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

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 BioProBench, a comprehensive resource for procedural reasoning in biology. BioProBench is grounded in BioProCorpus, a foundational collection of 27,000 human-written protocols. From this corpus, we systematically constructed a dataset of over 550,000 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 ProAgent, grounded in our corpus, ProAgent substantially advances the state-of-the-art. Code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/BioProBench/BioProBench .