BenchBench-Protocol: Evaluating Real-World Wet-Lab Protocol Reasoning and Modification

We introduce BenchBench-Protocol, a benchmark for large language models of 149 protocol-modification tasks recovered from modifications that scientists made to published protocols during real experimental work. Adapting a published protocol to a new experiment is a routine task for a wet-lab scientist, and a correct modification requires accounting for prior choices and downstream steps. Recent life-science benchmarks have moved toward open-ended, rubric-graded tasks, but tasks are typically elicited from experts rather than reconstructed from real-world modifications. BenchBench-Protocol tasks are derived from differences between a published protocol and a version a scientist modified, which provides the basis for the query and the weighted rubric elements for a correct response. The benchmark draws from 96 source protocols across nine domains of wet-lab biology and only includes tasks rated highly after review by domain experts. We evaluate nine closed and open models; Claude Opus 5 scores highest at 59.2% normalized rubric score, with other models between 34.1% and 47.1%, and the benchmark remains unsaturated when taking the best of ten attempts. As models are increasingly helpful in life-sciences research, evaluating them on routine wet-lab tasks becomes correspondingly important. We present BenchBench-Protocol as both a grounded assessment of wet-lab reasoning and evidence for the utility of real-world experiments to construct benchmark tasks.

ProtoAct: Turning Wet-Lab Protocols into Embodied Robotic Actions

Biological wet-lab protocols are written for trained researchers and often leave routine operations, state-dependent conditions, and contextual parameters implicit, making them difficult to translate into robot-executable actions. We present ProtoAct, a structured protocol-grounding framework that converts free-form biological procedures into state-aware, embodiment-ready action sequences. ProtoAct uses ProtoRAG to retrieve manually annotated examples for context-sensitive parsing, employs RefineChecker to detect and revise missing or inconsistent steps, and applies ActSchema to map the refined procedure into constrained JSON function sequences. We further introduce BioP2E, for which we manually annotate 22 cell-culture protocols into 258 monitoring conditions, 910 executable subtasks, and 962 grounded action calls. Evaluation across seven large language models demonstrates that ProtoAct can be effectively instantiated with different backbones. Ablations confirm that retrieval, posterior checking, and schema constraints make complementary contributions. The parsed subtasks further support demonstration collection and VLA model training, enabling successful execution in both simulation and real-robot settings. ProtoAct thus provides a practical interface between biological protocol understanding and embodied robotic execution.