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Functions614 in github.com/allenai/SciREX

↓ 1 callersFunctionpredict
(archive_folder, test_file, output_file, cuda_device)
scirex/predictors/predict_ner.py:23
↓ 1 callersFunctionpredict
coreference_scores_file (jsonl) - { 'doc_id' : str, 'pairwise_coreference_scores' : List[(s_1, e_1), (s_2, e_2), float (3 sig
scirex/predictors/predict_clusters.py:7
↓ 1 callersFunctionpredict
test_file contains atleast - doc_id, sections, sentences, ner in scirex format. output_file - { 'doc_id' : str, 'saliency' :
scirex/predictors/predict_salient_mentions.py:20
↓ 1 callersFunctionpredict
span_prediction_file (jsonl) needs atleast three fields - doc_id, words: List[str], field: List[Tuple[start_index, end_index, type]]
scirex/predictors/predict_pairwise_coreference.py:19
↓ 1 callersFunctionpredict
(clusters_file, saliency_file, output_file)
scirex/predictors/predict_salient_clusters.py:4
↓ 1 callersFunctionpredict_from_ensemble
(trigger_prediction_dirs, trigger_vocab_dirs, arg_prediction_dir, arg_vocab_dir, tes
dygiepp/dygie/commands/predict_from_ensemble.py:131
↓ 1 callersFunctionpredict_from_pair
(trigger_prediction_dir, arg_prediction_dir, vocab_dir, test_file, output_file)
dygiepp/dygie/commands/predict_from_pair.py:100
↓ 1 callersMethodpredict_labels
(self, relation_labels, output_dict, metadata)
dygiepp/dygie/models/relation.py:175
↓ 1 callersMethodpredict_labels
(self, relation_scores, relation_logits, relation_labels, output_dict)
scirex/models/relations/entity_relation.py:181
↓ 1 callersMethodpredict_labels
(self, output_dict)
scirex/models/relations/mention_binary_relation.py:100
↓ 1 callersMethodpredict_labels_doc
(self, output_dict)
dygiepp/dygie/models/coref.py:308
↓ 1 callersFunctionpredict_list
(archive_file, test_file_dir, test_file_list, output_dir, cuda_device, log_file)
dygiepp/dygie/commands/predict_dygie_whole_doc.py:167
↓ 1 callersFunctionpredict_one
(trig, arg, gold, trigger_vocabs, arg_vocab)
dygiepp/dygie/commands/predict_from_ensemble.py:110
↓ 1 callersFunctionpredict_one
(trig, arg, gold, vocab)
dygiepp/dygie/commands/predict_from_pair.py:79
↓ 1 callersFunctionprint_task
(cat_group)
scirex_utilities/add_paper_record_to_pwc.py:48
↓ 1 callersMethodprocess_annotation
The method that processes the children of a BeautifulSoup tag
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:213
↓ 1 callersFunctionprocess_back_to_dataframe
(span_labels: Dict[Tuple[int, int], dict], doc_text: str)
scirex_utilities/convert_brat_annotations_to_json.py:80
↓ 1 callersFunctionprocess_documents
(documents)
scirex/predictors/predict_ner.py:86
↓ 1 callersFunctionprocess_folder
(folder: str)
scirex_utilities/convert_brat_annotations_to_json.py:37
↓ 1 callersFunctionprocess_ner
(line, offset)
dygiepp/scripts/data/genia/convert_to_json.py:49
↓ 1 callersFunctionpropagate_annotations
(data_dict: Dict[str, Any])
scirex_utilities/convert_brat_annotations_to_json.py:539
↓ 1 callersFunctionread_grobid_file
(arxiv_id)
scirex_utilities/preprocessing/add_cleaned_text_to_pwc.py:22
↓ 1 callersFunctionread_latex_file
(arxiv_id)
scirex_utilities/preprocessing/add_cleaned_text_to_pwc.py:38
↓ 1 callersMethodrelation_forward
(self, output_span_embedding, metadata, relation_to_cluster_ids, span_cluster_labels)
scirex/models/scirex_model.py:231
↓ 1 callersMethodremove_whitespace
(self)
dygiepp/scripts/data/ace-event/parse_ace_event.py:214
↓ 1 callersMethodreset
(self)
scirex/metrics/span_f1_metrics.py:172
↓ 1 callersMethodreset
(self)
scirex/metrics/thresholding_f1_metric.py:79
↓ 1 callersMethodresize_sections_and_group
( self, sections: List[Span], sentences: List[List[Span]], entities: Dict[Span, EntityType] )
scirex/data/dataset_readers/scirex_full_reader.py:243
↓ 1 callersMethodsaliency_and_relation_forward
( self, output_span_embedding, metadata, span_saliency_labels, relatio
scirex/models/scirex_model.py:258
↓ 1 callersMethodsaliency_forward
( self, output_span_embedding, metadata, span_saliency_labels, span_cl
scirex/models/scirex_model.py:204
↓ 1 callersFunctionsave_list
Save a list as text, one entry per line.
dygiepp/scripts/data/genia/convert_to_json.py:13
↓ 1 callersFunctionscore_dygie_model
(predictions, gold_data)
scirex/evaluation_scripts/scierc_coref_evaluate.py:50
↓ 1 callersFunctionscore_scirex_model
(predictions, gold_data)
scirex/evaluation_scripts/scierc_coref_evaluate.py:37
↓ 1 callersFunctionsearch_es_by_arxiv_url
(paper_url)
scirex_utilities/add_paper_record_to_pwc.py:26
↓ 1 callersFunctionsearch_es_by_url
(paper_url)
scirex_utilities/add_paper_record_to_pwc.py:15
↓ 1 callersFunctionsentence_to_json
Get the tokens and NER tags. Ignore the POS tags.
dygiepp/scripts/data/genia/convert_to_json.py:60
↓ 1 callersMethodsetUp
(self)
dygiepp/dygie/tests/scripts/m2.py:15
↓ 1 callersFunctionsort_by_padding
Sorts the instances by their padding lengths, using the keys in ``sorting_keys`` (in the order in which they are provided). ``sorting_keys``
scirex/data/iterators/sampled_iterator.py:17
↓ 1 callersFunctionspan_match
(span_1, span_2)
scirex/metrics/span_f1_metrics.py:177
↓ 1 callersMethodspan_to_token
Returns the list of tokens that covers the given list of character spans
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:197
↓ 1 callersFunctionspans_to_bio_tags
(spans, length)
scirex/data/utils/span_utils.py:3
↓ 1 callersFunctionsplit_dataset
(input_file)
scirex_utilities/preprocessing/split_dataset_train_test.py:10
↓ 1 callersMethodtest_dataset
To compute coreference evaluation metrics, the evaluator needs access to the list of coreference clusters, given in the same form as
dygiepp/dygie/tests/scripts/m2.py:30
↓ 1 callersMethodtext_to_instance
TODO(dwadden) document me.
dygiepp/dygie/data/dataset_readers/ie_json.py:203
↓ 1 callersMethodtext_to_instance
( self, paragraph_num: int, paragraph: List[str], ner_dict: Dict[Span, str],
scirex/data/dataset_readers/scirex_full_reader.py:302
↓ 1 callersMethodtext_to_instance
( self, # type: ignore premise: str, hypothesis: str, metadata: Dict[str, Any
scirex/data/dataset_readers/coreference_eval_reader.py:66
↓ 1 callersMethodtext_to_instance
( self, doc_id: str, document: List[str], relation: Dict[BaseEntityType, str], label: int )
scirex/data/dataset_readers/doctaet_reader.py:98
↓ 1 callersMethodtext_to_instance
( self, # type: ignore premise: str, hypothesis: str, label: int, pro
scirex/data/dataset_readers/coreference_train_reader.py:89
↓ 1 callersMethodto_json
(self)
dygiepp/scripts/data/ace-event/parse_ace_event.py:719
↓ 1 callersFunctionunwrap
(trig_pred_dict)
dygiepp/dygie/commands/predict_from_ensemble.py:19
↓ 1 callersMethodupdate_span_embeddings
(self, span_embeddings, span_mask, top_span_embeddings, top_span_mask, top_span_indices)
dygiepp/dygie/models/dygie.py:322
↓ 1 callersMethodupdate_spans
(self, output_dict, span_embeddings_batched, indices)
dygiepp/dygie/models/coref.py:95
↓ 1 callersFunctionverify_json_dict
(json_dict)
scirex/data/dataset_readers/scirex_full_reader.py:105
↓ 1 callersFunctionverify_json_dict
(json_dict)
scirex/data/dataset_readers/doctaet_reader.py:47
↓ 1 callersFunctionwithin_sentence
(span)
dygiepp/dygie/data/dataset_readers/ie_json.py:56
Method__call__
(self, text)
scirex_utilities/convert_brat_annotations_to_json.py:26
Method__call__
(self, predictions: torch.Tensor, gold_labels: torch.Tensor,
dygiepp/dygie/training/ner_metrics.py:18
Method__call__
(self, predicted_relation_list, metadata_list)
dygiepp/dygie/training/relation_metrics.py:16
Method__call__
(self, predicted_relation_list, metadata_list)
dygiepp/dygie/training/relation_metrics.py:50
Method__call__
(self, predicted_events_list, metadata_list)
dygiepp/dygie/training/event_metrics.py:33
Method__call__
(self, predicted_events_list)
dygiepp/dygie/training/event_metrics.py:111
Method__call__
Loop over all event argument predictions. Check whether the event trigger and the argument ner tag agree with the role of the argumen
dygiepp/dygie/training/joint_metrics.py:23
Method__call__
(self, candidate_relation_list, candidate_relation_labels, candidate_relation_scores, doc_id)
scirex/metrics/n_ary_relation_metrics.py:15
Method__call__
(self, predictions: torch.Tensor, gold_labels: torch.Tensor,
scirex/metrics/span_f1_metrics.py:44
Method__call__
(self, predictions: torch.Tensor, gold_labels: torch.Tensor)
scirex/metrics/thresholding_f1_metric.py:28
Method__call__
(self, tensor)
scirex/models/gelu.py:6
Method__eq__
(self, other)
dygiepp/dygie/data/dataset_readers/data_structures.py:149
Method__eq__
(self, other)
dygiepp/dygie/data/dataset_readers/data_structures.py:187
Method__eq__
(self, other)
dygiepp/dygie/data/dataset_readers/data_structures.py:205
Method__getitem__
(self, ix)
dygiepp/dygie/data/dataset_readers/data_structures.py:25
Method__getitem__
(self, ix)
dygiepp/dygie/data/dataset_readers/data_structures.py:54
Method__getitem__
(self, i)
dygiepp/dygie/data/dataset_readers/data_structures.py:254
Method__getitem__
(self, ix)
dygiepp/dygie/data/dataset_readers/data_structures.py:300
Method__hash__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:192
Method__init__
(self, vocab)
scirex_utilities/convert_brat_annotations_to_json.py:23
Method__init__
(self, indices: List[Tuple[int, int]], row_field: SequenceField,
dygiepp/dygie/data/fields/adjacency_field_assym.py:43
Method__init__
(self, json_file)
dygiepp/dygie/data/dataset_readers/data_structures.py:20
Method__init__
(self, js)
dygiepp/dygie/data/dataset_readers/data_structures.py:33
Method__init__
(self, entry, sentence_start, sentence_ix)
dygiepp/dygie/data/dataset_readers/data_structures.py:84
Method__init__
(self, start, end, text, sentence_start)
dygiepp/dygie/data/dataset_readers/data_structures.py:137
Method__init__
(self, ix, text, sentence_start)
dygiepp/dygie/data/dataset_readers/data_structures.py:160
Method__init__
(self, token, label)
dygiepp/dygie/data/dataset_readers/data_structures.py:170
Method__init__
(self, span, role, event_type)
dygiepp/dygie/data/dataset_readers/data_structures.py:179
Method__init__
(self, ner, text, sentence_start, flavor=None)
dygiepp/dygie/data/dataset_readers/data_structures.py:197
Method__init__
(self, relation, text, sentence_start)
dygiepp/dygie/data/dataset_readers/data_structures.py:211
Method__init__
(self, event, text, sentence_start)
dygiepp/dygie/data/dataset_readers/data_structures.py:225
Method__init__
(self, events_json, text, sentence_start)
dygiepp/dygie/data/dataset_readers/data_structures.py:246
Method__init__
(self, cluster, cluster_id, document)
dygiepp/dygie/data/dataset_readers/data_structures.py:282
Method__init__
(self, span, ner, sentence, cluster_id)
dygiepp/dygie/data/dataset_readers/data_structures.py:305
Method__init__
(self, max_span_width: int, token_indexers: Dict[str, TokenIndexer] = None,
dygiepp/dygie/data/dataset_readers/ie_json.py:126
Method__init__
(self, number_of_classes: int, none_label: int=0)
dygiepp/dygie/training/ner_metrics.py:12
Method__init__
(self)
dygiepp/dygie/training/relation_metrics.py:12
Method__init__
(self)
dygiepp/dygie/training/relation_metrics.py:47
Method__init__
(self)
dygiepp/dygie/training/event_metrics.py:29
Method__init__
(self)
dygiepp/dygie/training/event_metrics.py:107
Method__init__
(self, valid_events)
dygiepp/dygie/training/joint_metrics.py:18
Method__init__
(self, num_classes)
dygiepp/dygie/models/one_hot.py:20
Method__init__
(self, vocab: Vocabulary, text_field_embedder: TextFieldEmbedder,
dygiepp/dygie/models/dygie.py:54
Method__init__
(self, vocab: Vocabulary, trigger_feedforward: FeedForward,
dygiepp/dygie/models/events.py:39
Method__init__
( self, pretrained_model: str, requires_grad: str = "none", top_layer_only: bo
dygiepp/dygie/models/bert_token_embedder_modified.py:30
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