├── QueryExtraction ├── .vscode │ └── settings.json ├── __init__.py ├── extraction.py ├── gensim_test_query.py ├── keybert_test_query.py ├── output.txt ├── rake_test_query.py ├── rakun_test_query.py ├── readme.md ├── spacy_test_query.py └── yake_test_query.py ├── README.md ├── allennlp ├── elmo-ner.py ├── loader.py └── sentiment.py ├── collated_tasks ├── README.md ├── non_mimic │ ├── deidentification │ │ ├── README.md │ │ ├── test.info │ │ ├── test.phi │ │ ├── test.res │ │ └── test.text │ ├── inference │ │ ├── MIMIC_NLI_tutorial.ipynb │ │ └── README.md │ └── question_answering │ │ ├── HeadQA_tutorial.ipynb │ │ ├── MedicalQADataset.ipynb │ │ └── readme.MD └── tasks │ ├── README.md │ ├── get_abbreviations.py │ ├── get_hyponyms.py │ ├── get_linked_entities.py │ ├── get_named_entities.py │ ├── get_translation.py │ └── utils │ ├── README.md │ ├── get_clusters.py │ ├── get_representations.py │ ├── get_sentences.py │ ├── get_similar_documents.py │ └── get_text_from_csv.py ├── ehrkit.jpg ├── ehrkit ├── .gitignore ├── README.md ├── __init__.py ├── classes.py ├── ehrkit.py └── solr_lib.py ├── environment.yml ├── extractiveSummarization ├── README.md ├── generate_summaries.py ├── requirements.txt ├── rouge_scores.py ├── scripts │ ├── bert_summaries.py │ └── noteevents_lexrank.py ├── setup.py ├── summarization_tests.py └── summarizers │ ├── __init__.py │ ├── evaluate │ ├── __init__.py │ └── folder2rouge.py │ └── lexrank.py ├── mimic_icd9_coding ├── .gitignore ├── coding_pipeline.py └── utils │ ├── BERTRunner.py │ ├── classifier.py │ ├── feature_extractor.py │ ├── mimic_data_preparation.py │ ├── preproc.py │ ├── preprocessing.py │ └── regressor.py ├── pubmed ├── README.md ├── download_pubmed.sh └── parse_articles.py ├── requirements.txt ├── summarization ├── pubmed_summarization │ ├── 10_exs_intro │ │ ├── test_files.txt │ │ └── training_files.txt │ ├── 5_exs_intro │ │ ├── nb │ │ │ ├── ROUGE.txt │ │ │ ├── feature_vecs.json │ │ │ ├── test_json │ │ │ │ └── PMC7400745.json │ │ │ └── test_summary │ │ │ │ └── PMC7400745.sum │ │ ├── test_files.txt │ │ └── training_files.txt │ ├── README.md │ ├── get_pubmed_nb_data.py │ └── pubmed_naive_bayes.py └── rouge_git │ ├── rouge.py │ └── rouge_score.py ├── tests ├── .gitignore ├── README.md ├── all_tests.py ├── pubmed_tests.py ├── test_functions_no_output.ipynb └── tests.py ├── tutorials ├── README.md ├── mimic_classifier.ipynb ├── mimic_classifier.py ├── naiveBayes.ipynb ├── query_extractor.ipynb └── run_tests.ipynb └── wrapper_functions ├── EHRKit.py ├── EHRKit_tutorials.ipynb ├── EHRLogo.png ├── README.md ├── demo.py ├── documentation.md ├── medspacy_functions.py ├── multi_doc_functions.py ├── scispacy_functions.py ├── stanza_functions.py ├── summarization_functions.py ├── transformer_functions.py └── utils.py /QueryExtraction/.vscode/settings.json: -------------------------------------------------------------------------------- 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