├── .gitignore ├── LICENSE ├── baseline ├── __init__.py ├── baseline_config.py ├── data_utils.py ├── experiment.py ├── feature_generation.py ├── readme.md ├── requirements.txt └── run.sh ├── config_experiment_sample.json ├── readme.md ├── requirements.txt ├── run.sh ├── run_batch_prediction.sh ├── run_json.sh ├── sample_data ├── dev.tsv ├── test.tsv └── train.tsv └── src ├── __init__.py ├── batch_prediction.py ├── brat_eval.py ├── config.py ├── data_processing ├── __init__.py ├── data_format_conf.py ├── io_utils.py ├── post_processing.py ├── preprocessing-batch.ipynb └── preprocessing.ipynb ├── data_utils.py ├── model_utils.py ├── models.py ├── relation_extraction.py ├── relation_extraction_json.py ├── run_app.py ├── task.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction/HEAD/.gitignore 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