wanglab/bioreason-pro-rl-reasoning-data

---
license: apache-2.0
language:
- en
tags:
- protein
- gene-ontology
- function-prediction
- biology
- bioinformatics
- reasoning
- reinforcement-learning
- grpo
size_categories:
- 1K<n<10K
---

<h1 align="center">
🧬 BioReason-Pro<br>Advancing Protein Function Prediction with<br>Multimodal Biological Reasoning
</h1>

<p align="center">
<a href="https://www.biorxiv.org/content/10.64898/2026.03.19.712954v1" target="_blank"><img src="https://img.shields.io/badge/bioRxiv-2026.03.19.712954-FF6B6B?style=for-the-badge&logo=arxiv&logoColor=white" alt="bioRxiv"></a>
<a href="https://github.com/bowang-lab/BioReason-Pro"><img src="https://img.shields.io/badge/GitHub-Code-4A90E2?style=for-the-badge&logo=github&logoColor=white" alt="GitHub"></a>
<a href="https://bioreason.net"><img src="https://img.shields.io/badge/Website-Online-00B89E?style=for-the-badge&logo=internet-explorer&logoColor=white" alt="Website"></a>
<a href="https://huggingface.co/collections/wanglab/bioreason-pro"><img src="https://img.shields.io/badge/HuggingFace-Models & Data-FFBF00?style=for-the-badge&logo=huggingface&logoColor=white" alt="HuggingFace"></a>
</p>

<br>

## BioReason-Pro RL Reasoning Data

Training dataset for reinforcement learning (GRPO) optimization of BioReason-Pro. Contains proteins with GO term annotations, InterPro domains, STRING protein-protein interactions, and protein metadata.

## Citation

If you find this work useful, please cite our papers:

```bibtex
@article {Fallahpour2026.03.19.712954,
author = {Fallahpour, Adibvafa and Seyed-Ahmadi, Arman and Idehpour, Parsa and Ibrahim, Omar and Gupta, Purav and Naimer, Jack and Zhu, Kevin and Shah, Arnav and Ma, Shihao and Adduri, Abhinav and G{\"u}loglu, Talu and Liu, Nuo and Cui, Haotian and Jain, Arihant and de Castro, Max and Fallahpour, Amirfaham and Cembellin-Prieto, Antonio and Stiles, John S. and Nem{\v c}ko, Filip and Nevue, Alexander A. and Moon, Hyungseok C. and Sosnick, Lucas and Markham, Olivia and Duan, Haonan and Lee, Michelle Y. Y. and Salvador, Andrea F. M. and Maddison, Chris J. and Thaiss, Christoph A. and Ricci-Tam, Chiara and Plosky, Brian S. and Burke, Dave P. and Hsu, Patrick D. and Goodarzi, Hani and Wang, Bo},
title = {BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning},
elocation-id = {2026.03.19.712954},
year = {2026},
doi = {10.64898/2026.03.19.712954},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2026/03/20/2026.03.19.712954},
eprint = {https://www.biorxiv.org/content/early/2026/03/20/2026.03.19.712954.full.pdf},
journal = {bioRxiv}
}

@misc{fallahpour2025bioreasonincentivizingmultimodalbiological,
title={BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model},
author={Adibvafa Fallahpour and Andrew Magnuson and Purav Gupta and Shihao Ma and Jack Naimer and Arnav Shah and Haonan Duan and Omar Ibrahim and Hani Goodarzi and Chris J. Maddison and Bo Wang},
year={2025},
eprint={2505.23579},
archivePrefix={arXiv},
primaryClass={cs.LG},
url={https://arxiv.org/abs/2505.23579},
}
```

license: Apache-2.0 许可证
language:
- 英语
tags:
- 蛋白质
- 基因本体（Gene Ontology）
- 功能预测
- 生物学
- 生物信息学
- 推理
- 强化学习（reinforcement learning）
- GRPO
size_categories:
- 1K < n < 10K
---

<h1 align="center">
🧬 BioReason-Pro 基于多模态生物学推理推进蛋白质功能预测
</h1>

<p align="center">
<a href="https://www.biorxiv.org/content/10.64898/2026.03.19.712954v1" target="_blank"><img src="https://img.shields.io/badge/bioRxiv-2026.03.19.712954-FF6B6B?style=for-the-badge&logo=arxiv&logoColor=white" alt="bioRxiv预印本"></a>
<a href="https://github.com/bowang-lab/BioReason-Pro"><img src="https://img.shields.io/badge/GitHub-代码库-4A90E2?style=for-the-badge&logo=github&logoColor=white" alt="GitHub代码库"></a>
<a href="https://bioreason.net"><img src="https://img.shields.io/badge/网站-已上线-00B89E?style=for-the-badge&logo=internet-explorer&logoColor=white" alt="官方网站"></a>
<a href="https://huggingface.co/collections/wanglab/bioreason-pro"><img src="https://img.shields.io/badge/HuggingFace-模型与数据集-FFBF00?style=for-the-badge&logo=huggingface&logoColor=white" alt="HuggingFace模型与数据集集合"></a>
</p>

<br>

## BioReason-Pro 强化学习推理数据集

本数据集用于BioReason-Pro的强化学习（GRPO）优化训练，包含带有基因本体（GO）术语注释、InterPro结构域、STRING蛋白质相互作用数据以及蛋白质元数据的蛋白质样本。

## 引用说明

若您认为本工作对您有所帮助，请引用以下论文：

bibtex
@article {Fallahpour2026.03.19.712954,
author = {Fallahpour, Adibvafa and Seyed-Ahmadi, Arman and Idehpour, Parsa and Ibrahim, Omar and Gupta, Purav and Naimer, Jack and Zhu, Kevin and Shah, Arnav and Ma, Shihao and Adduri, Abhinav and G{"u}loglu, Talu and Liu, Nuo and Cui, Haotian and Jain, Arihant and de Castro, Max and Fallahpour, Amirfaham and Cembellin-Prieto, Antonio and Stiles, John S. and Nem{v c}ko, Filip and Nevue, Alexander A. and Moon, Hyungseok C. and Sosnick, Lucas and Markham, Olivia and Duan, Haonan and Lee, Michelle Y. Y. and Salvador, Andrea F. M. and Maddison, Chris J. and Thaiss, Christoph A. and Ricci-Tam, Chiara and Plosky, Brian S. and Burke, Dave P. and Hsu, Patrick D. and Goodarzi, Hani and Wang, Bo},
title = {BioReason-Pro: 基于多模态生物学推理推进蛋白质功能预测},
elocation-id = {2026.03.19.712954},
year = {2026},
doi = {10.64898/2026.03.19.712954},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2026/03/20/2026.03.19.712954},
eprint = {https://www.biorxiv.org/content/early/2026/03/20/2026.03.19.712954.full.pdf},
journal = {bioRxiv}
}

@misc{fallahpour2025bioreasonincentivizingmultimodalbiological,
title={BioReason：激励DNA-大语言模型（DNA-LLM）开展多模态生物学推理},
author={Adibvafa Fallahpour and Andrew Magnuson and Purav Gupta and Shihao Ma and Jack Naimer and Arnav Shah and Haonan Duan and Omar Ibrahim and Hani Goodarzi and Chris J. Maddison and Bo Wang},
year={2025},
eprint={2505.23579},
archivePrefix={arXiv},
primaryClass={cs.LG},
url={https://arxiv.org/abs/2505.23579},
}