{"id":48436463,"url":"https://github.com/dmis-lab/bc9-medhop-qa","last_synced_at":"2026-04-06T13:03:07.340Z","repository":{"id":340501294,"uuid":"1165874520","full_name":"dmis-lab/bc9-medhop-qa","owner":"dmis-lab","description":null,"archived":false,"fork":false,"pushed_at":"2026-02-25T06:54:38.000Z","size":369,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-02-25T10:45:43.767Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dmis-lab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-02-24T16:31:28.000Z","updated_at":"2026-02-25T06:17:12.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/dmis-lab/bc9-medhop-qa","commit_stats":null,"previous_names":["dmis-lab/bc9-medhop-qa"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/dmis-lab/bc9-medhop-qa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmis-lab%2Fbc9-medhop-qa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmis-lab%2Fbc9-medhop-qa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmis-lab%2Fbc9-medhop-qa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmis-lab%2Fbc9-medhop-qa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dmis-lab","download_url":"https://codeload.github.com/dmis-lab/bc9-medhop-qa/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmis-lab%2Fbc9-medhop-qa/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31473275,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-06T08:36:52.050Z","status":"ssl_error","status_checked_at":"2026-04-06T08:36:51.267Z","response_time":112,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-04-06T13:03:03.478Z","updated_at":"2026-04-06T13:03:07.336Z","avatar_url":"https://github.com/dmis-lab.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# DMIS at BioCreative IX MedHopQA Track\n\nThis repository contains the code implementation of our methodology for generating answers to multi-step reasoning questions in the healthcare and biomedical domains, as introduced in the BioCreative IX MedhopQA Challenge.\n\n## Overview \u0026 Quick Links\n\n* **Task description**: The MedHopQA task requires the generation of answers to multi-step reasoning questions in the healthcare and biomedical domains. For detailed information, please visit to the official BC9 website (**[link](https://www.ncbi.nlm.nih.gov/research/bionlp/medhopqa)**) or see the overview paper (**[PDF](https://zenodo.org/records/16992154)**).\n* **System description**: Please check out our paper listed below.\n  * **[This paper](https://zenodo.org/records/16875789)** provides a brief description of our system.\n\n## Requirements\nThis repository has been tested on `Python==3.10`, `PyTorch==2.10`, and `Transformers==4.57.6`. See the `requirements.txt` file and instructions below.\n\n```bash\n# Download this project\ngit clone https://github.com/dmis-lab/bc9-medhop-qa.git\ncd bc9-medhop-qa\n\n# Create a conda environment\nconda create -n bc9 python=3.10\nconda activate bc9\n\n# Install all requirements\npip install -r requirements.txt\n```\n\n## File Structure\n\n```bash\nbc9-medhop-qa\n├── core\n│   ├── llm\n│   │   ├── gemini.py\n│   │   ├── gpt_4o.py\n│   │   ├── gpt_5_2.py\n│   │   └── o3.py\n│   ├── medhop_dataset.py\n│   ├── reranker\n│   │   ├── medcpt_reranker.py\n│   │   ├── qwen3_reranker.py\n│   │   └── reranker_base.py\n│   └── retriever\n│       ├── dense_wikipedia.py\n│       ├── elastic_wikipedia.py\n│       └── retriever_base.py\n├── data\n│   └── MedHopQA_Test_Dataset.csv\n├── decision_making.py\n├── output\n│   ├── result_decision_making.csv\n│   ├── result_q2d.csv\n│   ├── result_rag.csv\n│   ├── result_rationale.csv\n│   └── result_web_search.csv\n├── prompt\n│   ├── decision_making.py\n│   ├── query2doc.py\n│   ├── rationale.py\n│   └── web_search.py\n├── query2doc.py\n├── rationale.py\n├── README.md\n├── utils\n│   ├── merge_csvs.py\n│   └── normalize_long_answer.py\n└── web_search.py\n```\n\n## Excecution\n\n```bash\n# 1. Run Query2Doc\npython query2doc.py\n\n# 2. Run Rationale\npython ratinoale.py\n\n# 3. Run Web Search\npython web_search.py\n\n# 4. Merge outputs\npython utils/merge_csvs.py\n\n# 5. Run decision-making\npython decision-making.py\n\n```\n\n* Note: The Elasticsearch server and Wikipedia embeddings required for retrieval must be configured independently.\n\n## References\n\nPlease cite the papers below if you use our code, method, or if your work is inspired by ours.\n\n```bash\n@inproceedings{jung2025dmis,\n  author    = {Jung, J. and Hwang, H. and Park, Y. and Song, M. and Yoon, J. and Hwang, H. and Lee, S. and Sohn, J. and Kang, J.},\n  title     = {DMIS Lab at MedHopQA-2025: Ensemble Multi-Retrieval Methodologies with Reasoning Language Model Decision},\n  booktitle = {Proceedings of the BioCreative IX Challenge and Workshop (BC9): Large Language Models for Clinical and Biomedical NLP at the International Joint Conference on Artificial Intelligence (IJCAI)},\n  year      = {2025},\n  doi       = {10.5281/zenodo.16875789},\n  url       = {https://doi.org/10.5281/zenodo.16875789}\n}\n```\n\nAlso, it should be noted that appropriate references must be cited when using the MedHopQA dataset or citing BC9 challenge results, etc.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmis-lab%2Fbc9-medhop-qa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdmis-lab%2Fbc9-medhop-qa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmis-lab%2Fbc9-medhop-qa/lists"}