KarelDO/BioDEX
BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.
Pairs 256k+ expert-annotated drug safety reports with PubMed articles (19k full-text, 65k abstracts) to enable structured adverse event extraction. Built on encoder-decoder architectures (FLAN-T5) fine-tuned for report generation from clinical text, with modular Python objects for seamless data manipulation and published benchmark datasets (BioDEX-ICSR, BioDEX-Reactions) on Hugging Face. Supports both full ICSR report extraction and reaction-only classification tasks via in-context learning approaches.
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Jupyter Notebook
License
MIT
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Last pushed
Jan 29, 2024
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