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Functions614 in github.com/allenai/SciREX

Methodcount_vocab_items
(self, counter: Dict[str, Dict[str, int]])
scirex/data/dataset_readers/multi_label_field.py:102
Functioncumsum_shifted
Assumes `xs` is a 1-d array. The usual cumsum has elements [x[1], x[1] + x[2], ...]. This one has elements [0, x[1], x[1] + x[2], ...]. U
dygiepp/dygie/models/shared.py:8
Methodcustom_seg
(doc)
dygiepp/scripts/data/ace-event/parse_ace_event.py:299
Methoddecode
(self, output_dict: Dict[str, torch.Tensor])
dygiepp/dygie/models/ner.py:109
Methoddecode
Converts the list of spans and predicted antecedent indices into clusters of spans for each element in the batch. Parameters
dygiepp/dygie/models/coref.py:364
Methoddecode
(self, output_dict: Dict[str, torch.Tensor])
scirex/models/ner/ner_crf_tagger.py:98
Methoddecode
(self, output_dict: Dict[str, torch.Tensor])
scirex/models/span_classifiers/span_classifier.py:83
Methoddecode
(self, output_dict: Dict[str, torch.Tensor])
scirex/models/relations/entity_relation.py:205
Methoddecode
(self, output_dict: Dict[str, torch.Tensor])
scirex/models/relations/mention_binary_relation.py:139
Methoddecode
(self, output_dict: Dict[str, torch.Tensor])
scirex/models/coreference/bert_coreference.py:75
Methoddefault
(self, obj)
scirex_utilities/json_utilities.py:5
Functiondump_all_to_file
(input_file, output_dir)
scirex/data/utils/data_formatting.py:36
Functiondump_to_file
(input_file, output_dir, max_id, test_size=0.3, random_state=1001)
scirex/data/utils/data_formatting.py:22
Methodempty_field
(self)
dygiepp/dygie/data/fields/adjacency_field_assym.py:112
Methodequals
(self, ann2)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:114
Methodevent_type_matches
(self, argument)
dygiepp/dygie/data/dataset_readers/data_structures.py:264
Methodexact_match
(self, argument)
dygiepp/dygie/data/dataset_readers/data_structures.py:274
Functionextract_entites_from_document
(row)
scirex_utilities/analyse_pwc_entity_results.py:27
Functionextract_entities_from_sentence
(row)
scirex_utilities/analyse_pwc_entity_results.py:22
Functionfields_to_batches
The input is a dict whose items are batched tensors. The output is a list of dictionaries - one per entry in the batch - with the slices of t
dygiepp/scripts/data/genia/shared.py:50
Methodfind_cluster
Search through coreference clusters and return the one containing the query entity, if it's part of a cluster. If we don't find a mat
dygiepp/dygie/data/dataset_readers/data_structures.py:65
Functionfind_sub_list
(sl, l)
dygiepp/scripts/data/genia/shared.py:32
Functionfind_sub_lists
(sl,l)
dygiepp/scripts/data/genia/shared.py:41
Functionflatten
Flatten a nested list into a single list. Note this only works for lists nested one deep. For the general case we'd need recursion
dygiepp/scripts/data/genia/shared.py:22
Methodforward
(self, x)
dygiepp/dygie/models/one_hot.py:24
Methodforward
TODO(dwadden) change this.
dygiepp/dygie/models/dygie.py:127
Methodforward
TODO(dwadden) Write documentation. The trigger embeddings are just the contextualized token embeddings, and the trigger mask is
dygiepp/dygie/models/events.py:159
Methodforward
(self, trig_embeddings, arg_embeddings, trig_mask, arg_mask, trig_scores, arg_scores, trig_arg
dygiepp/dygie/models/span_prop.py:47
Methodforward
Extracts the top-k scoring items with respect to the scorer. We additionally return the indices of the top-k in their original order,
dygiepp/dygie/models/entity_beam_pruner.py:56
Methodforward
TODO(dwadden) Write documentation.
dygiepp/dygie/models/ner.py:65
Methodforward
TODO(dwadden) Write documentation.
dygiepp/dygie/models/relation.py:83
Methodforward
( self, # type: ignore tokens: Dict[str, torch.LongTensor], label: torch.IntTensor =
scirex/models/doctaet.py:56
Methodforward
( self, text, ner_type_labels, spans=None, span_cluster_labels=None,
scirex/models/scirex_model.py:73
Methodforward
( self, # type: ignore text_embeddings: torch.FloatTensor, text_mask: torch.IntTensor
scirex/models/ner/ner_crf_tagger.py:58
Methodforward
( self, # type: ignore spans: torch.IntTensor, # (Batch Size, Number of Spans, 2) sp
scirex/models/span_classifiers/span_classifier.py:40
Methodforward
(self, **kwargs)
scirex/models/relations/entity_relation.py:65
Methodforward
( self, # type: ignore tokens: Dict[str, torch.LongTensor], label: torch.IntTensor =
scirex/models/coreference/bert_coreference.py:43
Functionfuzzy_match_with_any
(w1: str, w2: str)
scirex_utilities/entity_matching_algorithms.py:58
Functiongenerate_brat_annotations
( pwc_doc_file, pwc_sentence_file, pwc_prediction_file, brat_anno_folder, after_doc_id=None )
scirex_utilities/convert_pwc_to_brat.py:155
Functiongenerate_brat_annotations
(documents, brat_anno_folder)
scirex_utilities/convert_predictions_to_brat.py:151
Functionget_arxiv_id
(paper_url)
scirex_utilities/preprocessing/add_cleaned_text_to_pwc.py:17
Functionget_cleaned_text_if_available
(row)
scirex_utilities/preprocessing/add_cleaned_text_to_pwc.py:70
Methodget_cluster_assignment
(coref)
dygiepp/scripts/data/genia/merge_coref.py:139
Functionget_coref_types
Get the different types of coref in the GENIA data set, and save to file. Once this is done once, just hard-code the list of coref types.
dygiepp/scripts/data/genia/merge_coref.py:33
Methodget_flavor
(self, argument)
dygiepp/dygie/data/dataset_readers/data_structures.py:125
Methodget_metric
(self, reset=False)
dygiepp/dygie/training/relation_metrics.py:27
Methodget_metric
(self, reset=False)
dygiepp/dygie/training/relation_metrics.py:58
Methodget_metric
(self, reset=False)
dygiepp/dygie/training/event_metrics.py:70
Methodget_metric
(self, reset=False)
dygiepp/dygie/training/event_metrics.py:125
Methodget_metric
(self, reset=False)
dygiepp/dygie/training/joint_metrics.py:43
Methodget_metric
(self, reset=False)
scirex/metrics/n_ary_relation_metrics.py:38
Methodget_metric
(self, reset: bool = False)
scirex/metrics/thresholding_f1_metric.py:50
Methodget_metrics
Get all metrics from all modules. For the ones that shouldn't be displayed, prefix their keys with an underscore.
dygiepp/dygie/models/dygie.py:369
Methodget_metrics
(self, reset: bool = False)
dygiepp/dygie/models/events.py:326
Methodget_metrics
(self, reset)
dygiepp/dygie/models/dummy.py:5
Methodget_metrics
(self, reset: bool = False)
dygiepp/dygie/models/ner.py:134
Methodget_metrics
(self, reset: bool = False)
dygiepp/dygie/models/relation.py:227
Methodget_metrics
(self, reset: bool = False)
dygiepp/dygie/models/coref.py:438
Methodget_metrics
(self, reset: bool = False)
scirex/models/doctaet.py:88
Methodget_metrics
Get all metrics from all modules. For the ones that shouldn't be displayed, prefix their keys with an underscore.
scirex/models/scirex_model.py:389
Methodget_metrics
(self, reset: bool = False)
scirex/models/ner/ner_crf_tagger.py:146
Methodget_metrics
(self, reset: bool = False)
scirex/models/span_classifiers/span_classifier.py:93
Methodget_metrics
(self, reset: bool = False)
scirex/models/relations/entity_relation.py:220
Methodget_metrics
(self, reset: bool = False)
scirex/models/relations/mention_binary_relation.py:152
Methodget_metrics
(self, reset: bool = False)
scirex/models/coreference/bert_coreference.py:79
Methodget_num_batches
(self, instances)
dygiepp/dygie/data/iterators/multitask_iterator.py:73
Methodget_num_batches
Get the number of batches.
dygiepp/dygie/data/iterators/document_iterator.py:44
Methodget_num_batches
(self, instances)
scirex/data/iterators/batch_iterator.py:56
Methodget_padding_lengths
(self)
dygiepp/dygie/data/fields/adjacency_field_assym.py:96
Functionget_pwc_data_and_output
(pwc_doc_file: str, pwc_sentence_file: str, pwc_prediction_file: str)
scirex_utilities/analyse_pwc_entity_results.py:65
Functionget_result_matrix_for_match_method
(pwc_df, pwc_sentences, comparison_method)
scirex_utilities/analyse_pwc_entity_results.py:115
Methodget_text
(self)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:93
Functiongroup_sentences_to_sections
(sentences: List[Span], sections: List[Span])
scirex/data/utils/paragraph_alignment.py:86
Methodin_range
(candidate)
dygiepp/scripts/data/ace-event/parse_ace_event.py:667
Functionis_exact_match_in_any
(true_value: str, predicted_value_list: List[str])
scirex_utilities/entity_matching_algorithms.py:90
Functionis_exact_match_in_concatenated
(true_value: str, predicted_value_list: List[str])
scirex_utilities/entity_matching_algorithms.py:82
Functionis_exact_match_with_any
(true_value: str, predicted_value_list: List[str])
scirex_utilities/entity_matching_algorithms.py:86
Functionis_fuzzy_match_with_any
(true_value: str, predicted_value_list: List[str], min_ratio: int = 70)
scirex_utilities/entity_matching_algorithms.py:94
Functionload_list
Make each line of a file into a list entry. Apply a conversion function to each line (e.g. convert to int). By default, the conversion does n
dygiepp/scripts/data/genia/shared.py:10
Methodmatches_except_event_type
(self, argument)
dygiepp/dygie/data/dataset_readers/data_structures.py:268
Methodn_tokens
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:79
Functionno_tags
(line)
dygiepp/scripts/data/genia/convert_to_json.py:45
Functionnormalize_spans
(row)
scirex_utilities/convert_brat_annotations_to_json.py:220
Methodoverlaps
(self, ann2)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:96
FunctionparseStanfordOld
(stanfordfn)
dygiepp/scripts/data/ace05/preprocess/ace2json.py:35
Functionparse_bibliography
Finds all bibliography entries in a grobid xml.
scirex_utilities/preprocessing/grobid_util.py:28
Methodprint_plaintext
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:60
Methodremove_whitespace
(self)
dygiepp/scripts/data/ace-event/parse_ace_event.py:158
Functionsave_list
Save a list as text, one entry per line.
dygiepp/scripts/data/genia/shared.py:3
MethodsetUp
(self)
dygiepp/dygie/tests/data/ie_json_test.py:19
MethodsetUp
(self)
dygiepp/dygie/tests/models/relation_test.py:17
MethodsetUp
(self)
dygiepp/dygie/tests/models/dygie_test.py:11
MethodsetUp
(self)
dygiepp/dygie/tests/models/coref_test.py:15
Functionsplit_train_dev_test
(sentences, train_pct=0.8, dev_pct=0.1, test_pct=0.1)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:396
MethodtearDown
(self)
dygiepp/dygie/tests/data/ie_json_test.py:26
Methodtest_compute_relation_scores
(self)
dygiepp/dygie/tests/models/relation_test.py:66
Methodtest_compute_span_pair_embeddings
(self)
dygiepp/dygie/tests/models/relation_test.py:51
Methodtest_coref_correct_scierc
(self)
dygiepp/dygie/tests/data/ie_json_test.py:48
Methodtest_coref_make_evaluation_metadata
To compute coreference evaluation metrics, the evaluator needs access to the list of coreference clusters, given in the same form as
dygiepp/dygie/tests/models/coref_test.py:29
Methodtest_cross_entropy_ignore_index
(self)
dygiepp/dygie/tests/models/relation_test.py:113
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