole_doc.py:109
↓ 1 callersFunctionload_json
(test_file)
dygiepp/dygie/commands/predict_dygie.py:109
↓ 1 callersFunctionmain
()
scirex_utilities/bioul_to_spans.py:40
↓ 1 callersFunctionmain
()
dygiepp/dygie/commands/predict_dygie_whole_doc.py:193
↓ 1 callersFunctionmain
()
dygiepp/dygie/commands/predict_from_ensemble.py:146
↓ 1 callersFunctionmain
()
dygiepp/dygie/commands/predict_dygie.py:175
↓ 1 callersFunctionmain
()
dygiepp/dygie/commands/predict_from_pair.py:112
↓ 1 callersFunctionmain
()
dygiepp/scripts/data/ace-event/parse_ace_event.py:752
↓ 1 callersFunctionmain
()
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:435
↓ 1 callersFunctionmain
()
dygiepp/scripts/data/genia/align_articles.py:108
↓ 1 callersFunctionmain
()
dygiepp/scripts/data/genia/convert_to_json.py:123
↓ 1 callersFunctionmain
()
dygiepp/scripts/data/genia/resolve_differences.py:77
↓ 1 callersFunctionmain
()
dygiepp/scripts/data/genia/merge_coref.py:237
↓ 1 callersFunctionmain
(args)
scirex/evaluation_scripts/scirex_relation_evaluate.py:71
↓ 1 callersFunctionmain
()
scirex/predictors/predict_ner.py:113
↓ 1 callersFunctionmain
()
scirex/predictors/predict_salient_mentions.py:77
↓ 1 callersFunctionmain
()
scirex/predictors/predict_pairwise_coreference.py:75
↓ 1 callersFunctionmake_cluster_dict
Returns a dict whose keys are spans, and values are the ID of the cluster of which the span is a member.
dygiepp/dygie/data/dataset_readers/ie_json.py:44
↓ 1 callersFunctionmake_comparator
()
dygiepp/scripts/data/genia/align_articles.py:66
↓ 1 callersFunctionmake_comparator
()
dygiepp/scripts/data/genia/resolve_differences.py:20
↓ 1 callersFunctionmake_lookups
Need to match the ner data and the coref data by sentence. Create dictionaries where the keys are the document ID's and the values are the
dygiepp/scripts/data/genia/align_articles.py:23
↓ 1 callersFunctionmake_sentences
(lines)
dygiepp/scripts/data/genia/convert_to_json.py:20
↓ 1 callersFunctionmap_back_to_spans
(document, span_field, labels)
scirex/models/clustering/clustering.py:41
↓ 1 callersMethodmap_cluster_to_type_embeddings
(self, type_to_cluster_map: Dict[str, List[int]])
scirex/models/relations/entity_relation.py:55
↓ 1 callersFunctionmatch_abbr
(a, b)
scirex_utilities/entity_matching_algorithms.py:6
↓ 1 callersFunctionmatch_entity_with_best_truth
(enttype, entity, true_list)
scirex_utilities/entity_matching_algorithms.py:70
↓ 1 callersFunctionmatch_predicted_clusters_to_gold
( predicted_clusters: Dict[str, List[Tuple[int, int]]], gold_clusters: Dict[str, List[Tuple[int, int]]
scirex/metrics/clustering_metrics.py:6
↓ 1 callersFunctionmodal_prediction
(predictions)
dygiepp/dygie/commands/predict_from_ensemble.py:31
↓ 1 callersFunctionner_metrics
(gold_data, predicted_data)
scirex/evaluation_scripts/scirex_relation_evaluate.py:27
↓ 1 callersMethodoffset_span_by_para_start
(metadata, spans, span_mask)
scirex/models/scirex_model.py:322
↓ 1 callersFunctionone_fold
(fold, output_dir, heads_only=True, real_entities_only=True, include_pronouns=False)
dygiepp/scripts/data/ace-event/parse_ace_event.py:733
↓ 1 callersFunctionone_fold
Add coref field to json, one fold.
dygiepp/scripts/data/genia/merge_coref.py:207
↓ 1 callersFunctionoverlap_score
(cluster_1, cluster_2)
scirex/evaluation_scripts/scierc_coref_evaluate.py:8
↓ 1 callersMethodparse_lex
(lex, sem)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:265
↓ 1 callersFunctionpredict
(model, dataset_reader, test_file, output_file, cuda_device)
dygiepp/dygie/commands/predict_dygie_whole_doc.py:128
↓ 1 callersFunctionpredict
(archive_file, test_file, output_file, cuda_device, score_dir)
dygiepp/dygie/commands/predict_dygie.py:137
↓ 1 callersFunctionpredict
(archive_folder, span_file, cluster_file, output_file, cuda_device)
scirex/predictors/predict_n_ary_relations.py:44
↓ 1 callersFunctionpredict
(clusters_file, gold_file, output_file)
scirex/predictors/predict_salient_clusters_using_gold.py:19
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