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arXiv · 2606.31763

A Self-Evolving Agentic System for Automated Generation and Execution of Biological Protocols

Yankai Jiang·Weiting Tang·Haoran Sun·Zhenyu Tang·Yuejie Hou·Yingnan Han·Rubo Wang·Yueyuxiao Yang·Cheng Liang·Lilong Wang·Wenjie Lou·Xiaosong Wang·Lei Bai·Meng Yang
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Abstract

Autonomous wet-lab experimentation requires more than plausible protocol text: biological intent, quantitative procedures, device constraints and experimental feedback must remain aligned from protocol and SOP design to code and physical execution. We developed ProtoPilot, a self-evolving multi-agent system, together with an expert-grounded benchmark and evaluation framework for testing this conversion as an experimental automation problem. The framework spans 294 synthetic-biology and molecular-biology tasks derived from 98 gold-standard protocols, wet-lab expert rubrics, device-level validity gates and real experimental tests. ProtoPilot incorporates layer-wise verifiability, multi-agent orchestration and a runtime-updated skill library to generate protocols, expand SOPs, synthesize SDK-compliant code and revise workflows from wet-lab feedback. It achieved a Top@3 expert-preference rate of 90.2%, an overall protocol-to-code gate pass rate of 89.5% and an Opentrons pass rate of 88.24%, compared with 32.35% for OpenTrons-AI. Wet-lab validation produced interpretable readouts, Sanger-confirmed products and feedback-corrected PCA-assembled DNA targets, establishing a verifiable route to autonomous experimentation. Together, these results show that the evaluation framework captures execution-relevant requirements for autonomous wet-lab automation, and that ProtoPilot can meet them by converting protocol and code generation into validated execution and feedback-guided revision.

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Yankai Jiang, Weiting Tang, Haoran Sun, Zhenyu Tang, Yuejie Hou, Yingnan Han, Rubo Wang, Yueyuxiao Yang, Cheng Liang, Lilong Wang, Wenjie Lou, Xiaosong Wang, Lei Bai, Meng Yang. 2026-06-30. A Self-Evolving Agentic System for Automated Generation and Execution of Biological Protocols. https://arxiv.org/abs/2606.31763

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