README.md

---
license: apache-2.0
tags:
- biology
- dna
- reasoning
---

<h1 align="center">
🧬 BioReason<br>Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model
</h1>

<p align="center">
  <a href="https://www.arxiv.org/abs/2505.23579" target="_blank"><img src="https://img.shields.io/badge/arXiv-2505.23579-FF6B6B?style=for-the-badge&logo=arxiv&logoColor=white" alt="arXiv"></a>
  <a href="https://github.com/bowang-lab/BioReason"><img src="https://img.shields.io/badge/GitHub-Code-4A90E2?style=for-the-badge&logo=github&logoColor=white" alt="GitHub"></a>
  <a href="https://bowang-lab.github.io/BioReason/"><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-683cd17172a037a31d208f70"><img src="https://img.shields.io/badge/HuggingFace-Dataset-FFBF00?style=for-the-badge&logo=huggingface&logoColor=white" alt="HuggingFace Dataset"></a>
</p>

<br>

# Variant Effect Coding Dataset

50,083 core variant entries from GPN-MSA study using ClinVar pathogenic variants and gnomAD benign variants (MAF>5%), split by chromosome (Chr 1-7,9-22,X,Y for train, Chr 8 for test) for pathogenic/benign classification.


## Usage

```python
from datasets import load_dataset

dataset = load_dataset("wanglab/variant_effect_coding")
example = dataset["train"][0]
print(example)
```


## Citation

```
@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}, 
}
```