├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .gitmodules ├── CONTRIBUTORS.md ├── LICENSE ├── README.md ├── derek-demo ├── __init__.py ├── processors │ └── app.py ├── requirements.txt └── ui │ ├── app.py │ └── templates │ ├── index.html │ ├── layout.html │ └── news.html ├── derek ├── __init__.py ├── common │ ├── __init__.py │ ├── evaluation │ │ ├── __init__.py │ │ ├── helper.py │ │ ├── metrics.py │ │ └── results_controllers.py │ ├── feature_computation │ │ ├── __init__.py │ │ ├── computers.py │ │ └── manager.py │ ├── feature_extraction │ │ ├── __init__.py │ │ ├── continuous_converters.py │ │ ├── converters.py │ │ ├── embeddings.py │ │ ├── factory.py │ │ ├── factory_helper.py │ │ ├── feature_extractor.py │ │ ├── features_meta.py │ │ ├── gazetteer_feature_extractor.py │ │ ├── helper.py │ │ ├── ne_feature_extractor.py │ │ └── token_position_feature_extractor.py │ ├── helper.py │ ├── hooks.py │ ├── io.py │ ├── logger.py │ ├── nn │ │ ├── __init__.py │ │ ├── aggregation_strategies.py │ │ ├── batchers.py │ │ ├── features_lookups.py │ │ ├── graph_factory.py │ │ ├── tf_io.py │ │ ├── tf_layers.py │ │ ├── tf_losses.py │ │ ├── tf_trainers.py │ │ ├── tf_utils.py │ │ ├── trainers.py │ │ └── transformer.py │ └── vectorizers.py ├── coref │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ ├── chains_collection.py │ │ ├── conll_serializer.py │ │ ├── model.py │ │ └── readers.py │ ├── feature_extraction │ │ ├── __init__.py │ │ ├── entity_feature_extractor.py │ │ ├── factory.py │ │ ├── feature_extractor.py │ │ ├── heuristics.py │ │ └── sampling_strategies.py │ └── nn │ │ ├── __init__.py │ │ ├── classifier.py │ │ └── graph_factory.py ├── data │ ├── __init__.py │ ├── babylondigger_processor.py │ ├── collapser_helper.py │ ├── entities_collapser.py │ ├── helper.py │ ├── model.py │ ├── nltk_segmenter.py │ ├── processing_helper.py │ ├── readers.py │ ├── sdp_extraction.py │ ├── texterra_processing.py │ ├── transformers.py │ └── udpipe_processor.py ├── evaluators.py ├── managers.py ├── ner │ ├── __init__.py │ ├── chained_ner_classifier.py │ ├── evaluation.py │ ├── feature_extraction │ │ ├── __init__.py │ │ ├── augmentations.py │ │ ├── feature_extractor.py │ │ └── labelling_strategies.py │ ├── nn │ │ ├── __init__.py │ │ ├── classifier.py │ │ └── graph_factory.py │ └── post_processing │ │ ├── __init__.py │ │ └── process_similar_entities.py ├── net │ ├── __init__.py │ ├── evaluation.py │ ├── feature_extraction │ │ ├── __init__.py │ │ └── feature_extractor.py │ └── nn │ │ ├── __init__.py │ │ ├── classifier.py │ │ └── graph_factory.py ├── preprocessors.py ├── rel_ext │ ├── __init__.py │ ├── evaluation.py │ ├── feature_extraction │ │ ├── __init__.py │ │ ├── factory.py │ │ ├── feature_extractor.py │ │ ├── feature_meta.py │ │ ├── sampling_strategies.py │ │ └── spans_feature_extractor.py │ ├── nn │ │ ├── __init__.py │ │ ├── classifier.py │ │ └── graph_factory.py │ └── syntactic │ │ ├── __init__.py │ │ ├── parser │ │ ├── __init__.py │ │ └── feature_extraction │ │ │ ├── __init__.py │ │ │ ├── factory.py │ │ │ ├── feature_extractor.py │ │ │ └── sampling_strategies.py │ │ └── shortest_path │ │ ├── __init__.py │ │ ├── feature_extraction │ │ ├── __init__.py │ │ └── feature_extractor.py │ │ └── nn │ │ ├── __init__.py │ │ └── graph_factory.py └── transformers.py ├── requirements.txt ├── tests ├── __init__.py ├── common │ ├── __init__.py │ ├── batchers.py │ ├── converters.py │ ├── evaluation.py │ └── results_controllers.py ├── data │ ├── embeddings │ │ ├── glove.txt │ │ └── w2v.txt │ ├── feature_extractor │ │ ├── feature_extraction_result.json │ │ ├── gazetteer.txt │ │ ├── geo_bact_replacement.json │ │ └── props.json │ └── parser_feature_extractor │ │ ├── feature_extraction_result.json │ │ ├── geo_bact_replacement.json │ │ ├── pos_sampling_feature_extraction_result.json │ │ ├── props.json │ │ └── props_pos_sampling.json ├── datamodel │ ├── __init__.py │ ├── chain_collection.py │ ├── datamodel.py │ └── easy_first_mention.py ├── feature_extraction │ ├── __init__.py │ ├── candidates_extraction.py │ ├── coref_sampling_strategy.py │ ├── embeddings.py │ ├── feature_computation.py │ ├── feature_extraction.py │ ├── grouping_feature_extractor.py │ ├── ner_labelling_strategies.py │ └── root_path_extraction.py ├── managers │ ├── __init__.py │ ├── coref_manager.py │ ├── nerc_managers.py │ └── rel_ext_manager.py ├── processing │ ├── __init__.py │ ├── align_entities.py │ ├── collapse_intersecting.py │ ├── entities_collapser.py │ ├── process_similar_entities.py │ ├── processing.py │ ├── sentence_adjustment.py │ ├── tasks_preprocessing.py │ └── unquote_augmentor.py ├── run_unit_tests.sh ├── test_helper.py └── tools_tests │ ├── __init__.py │ ├── generate_dataset_argparser.py │ └── props_searching.py └── tools ├── __init__.py ├── common ├── __init__.py ├── argparsers.py ├── bllip_processor.py ├── experiment_runner.py ├── helper.py ├── read_conllu.py └── setup_variables.sh ├── coref ├── __init__.py ├── coref_trainer.py ├── generate_dataset.sh ├── param_search.py ├── setup.sh └── test.sh ├── cross-validation.sh ├── doc_converters ├── __init__.py ├── digger_converter.py └── genia_to_ud.py ├── evaluate.py ├── factrueval ├── __init__.py └── factrueval_submit.py ├── gazetteer_lemmatizer.py ├── generate_brat_dataset.sh ├── generate_dataset.py ├── holdout.sh ├── param_search.py ├── preprocess_dataset.py ├── process_after_segment.py ├── pubmed_extraction ├── __init__.py ├── conllu_parse.py └── parse_xmls.py ├── rel_ext ├── __init__.py ├── bionlp_submit.py ├── generate_dataset.sh └── setup_variables.sh ├── requirements.txt ├── segment.py └── server.py /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ispras-texterra/derek/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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