├── .gitignore ├── CXRMetric ├── CheXbert │ ├── .gitignore │ ├── LICENSE.pdf │ ├── README.md │ ├── environment.yml │ ├── figures │ │ └── chexbert.png │ ├── out │ │ └── labeled_reports.csv │ ├── requirements.txt │ └── src │ │ ├── Pruning.ipynb │ │ ├── Sentences.ipynb │ │ ├── all_sentences.csv │ │ ├── bert_tokenizer.py │ │ ├── compress.png │ │ ├── compress_sentences.png │ │ ├── constants.py │ │ ├── datasets │ │ ├── impressions_dataset.py │ │ └── unlabeled_dataset.py │ │ ├── encode.py │ │ ├── label.py │ │ ├── labeled_reports.csv │ │ ├── models │ │ ├── bert_encoder.py │ │ └── bert_labeler.py │ │ ├── run_bert.py │ │ ├── sample_reports.csv │ │ ├── sentences.csv │ │ ├── sentences_embed.csv │ │ ├── sim.py │ │ ├── temp.py │ │ └── utils.py ├── __init__.py ├── composite_metric_model.pkl ├── dygiepp │ ├── .dockerignore │ ├── .gitignore │ ├── Dockerfile │ ├── LICENSE │ ├── README.md │ ├── TODO.md │ ├── doc │ │ ├── config.md │ │ ├── contributions.md │ │ ├── data.md │ │ └── model.md │ ├── dygie │ │ ├── __init__.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── dataset_readers │ │ │ │ ├── document.py │ │ │ │ └── dygie.py │ │ │ └── fields │ │ │ │ └── adjacency_field_assym.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── coref.py │ │ │ ├── dygie.py │ │ │ ├── entity_beam_pruner.py │ │ │ ├── events.py │ │ │ ├── ner.py │ │ │ ├── relation.py │ │ │ └── shared.py │ │ ├── predictors │ │ │ ├── __init__.py │ │ │ └── dygie.py │ │ ├── pytest.ini │ │ ├── spacy_interface │ │ │ ├── __init__.py │ │ │ └── spacy_interface.py │ │ ├── tests │ │ │ ├── data │ │ │ │ ├── __init__.py │ │ │ │ ├── annotated_doc_test.py │ │ │ │ ├── collate_test.py │ │ │ │ ├── document_test.py │ │ │ │ ├── dygie_test.py │ │ │ │ └── spacy_interface_test.py │ │ │ ├── fixtures │ │ │ │ ├── ace_event_article.json │ │ │ │ ├── ace_event_coref_article.json │ │ │ │ ├── collate │ │ │ │ │ ├── ace-event │ │ │ │ │ │ ├── dev.json │ │ │ │ │ │ ├── test.json │ │ │ │ │ │ └── train.json │ │ │ │ │ └── scierc │ │ │ │ │ │ ├── dev.json │ │ │ │ │ │ ├── test.json │ │ │ │ │ │ └── train.json │ │ │ │ ├── dygie_test.jsonnet │ │ │ │ ├── dygie_test_full.jsonnet │ │ │ │ ├── multi_dataset │ │ │ │ │ ├── dev.jsonl │ │ │ │ │ ├── test.jsonl │ │ │ │ │ └── train.jsonl │ │ │ │ └── scierc_article.json │ │ │ └── models │ │ │ │ ├── __init__.py │ │ │ │ ├── coref_test.py │ │ │ │ ├── dygie_test.py │ │ │ │ ├── multi_dataset_test.sh │ │ │ │ └── relation_test.py │ │ └── training │ │ │ ├── event_metrics.py │ │ │ ├── f1.py │ │ │ ├── ner_metrics.py │ │ │ └── relation_metrics.py │ ├── notebooks │ │ ├── document.ipynb │ │ └── spacy-interface-example.ipynb │ ├── requirements.txt │ ├── scripts │ │ ├── data │ │ │ ├── ace-event │ │ │ │ ├── collect_ace_event.sh │ │ │ │ ├── event-split │ │ │ │ │ ├── dev.filelist │ │ │ │ │ ├── test.filelist │ │ │ │ │ └── train.filelist │ │ │ │ ├── parse_ace_event.py │ │ │ │ └── requirements.txt │ │ │ ├── ace05 │ │ │ │ ├── common │ │ │ │ │ ├── conll2txt.py │ │ │ │ │ ├── dep2so.prl │ │ │ │ │ ├── fix_sentence_break.py │ │ │ │ │ ├── props_fixed │ │ │ │ │ ├── props_ssplit │ │ │ │ │ └── standoff.py │ │ │ │ ├── get_corenlp.sh │ │ │ │ └── preprocess │ │ │ │ │ ├── ace2ann.py │ │ │ │ │ ├── ace2json.py │ │ │ │ │ ├── run.zsh │ │ │ │ │ ├── split │ │ │ │ │ ├── dev │ │ │ │ │ ├── test │ │ │ │ │ └── train │ │ │ │ │ ├── train_list │ │ │ │ │ └── train_list_fixed │ │ │ ├── chemprot │ │ │ │ ├── 01_rename_test.py │ │ │ │ ├── 02_chemprot_to_input.py │ │ │ │ ├── 03_spot_check.py │ │ │ │ ├── _old_02_chemprot_to_input.py │ │ │ │ └── requirements.txt │ │ │ ├── genia │ │ │ │ ├── align_articles.py │ │ │ │ ├── check_genia_xml_sutd.py │ │ │ │ ├── convert_to_json.py │ │ │ │ ├── exclude.txt │ │ │ │ ├── genia_xml_to_inline_sutd.py │ │ │ │ ├── merge_coref.py │ │ │ │ ├── normalize_genia.py │ │ │ │ ├── resolve_differences.py │ │ │ │ ├── run_genia_sutd.sh │ │ │ │ ├── shared.py │ │ │ │ └── split_folds.py │ │ │ ├── get_ace05.sh │ │ │ ├── get_chemprot.sh │ │ │ ├── get_genia.sh │ │ │ ├── get_mechanic.sh │ │ │ ├── get_scierc.sh │ │ │ └── shared │ │ │ │ ├── check_sentence_length.py │ │ │ │ ├── collate.py │ │ │ │ ├── normalize.py │ │ │ │ └── uncollate.py │ │ ├── debug │ │ │ ├── debug_forward_pass.py │ │ │ └── print_label_namespaces.py │ │ ├── new-dataset │ │ │ ├── annotated_doc.py │ │ │ ├── brat_to_input.py │ │ │ └── format_new_dataset.py │ │ ├── pretrained │ │ │ └── get_dygiepp_pretrained.sh │ │ ├── train.sh │ │ └── tuning │ │ │ └── optuna_train.py │ └── training_config │ │ ├── ace05_event.jsonnet │ │ ├── ace05_event_optuna.jsonnet │ │ ├── ace05_relation.jsonnet │ │ ├── chemprot.jsonnet │ │ ├── genia.jsonnet │ │ ├── genia_lightweight.jsonnet │ │ ├── multi_dataset.jsonnet │ │ ├── scierc.jsonnet │ │ ├── scierc_lightweight.jsonnet │ │ └── template.libsonnet ├── normalizer.pkl ├── radcliq-v1.pkl ├── radgraph_evaluate_model.py ├── radgraph_inference │ ├── __pycache__ │ │ └── inference.cpython-37.pyc │ └── inference.py └── run_eval.py ├── LICENSE ├── README.md ├── config.py ├── dygie ├── __init__.py ├── __pycache__ │ └── __init__.cpython-37.pyc ├── data │ ├── __init__.py │ ├── __pycache__ │ │ └── __init__.cpython-37.pyc │ ├── dataset_readers │ │ ├── __pycache__ │ │ │ ├── document.cpython-37.pyc │ │ │ └── dygie.cpython-37.pyc │ │ ├── document.py │ │ └── dygie.py │ └── fields │ │ ├── __pycache__ │ │ └── adjacency_field_assym.cpython-37.pyc │ │ └── adjacency_field_assym.py ├── models │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── coref.cpython-37.pyc │ │ ├── dygie.cpython-37.pyc │ │ ├── entity_beam_pruner.cpython-37.pyc │ │ ├── events.cpython-37.pyc │ │ ├── ner.cpython-37.pyc │ │ ├── relation.cpython-37.pyc │ │ └── shared.cpython-37.pyc │ ├── coref.py │ ├── dygie.py │ ├── entity_beam_pruner.py │ ├── events.py │ ├── ner.py │ ├── relation.py │ └── shared.py ├── predictors │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ └── dygie.cpython-37.pyc │ └── dygie.py ├── pytest.ini ├── spacy_interface │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ └── spacy_interface.cpython-37.pyc │ └── spacy_interface.py ├── tests │ ├── data │ │ ├── __init__.py │ │ ├── annotated_doc_test.py │ │ ├── collate_test.py │ │ ├── document_test.py │ │ ├── dygie_test.py │ │ └── spacy_interface_test.py │ ├── fixtures │ │ ├── ace_event_article.json │ │ ├── ace_event_coref_article.json │ │ ├── collate │ │ │ ├── ace-event │ │ │ │ ├── dev.json │ │ │ │ ├── test.json │ │ │ │ └── train.json │ │ │ └── scierc │ │ │ │ ├── dev.json │ │ │ │ ├── test.json │ │ │ │ └── train.json │ │ ├── dygie_test.jsonnet │ │ ├── dygie_test_full.jsonnet │ │ ├── multi_dataset │ │ │ ├── dev.jsonl │ │ │ ├── test.jsonl │ │ │ └── train.jsonl │ │ └── scierc_article.json │ └── models │ │ ├── __init__.py │ │ ├── coref_test.py │ │ ├── dygie_test.py │ │ ├── multi_dataset_test.sh │ │ └── relation_test.py └── training │ ├── __pycache__ │ ├── event_metrics.cpython-37.pyc │ ├── f1.cpython-37.pyc │ ├── ner_metrics.cpython-37.pyc │ └── relation_metrics.cpython-37.pyc │ ├── 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