README.md

# 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](https://huggingface.co/datasets/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.