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arXiv · 2505.07889

BioProBench: A Corpus and Benchmark for Biological Protocol Reasoning in Autonomous Science

Yuyang Liu·Liuzhenghao Lv·Xiancheng Zhang·Jingya Wang Li Yuan·Yonghong Tian
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Abstract

The realization of autonomous scientific experimentation is currently limited by LLMs' struggle to grasp the strict procedural logic and accuracy required by biological protocols. To address this fundamental challenge, we present \textbf{BioProBench}, a comprehensive resource for procedural reasoning in biology. BioProBench is grounded in \textbf{BioProCorpus}, a foundational collection of 22,413 human-written protocols. From this corpus, we systematically constructed a dataset of 523,784 task instances, offering both a large-scale training resource and a rigorous benchmark with novel metrics. Evaluating 10 mainstream LLMs, we find that while general comprehension is high, performance drops significantly on tasks demanding deep reasoning, quantitative precision, and safety awareness. To demonstrate the value of BioProCorpus in mitigating these issues, we developed \textbf{ProAgent}, grounded in our corpus, ProAgent substantially advances the state-of-the-art. https://github.com/YuyangSunshine/bioprobench and https://huggingface.co/BioProBench.

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Yuyang Liu, Liuzhenghao Lv, Xiancheng Zhang, Jingya Wang Li Yuan, Yonghong Tian. 2025-05-11. BioProBench: A Corpus and Benchmark for Biological Protocol Reasoning in Autonomous Science. https://arxiv.org/abs/2505.07889

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