Code
Hub
Workspaces
Following
Trending
Connect
MCP
copy
Create free account
hub
/
github.com/allenai/SciREX
/ functions
Functions
614 in github.com/allenai/SciREX
⨍
Functions
614
◇
Types & classes
84
↳
Endpoints
2
Method
__init__
(self, vocab: Vocabulary, n_span_prop: int, emb_dim: int,
dygiepp/dygie/models/span_prop.py:20
Method
__init__
(self, scorer: torch.nn.Module, entity_beam: bool = False, gold_beam: bool = False, min_score
dygiepp/dygie/models/entity_beam_pruner.py:45
Method
__init__
(self, vocab: Vocabulary, mention_feedforward: FeedForward,
dygiepp/dygie/models/ner.py:36
Method
__init__
(self, vocab: Vocabulary, mention_feedforward: FeedForward,
dygiepp/dygie/models/relation.py:29
Method
__init__
(self, vocab: Vocabulary, mention_feedforward: FeedForward,
dygiepp/dygie/models/coref.py:49
Method
__init__
(self, entries, doc_key)
dygiepp/scripts/data/ace-event/parse_ace_event.py:210
Method
__init__
A base class for ACE xml annotation :param annotation_path: :param text_path:
dygiepp/scripts/data/ace-event/parse_ace_event.py:267
Method
__init__
Token object to faithfully represent a token To be represented faithfully, a token needs to hold: - text: The text it is covering, mi
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:30
Method
__init__
Span object represents any span with start and end indices
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:54
Method
__init__
Annotation object defines an annotation by a list of spans and its label. Optionally, this object can hold the containing text, so that the t
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:81
Method
__init__
(self, sentence_xml)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:131
Method
__init__
(self, article_xml)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:375
Method
__init__
Get the text, id, referrent, and text span.
dygiepp/scripts/data/genia/merge_coref.py:58
Method
__init__
(self, soup, sents_flat, coref_types)
dygiepp/scripts/data/genia/merge_coref.py:112
Method
__init__
(self)
scirex/metrics/n_ary_relation_metrics.py:11
Method
__init__
(self, label_vocabulary: Dict[int, str], ignore_classes: List[str] = None,
scirex/metrics/span_f1_metrics.py:27
Method
__init__
Args: bins: number of threshold bins for the fast computation of AP
scirex/metrics/thresholding_f1_metric.py:17
Method
__init__
(self, sorting_keys: List[Tuple[str, str]], padding_noise: float = 0.1,
scirex/data/iterators/sampled_iterator.py:87
Method
__init__
( self, token_indexers: Dict[str, TokenIndexer] = None, max_paragraph_length: int = 30
scirex/data/dataset_readers/scirex_full_reader.py:123
Method
__init__
( self, field: str, tokenizer: Tokenizer = None, token_indexers: Dict[str, Tok
scirex/data/dataset_readers/coreference_eval_reader.py:18
Method
__init__
( self, labels: Sequence[Union[str, int]], label_namespace: str = "labels", sk
scirex/data/dataset_readers/multi_label_field.py:53
Method
__init__
(self, token_indexers: Dict[str, TokenIndexer] = None, lazy: bool = False)
scirex/data/dataset_readers/doctaet_reader.py:58
Method
__init__
( self, sample_train: bool = False, tokenizer: Tokenizer = None, token_indexer
scirex/data/dataset_readers/coreference_train_reader.py:19
Method
__init__
( self, pretrained_model: str, requires_grad: str = "none", top_layer_only: bo
scirex/models/bert_token_embedder_modified.py:30
Method
__init__
( self, vocab: Vocabulary, bert_model: PretrainedBertEmbedder, aggregate_feedf
scirex/models/doctaet.py:16
Method
__init__
( self, vocab: Vocabulary, text_field_embedder: TextFieldEmbedder, context_lay
scirex/models/scirex_model.py:26
Method
__init__
( self, vocab: Vocabulary, mention_feedforward: FeedForward, label_namespace:
scirex/models/ner/ner_crf_tagger.py:17
Method
__init__
( self, vocab: Vocabulary, mention_feedforward: FeedForward, label_namespace:
scirex/models/span_classifiers/span_classifier.py:21
Method
__init__
( self, vocab: Vocabulary = None, antecedent_feedforward: FeedForward = None,
scirex/models/relations/entity_relation.py:23
Method
__init__
( self, vocab: Vocabulary, antecedent_feedforward: FeedForward, relation_cover
scirex/models/relations/mention_binary_relation.py:18
Method
__init__
( self, vocab: Vocabulary, bert_model: PretrainedBertEmbedder, aggregate_feedf
scirex/models/coreference/bert_coreference.py:16
Method
__len__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:28
Method
__len__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:57
Method
__len__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:122
Method
__len__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:251
Method
__len__
(self)
scirex/data/dataset_readers/multi_label_field.py:143
Method
__missing__
(self, key)
dygiepp/dygie/data/dataset_readers/ie_json.py:41
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:51
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:111
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:146
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:165
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:174
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:184
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:220
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:236
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:257
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:297
Method
__repr__
(self)
dygiepp/dygie/data/dataset_readers/data_structures.py:311
Method
__str__
(self)
dygiepp/dygie/data/fields/adjacency_field_assym.py:122
Method
__str__
(self)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:74
Method
__str__
(self)
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:124
Method
__str__
(self)
scirex/data/dataset_readers/multi_label_field.py:138
Method
_create_batches
(self, instances: Iterable[Instance], shuffle: bool)
dygiepp/dygie/data/iterators/batch_iterator.py:25
Method
_create_batches
(self, instances: Iterable[Instance], shuffle: bool)
dygiepp/dygie/data/iterators/multitask_iterator.py:28
Method
_create_batches
(self, instances: Iterable[Instance], shuffle: bool)
dygiepp/dygie/data/iterators/document_iterator.py:23
Method
_create_batches
(self, instances: Iterable[Instance], shuffle: bool)
scirex/data/iterators/batch_iterator.py:21
Method
_create_batches
(self, instances: Iterable[Instance], shuffle: bool)
scirex/data/iterators/sampled_iterator.py:109
Method
_flatten_span_info
(span_info_batched, span_ix)
scirex/models/scirex_model.py:309
Method
_instances_from_cache_file
(self, cache_filename)
dygiepp/dygie/data/dataset_readers/ie_json.py:314
Method
_instances_to_cache_file
(self, cache_filename, instances)
dygiepp/dygie/data/dataset_readers/ie_json.py:320
Method
_read
(self, file_path: str)
dygiepp/dygie/data/dataset_readers/ie_json.py:141
Method
_read
(self, file_path: str)
scirex/data/dataset_readers/scirex_full_reader.py:140
Method
_read
(self, file_path: str)
scirex/data/dataset_readers/coreference_eval_reader.py:32
Method
_read
(self, file_path: str)
scirex/data/dataset_readers/coreference_train_reader.py:32
Function
add_token_index
(row)
scirex_utilities/convert_brat_annotations_to_json.py:272
Function
add_type_to_gold
(x)
scirex_utilities/decoding.py:18
Method
adjust
(self, tok)
dygiepp/scripts/data/ace-event/parse_ace_event.py:47
Method
adjust
(self, tok)
dygiepp/scripts/data/ace-event/parse_ace_event.py:86
Method
adjust_spans_doc
(self, entry_start)
dygiepp/scripts/data/ace-event/parse_ace_event.py:56
Method
adjust_spans_doc
(self, entry_start)
dygiepp/scripts/data/ace-event/parse_ace_event.py:90
Method
adjust_spans_doc
(self, entry_start)
dygiepp/scripts/data/ace-event/parse_ace_event.py:125
Method
adjust_spans_doc
(self, entry_start)
dygiepp/scripts/data/ace-event/parse_ace_event.py:176
Method
align
(self, sent)
dygiepp/scripts/data/ace-event/parse_ace_event.py:41
Method
align
(self, sent)
dygiepp/scripts/data/ace-event/parse_ace_event.py:82
Method
as_tensor
(self, padding_lengths: Dict[str, int])
dygiepp/dygie/data/fields/adjacency_field_assym.py:101
Method
as_tensor
(self, padding_lengths: Dict[str, int])
scirex/data/dataset_readers/multi_label_field.py:122
Method
authors
(self)
scirex_utilities/preprocessing/grobid_util.py:12
Function
batch_identity
Tile the identity matrix along axis 0, `batch_size` times.
dygiepp/dygie/models/shared.py:19
Function
check_against_sutd_processed
Grab one of my processed documents. Make sure I can find a match in one of the SUTD processed files.
dygiepp/scripts/data/genia/check_genia_xml_sutd.py:49
Function
check_against_xml_source
Make sure my processed documents are consistent with the source XML
dygiepp/scripts/data/genia/check_genia_xml_sutd.py:13
Function
clean_predictions
(pwc_prediction_file: str)
scirex_utilities/analyse_pwc_entity_results.py:32
Function
cleanup_coref
Convert from nested list of tuples to nested list of lists.
dygiepp/dygie/commands/predict_dygie_whole_doc.py:49
Function
cleanup_coref
Convert from nested list of tuples to nested list of lists.
dygiepp/dygie/commands/predict_dygie.py:49
Function
cleanup_event
(decoded, sentence_starts)
dygiepp/dygie/commands/predict_dygie_whole_doc.py:86
Function
cleanup_event
(decoded, sentence_starts)
dygiepp/dygie/commands/predict_dygie.py:86
Function
cleanup_ner
(decoded, sentence_starts)
dygiepp/dygie/commands/predict_dygie_whole_doc.py:61
Function
cleanup_ner
(decoded, sentence_starts)
dygiepp/dygie/commands/predict_dygie.py:61
Function
cleanup_relation
Add sentence offsets to relation results.
dygiepp/dygie/commands/predict_dygie_whole_doc.py:73
Function
cleanup_relation
Add sentence offsets to relation results.
dygiepp/dygie/commands/predict_dygie.py:73
Function
cluster_with_connected_components
(matrix, threshold, plot)
scirex/models/clustering/clustering.py:36
Function
combine
(rows)
scirex_utilities/convert_pwc_to_brat.py:170
Function
compare
(str1, str2)
dygiepp/scripts/data/genia/resolve_differences.py:23
Function
compare_fields
(row)
scirex_utilities/analyse_pwc_entity_results.py:101
Function
compute_f1
(predicted, gold, matched, m=100)
scirex/metrics/f1.py:15
Method
compute_representations
Run the forward pass for a single document. Important: This function assumes that sentences are going to be passed in in sorted orde
scirex/models/relations/mention_binary_relation.py:37
Method
convert
(x)
dygiepp/dygie/tests/models/relation_test.py:24
Function
convert_ner_to_dict
(ner: Tuple[int, int, str])
scirex/predictors/utils.py:62
Function
convert_ner_to_typed_list
(ner: Dict[Tuple[int, int], str])
scirex/predictors/utils.py:65
Function
convert_row_to_sentences
(row_tup)
scirex_utilities/preprocessing/process_pwc_to_sentences.py:47
Method
count_vocab_items
(self, counter: Dict[str, Dict[str, int]])
dygiepp/dygie/data/fields/adjacency_field_assym.py:84
← previous
next →
401–500 of 614, ranked by callers