├── .gitignore ├── LICENSE.txt ├── README.md ├── blue ├── __init__.py ├── bert │ ├── __init__.py │ ├── create_cdr_bert.py │ ├── create_chemprot_bert.py │ ├── create_clefe_bert.py │ ├── create_ddi_bert.py │ ├── create_i2b2_bert.py │ └── create_mednli_bert.py ├── create_bert.sh ├── create_gs.sh ├── eval_hoc.py ├── eval_mednli.py ├── eval_ner.py ├── eval_rel.py ├── eval_sts.py ├── ext │ ├── __init__.py │ ├── data_structure.py │ ├── pmetrics.py │ ├── preprocessing.py │ ├── pstring.py │ └── pubtator.py └── gs │ ├── __init__.py │ ├── create_cdr_test_gs.py │ ├── create_chemprot_test_gs.py │ ├── create_clefe_test_gs.py │ ├── create_ddi_test_gs.py │ ├── create_hoc.py │ ├── create_i2b2_test_gs.py │ └── create_mednli_test_gs.py ├── blue_plus ├── README.md ├── __init__.py ├── dataset.py └── example_dataset │ ├── __init__.py │ ├── biosses.yml │ ├── biosses_dataset.py │ └── requirements.txt └── requirements.txt /.gitignore: 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