{"data":{"kind":"file","path":"README.md","version_id":"k5ffnwtj5l6rt9pavom0hntr","entry":{"name":"README.md","path":"README.md","is_directory":false,"size":3157,"modified_at":"2026-01-14T14:43:38.835000","content_hash":"4a9c82cb1b7dd2b05ff5f259a91c4314d766dc6544e43e39b189b86f06fdbab1"},"entries":[],"content":"# OpenMed BioASQ Environment\n\nBiomedical question answering environment for RL fine-tuning using the PubMedQA dataset.\n\n## Task Description\n\nGiven a biomedical research question and PubMed abstract context, classify the answer:\n\n| Class | Label | Description |\n|-------|-------|-------------|\n| A | YES | Evidence supports an affirmative answer to the research question |\n| B | NO | Evidence supports a negative answer to the research question |\n| C | MAYBE | Evidence is inconclusive, unclear, or insufficient |\n\n## Dataset\n\n- **Source**: PubMedQA (Jin et al., EMNLP 2019)\n- **HuggingFace**: [qiaojin/PubMedQA](https://huggingface.co/datasets/qiaojin/PubMedQA)\n- **Training**: pqa_artificial - 211,269 artificially generated QA instances\n- **Evaluation**: pqa_labeled - 1,000 expert-annotated instances\n- **Domain**: Biomedical research from PubMed abstracts\n\n## Reward Structure\n\n| Component | Weight | Description |\n|-----------|--------|-------------|\n| Accuracy | 80% | Exact match on answer classification (A-C) |\n| Thinking | 15% | Quality of reasoning in `<think>` tags |\n| Format | 5% | Proper `\\\\boxed{}` answer format |\n\n## Example\n\n**Input:**\n```\nResearch Question: Do mitochondria play a role in remodelling lace plant leaves during programmed cell death?\n\nPubMed Abstract:\nBACKGROUND: Programmed cell death (PCD) is the regulated death of cells within an organism. The lace plant (Aponogeton madagascariensis) produces perforations in its leaves through PCD...\n\nRESULTS: The results showed that mitochondria were responsible for some of the H2O2 production during PCD. Mitochondrial dynamics changed significantly during PCD, with elongated mitochondria present in early stages and fragmented mitochondria in later stages...\n\nCONCLUSIONS: This study is the first to document mitochondrial dynamics during PCD in vivo. The results suggest that mitochondria play an active role in cell death...\n```\n\n**Expected Output:**\n```\n<think>\nThe research question asks whether mitochondria play a role in programmed cell death during lace plant leaf remodelling. The abstract clearly states that \"mitochondria were responsible for some of the H2O2 production during PCD\" and shows that \"mitochondrial dynamics changed significantly during PCD.\" The conclusion explicitly states that \"mitochondria play an active role in cell death.\" This is direct evidence supporting an affirmative answer to the research question.\n</think>\n\\\\boxed{A}\n```\n\n## Usage\n\n```python\nfrom OpenMed_BioASQ import load_environment\n\nenv = load_environment()\n```\n\n## Citation\n\n```bibtex\n@inproceedings{jin-etal-2019-pubmedqa,\n    title = \"{P}ub{M}ed{QA}: A Dataset for Biomedical Research Question Answering\",\n    author = \"Jin, Qiao  and\n      Dhingra, Bhuwan  and\n      Liu, Zhengping  and\n      Cohen, William  and\n      Lu, Xinghua\",\n    booktitle = \"Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP)\",\n    year = \"2019\",\n    url = \"https://aclanthology.org/D19-1259\",\n    doi = \"10.18653/v1/D19-1259\",\n    pages = \"2567--2577\",\n}\n```\n\n## License\n\nMIT\n","encoding":"utf-8","truncated":false,"total_bytes":3157},"status":null}