wanglab/variant_effect_coding
🧬 BioReasonIncentivizing Multimodal Biological Reasoning within a DNA-LLM Model 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 from datasets import load_dataset dataset = load_dataset("wanglab/variant_effect_coding") example =… See the full description on the dataset page: https://huggingface.co/datasets/wanglab/variant_effect_coding.
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1---2license: apache-2.03tags:4- biology5- dna6- reasoning7---8 9<h1 align="center">10🧬 BioReason<br>Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model11</h1>12 13<p align="center">14 <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>15 <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>16 <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>17 <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>18</p>19 20<br>21 22# Variant Effect Coding Dataset23 2450,083 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.25 26 27## Usage28 29```python30from datasets import load_dataset31 32dataset = load_dataset("wanglab/variant_effect_coding")33example = dataset["train"][0]34print(example)35```36 37 38## Citation39 40```41@misc{fallahpour2025bioreasonincentivizingmultimodalbiological,42 title={BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model}, 43 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},44 year={2025},45 eprint={2505.23579},46 archivePrefix={arXiv},47 primaryClass={cs.LG},48 url={https://arxiv.org/abs/2505.23579}, 49}50```