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github.com/allenai/SciREX
/ types & classes
Types & classes
84 in github.com/allenai/SciREX
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Functions
614
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Types & classes
84
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Endpoints
2
↓ 9 callers
Class
Token
dygiepp/dygie/data/dataset_readers/data_structures.py:159
↓ 7 callers
Class
Span
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:53
↓ 6 callers
Class
MultiLabelField
A `MultiLabelField` is an extension of the :class:`LabelField` that allows for multiple labels. It is particularly useful in multi-label clas
scirex/data/dataset_readers/multi_label_field.py:14
↓ 5 callers
Class
Annotation
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:80
↓ 5 callers
Class
BinaryThresholdF1
F1 measure optimised for validation set
scirex/metrics/thresholding_f1_metric.py:12
↓ 5 callers
Class
MissingDict
If key isn't there, returns default value. Like defaultdict, but it doesn't store the missing keys that were queried.
dygiepp/dygie/data/dataset_readers/ie_json.py:29
↓ 5 callers
Class
Span
dygiepp/dygie/data/dataset_readers/data_structures.py:136
↓ 3 callers
Class
Entity
dygiepp/scripts/data/ace-event/parse_ace_event.py:61
↓ 3 callers
Class
NER
dygiepp/dygie/data/dataset_readers/data_structures.py:196
↓ 3 callers
Class
Pruner
This module scores and prunes items in a list using a parameterised scoring function and a threshold. Parameters ---------- scor
dygiepp/dygie/models/entity_beam_pruner.py:27
↓ 3 callers
Class
Relation
dygiepp/scripts/data/ace-event/parse_ace_event.py:77
↓ 2 callers
Class
AdjacencyFieldAssym
There are cases where we need to express adjacency relations between elements in two different fields - for instance a TextField and a SpanFi
dygiepp/dygie/data/fields/adjacency_field_assym.py:16
↓ 2 callers
Class
Cluster
dygiepp/dygie/data/dataset_readers/data_structures.py:281
↓ 2 callers
Class
Doc
dygiepp/scripts/data/ace-event/parse_ace_event.py:209
↓ 2 callers
Class
Events
dygiepp/dygie/data/dataset_readers/data_structures.py:245
↓ 2 callers
Class
Relation
dygiepp/dygie/data/dataset_readers/data_structures.py:210
↓ 2 callers
Class
Token
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:29
↓ 1 callers
Class
Argument
dygiepp/dygie/data/dataset_readers/data_structures.py:178
↓ 1 callers
Class
ArgumentStats
Compute the fraction of predicted event arguments that are associated with multiple triggers.
dygiepp/dygie/training/event_metrics.py:103
↓ 1 callers
Class
Article
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:374
↓ 1 callers
Class
BatchIterator
For multi-task IE, we want the training instances in a batch to be successive sentences from the same document. Otherwise the coreference lab
dygiepp/dygie/data/iterators/batch_iterator.py:17
↓ 1 callers
Class
CandidateRecall
Computes relation candidate recall.
dygiepp/dygie/training/relation_metrics.py:43
↓ 1 callers
Class
ClusterMember
dygiepp/dygie/data/dataset_readers/data_structures.py:304
↓ 1 callers
Class
Coref
Represents a single coreference.
dygiepp/scripts/data/genia/merge_coref.py:55
↓ 1 callers
Class
Corefs
Holds all corefs and represents relations between them.
dygiepp/scripts/data/genia/merge_coref.py:109
↓ 1 callers
Class
Document
dygiepp/dygie/data/dataset_readers/data_structures.py:32
↓ 1 callers
Class
Document
dygiepp/scripts/data/ace-event/parse_ace_event.py:266
↓ 1 callers
Class
DocumentIterator
For multi-task IE, we want the training instances in a batch to be successive sentences from the same document. Otherwise the coreference lab
dygiepp/dygie/data/iterators/document_iterator.py:15
↓ 1 callers
Class
Entry
dygiepp/scripts/data/ace-event/parse_ace_event.py:144
↓ 1 callers
Class
Event
dygiepp/dygie/data/dataset_readers/data_structures.py:224
↓ 1 callers
Class
Event
dygiepp/scripts/data/ace-event/parse_ace_event.py:111
↓ 1 callers
Class
EventArgument
dygiepp/scripts/data/ace-event/parse_ace_event.py:105
↓ 1 callers
Class
EventMetrics
Computes precision, recall, and micro-averaged F1 for triggers and arguments.
dygiepp/dygie/training/event_metrics.py:25
↓ 1 callers
Class
EventTrigger
dygiepp/scripts/data/ace-event/parse_ace_event.py:99
↓ 1 callers
Class
GrobidBibliographyEntry
scirex_utilities/preprocessing/grobid_util.py:6
↓ 1 callers
Class
IEJsonReader
Reads a single JSON-formatted file. This is the same file format as used in the scierc, but is preprocessed
dygiepp/dygie/data/dataset_readers/ie_json.py:121
↓ 1 callers
Class
MultiTokenTrigerException
dygiepp/scripts/data/ace-event/parse_ace_event.py:26
↓ 1 callers
Class
NAryRelationMetrics
scirex/metrics/n_ary_relation_metrics.py:10
↓ 1 callers
Class
NERMetrics
Computes precision, recall, and micro-averaged F1 from a list of predicted and gold labels.
dygiepp/dygie/training/ner_metrics.py:8
↓ 1 callers
Class
OneHotEncoder
A one-hot encoder class. Only a module in the trivial sense.
dygiepp/dygie/models/one_hot.py:16
↓ 1 callers
Class
RelationArgument
dygiepp/scripts/data/ace-event/parse_ace_event.py:71
↓ 1 callers
Class
RelationMetrics
Computes precision, recall, and micro-averaged F1 from a list of predicted and gold spans.
dygiepp/dygie/training/relation_metrics.py:8
↓ 1 callers
Class
Result
scirex_utilities/result_from_pwc_table.py:8
↓ 1 callers
Class
ScirexFullReader
scirex/data/dataset_readers/scirex_full_reader.py:122
↓ 1 callers
Class
Section
scirex_utilities/preprocessing/grobid_util.py:49
↓ 1 callers
Class
Sentence
dygiepp/dygie/data/dataset_readers/data_structures.py:83
↓ 1 callers
Class
Sentence
dygiepp/scripts/data/genia/genia_xml_to_inline_sutd.py:130
↓ 1 callers
Class
SpanBasedF1Measure
Copied (Span Based F1 Measure from allennlp)
scirex/metrics/span_f1_metrics.py:22
↓ 1 callers
Class
TestDyGIE
dygiepp/dygie/tests/scripts/m2.py:14
↓ 1 callers
Class
Trigger
dygiepp/dygie/data/dataset_readers/data_structures.py:169
↓ 1 callers
Class
WhitespaceTokenizer
scirex_utilities/convert_brat_annotations_to_json.py:22
Class
AceException
dygiepp/scripts/data/ace-event/parse_ace_event.py:18
Class
BatchIterator
scirex/data/iterators/batch_iterator.py:20
Class
BertCoreference
scirex/models/coreference/bert_coreference.py:15
Class
BucketSampleIterator
An iterator which by default, pads batches with respect to the maximum input lengths `per batch`. Additionally, you can provide a list of fie
scirex/data/iterators/sampled_iterator.py:45
Class
CorefResolver
TODO(dwadden) document correctly. Parameters ---------- mention_feedforward : ``FeedForward`` This feedforward network is ap
dygiepp/dygie/models/coref.py:23
Class
CrossSentenceException
dygiepp/scripts/data/ace-event/parse_ace_event.py:22
Class
Dataset
dygiepp/dygie/data/dataset_readers/data_structures.py:19
Class
DoctaetModel
scirex/models/doctaet.py:15
Class
DoctaetReader
scirex/data/dataset_readers/doctaet_reader.py:57
Class
Dummy
Placeholder class to avoid wasting model parameters on stuff that we don't use.
dygiepp/dygie/models/dummy.py:1
Class
DyGIE
TODO(dwadden) document me. Parameters ---------- vocab : ``Vocabulary`` text_field_embedder : ``TextFieldEmbedder`` Used
dygiepp/dygie/models/dygie.py:28
Class
EventExtractor
Event extraction for DyGIE.
dygiepp/dygie/models/events.py:34
Class
GELU
scirex/models/gelu.py:5
Class
JointMetrics
Right now, counts how many event predictions are valid. I.e. the trigger / argument and argument / ner labels are compatible.
dygiepp/dygie/training/joint_metrics.py:13
Class
MultiTaskIterator
To use when we're co-training on Ontonotes and ACE.
dygiepp/dygie/data/iterators/multitask_iterator.py:24
Class
NERTagger
Named entity recognition module of DyGIE model. Parameters ---------- mention_feedforward : ``FeedForward`` This feedforward
dygiepp/dygie/models/ner.py:17
Class
NERTagger
scirex/models/ner/ner_crf_tagger.py:16
Class
NumpyEncoder
scirex_utilities/json_utilities.py:4
Class
PretrainedBertEmbedder
Parameters ---------- pretrained_model: ``str`` Either the name of the pretrained model to use (e.g. 'bert-base-uncased'),
dygiepp/dygie/models/bert_token_embedder_modified.py:8
Class
PretrainedBertEmbedder
Parameters ---------- pretrained_model: ``str`` Either the name of the pretrained model to use (e.g. 'bert-base-uncased'),
scirex/models/bert_token_embedder_modified.py:8
Class
RelationExtractor
Relation extraction module of DyGIE model.
dygiepp/dygie/models/relation.py:24
Class
RelationExtractor
scirex/models/relations/entity_relation.py:22
Class
RelationExtractor
scirex/models/relations/mention_binary_relation.py:17
Class
ScirexCoreferenceEvalReader
scirex/data/dataset_readers/coreference_eval_reader.py:17
Class
ScirexCoreferenceTrainReader
scirex/data/dataset_readers/coreference_train_reader.py:18
Class
ScirexModel
scirex/models/scirex_model.py:25
Class
SpanClassifier
scirex/models/span_classifiers/span_classifier.py:20
Class
SpanProp
dygiepp/dygie/models/span_prop.py:19
Class
TestCoref
dygiepp/dygie/tests/models/coref_test.py:14
Class
TestDyGIE
dygiepp/dygie/tests/models/dygie_test.py:10
Class
TestIEJsonReader
Read in data and do some spot-checks.
dygiepp/dygie/tests/data/ie_json_test.py:15
Class
TestRelation
dygiepp/dygie/tests/models/relation_test.py:16
Class
TokSpan
dygiepp/scripts/data/ace-event/parse_ace_event.py:35