toolevalxm/BioBench-Genomics

BioBench: A Bioinformatics Code Reasoning Benchmark

<p align="left"> 📑 <a href="https://huggingface.co/papers/xxxx.xxxxx" target="blank">Paper</a> &nbsp&nbsp | &nbsp&nbsp 🌐 <a href="https://biobench.github.io/" target="blank">Project Page</a> &nbsp&nbsp | &nbsp&nbsp 💾 <a href="https://huggingface.co/collections/toolevalxm/biobench-67a978e28fd926b56a4f55a2" target="blank">Released Resources</a> &nbsp&nbsp | &nbsp&nbsp 📦 <a href="https://github.com/xmhtoolathlon/Annoy-DataSync" target="blank">Repo</a>

This is the synthesized BioBench-Genomics dataset, designed for training LLMs on bioinformatics reasoning tasks.

Dataset <table> <tr> <th>Dataset</th> <th>Link</th> </tr> <tr> <td>BioBench-Genomics</td> <td style="background-color: #e6f3ff; text-align: center; vertical-align: middle;"> <a href="https://huggingface.co/datasets/toolevalxm/BioBench-Genomics">🤗</a> </td> </tr> </table> Please also check the raw data after our processing if you are interested: toolevalxm/BioBench-Genomics-Raw.

Models <table> <tr> <th rowspan="2">Base Model / Training</th> <th colspan="2">BioBench</th> <th colspan="2">BioBench++</th> </tr> <tr> <th>Stage 1</th> <th>Stage 2</th> <th>Stage 1</th> <th>Stage 2</th> </tr> <tr> <td>Qwen 2.5 7B Coder</td> <td style="text-align: center; vertical-align: middle;">🤗</td> <td style="text-align: center; vertical-align: middle;">🤗</td> <td style="text-align: center; vertical-align: middle;">🤗</td> <td style="text-align: center; vertical-align: middle;">🤗</td> </tr> </table>

Introduction

BioBench transforms bioinformatics code patterns into natural language Chain-of-Thought rationales. We use a fully LLM-based approach for synthesizing all the desired responses using Qwen2.5-72B-Instruct, as it excels at scientific reasoning with competitive cost compared to other advanced LLMs.

*Due to collaborator compliance requirements, we only release the Genomics subset (this page) of the full BioBench dataset.

License

The license for this dataset is other.