├── .github └── workflows │ └── codeql-analysis.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── SECURITY.md ├── SUPPORT.md ├── data ├── BC5CDR │ └── raw │ │ ├── BC5CDR_Evaluation-0.0.3 │ │ ├── BioC.dtd │ │ ├── DISCLAIMER.txt │ │ ├── bc5cdr_eval.jar │ │ ├── data │ │ │ ├── gold │ │ │ │ ├── CDR_sample.gold.BioC.xml │ │ │ │ └── CDR_sample.gold.PubTator │ │ │ └── test │ │ │ │ ├── CDR_sample.old.test.CID.BioC.xml │ │ │ │ ├── CDR_sample.old.test.DNER.BioC.xml │ │ │ │ ├── CDR_sample.test.CID.BioC.xml │ │ │ │ ├── CDR_sample.test.CID.PubTator │ │ │ │ ├── CDR_sample.test.DNER.BioC.xml │ │ │ │ ├── CDR_sample.test.DNER.PubTator │ │ │ │ ├── my.txt │ │ │ │ └── rment.py │ │ ├── eval_id.sh │ │ ├── eval_mention.sh │ │ ├── eval_relation.sh │ │ ├── my.txt │ │ └── readme.txt │ │ ├── CDR_Data │ │ ├── BC5CDR.corpus.pdf │ │ ├── BC5CDR.overview.pdf │ │ ├── BC5CDR.presentation.pdf │ │ ├── CDR.Corpus.v010516 │ │ │ ├── CDR_DevelopmentSet.BioC.xml │ │ │ ├── CDR_DevelopmentSet.PubTator.txt │ │ │ ├── CDR_TestSet.BioC.xml │ │ │ ├── CDR_TestSet.PubTator.txt │ │ │ ├── CDR_TrainingSet.BioC.xml │ │ │ └── CDR_TrainingSet.PubTator.txt │ │ ├── DNorm.TestSet │ │ │ ├── TestSet.DNorm.BioC.xml │ │ │ └── TestSet.DNorm.PubTator.txt │ │ ├── README.txt │ │ └── tmChem.TestSet │ │ │ ├── TestSet.tmChem.BioC.xml │ │ │ └── TestSet.tmChem.PubTator.txt │ │ ├── test.entities.json │ │ ├── test.json │ │ ├── train.entities.json │ │ ├── train.json │ │ ├── valid.entities.json │ │ └── valid.json ├── BioGPT-Large │ ├── bpecodes │ └── dict.txt ├── BioGPT │ ├── bpecodes │ └── dict.txt ├── DDI │ └── raw │ │ ├── test.json │ │ ├── train.json │ │ └── valid.json ├── HoC │ └── raw │ │ ├── test.tsv │ │ ├── train.tsv │ │ └── valid.tsv ├── KD-DTI │ └── raw │ │ ├── test.json │ │ ├── train.json │ │ └── valid.json ├── biogpt_large_bpecodes ├── biogpt_large_dict.txt ├── bpecodes └── dict.txt ├── examples ├── DC-HoC │ ├── README.md │ ├── hard_match_evaluation.py │ ├── infer.sh │ ├── postprocess.py │ ├── preprocess.sh │ ├── rebuild_data.py │ └── train.sh ├── QA-PubMedQA │ ├── README.md │ ├── hard_match_evaluation.py │ ├── infer.sh │ ├── infer_large.sh │ ├── postprocess.py │ ├── preprocess.sh │ ├── preprocess_large.sh │ └── rebuild_data.py ├── RE-BC5CDR │ ├── README.md │ ├── infer.sh │ ├── postprocess.py │ ├── preprocess.sh │ ├── rebuild_data.py │ └── train.sh ├── RE-DDI │ ├── README.md │ ├── hard_match_evaluation.py │ ├── infer.sh │ ├── postprocess.py │ ├── preprocess.sh │ ├── rebuild_data.py │ └── train.sh ├── RE-DTI │ ├── README.md │ ├── hard_match_evaluation.py │ ├── infer.sh │ ├── postprocess.py │ ├── preprocess.sh │ ├── rebuild_data.py │ └── train.sh └── text-generation │ ├── README.md │ └── interactive.py ├── inference.py ├── requirements.txt ├── scripts └── average_checkpoints.py └── src ├── __init__.py ├── constrained_generator.py ├── language_model_prompt_dataset.py ├── language_modeling_prompt.py └── transformer_lm_prompt.py /.github/workflows/codeql-analysis.yml: 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