DrugHarness: An Evolvable Agent Harness for Computational Drug Discovery

Yuxing Chen; Zhisheng Zhang; Cheng Tang; Wei Li; Minghui Zhang; Ziyan Huang; Shaocong Wei; Jiawei Chen; Junru Hu; Hongze Zhu; Jianghan Shen; Min Cen; Xinyuan Zhu; Yaxue Zhao; Jubo Wang; Yuqiang Li; Chun-Mei Feng; Zongyuan Ge; Rui Su; Jie Xu; Yirong Chen; Xi Xu; Ming Hu

arXiv · 2610.23791

DrugHarness: An Evolvable Agent Harness for Computational Drug Discovery

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Abstract

Computational drug discovery requires agents to compose scientific operations and adapt to changing evidence and constraints. Here we introduce DrugHarness, an evolvable agent harness coupling composable scientific execution with conditional skill induction. Its environment integrates over 80 scientific operations, biomedical resources and task-specific code, preserving associations among candidates, results and artifacts. From execution trajectories and outcome feedback, DrugHarness induces action hypotheses with observable applicability conditions, recommended actions and supporting evidence. An independent review agent evaluates candidate skills derived from these hypotheses through source verification and, when needed, targeted execution trials. Admitted skills guide subsequent tasks and are revised through feedback. Evaluation on MolBench and SMDD-Bench demonstrates capabilities in molecular screening, optimization and constrained design. Without evolution, DrugHarness exceeds reported MolClaw-CC results by 10.8 percentage points in affinity-comparison accuracy and 55% in mean top-three active hits on MolBench. Retrospective evaluation on skill-development tasks shows that evolution increases Qwen's affinity-comparison accuracy from 62.2% to 81.1% and optimization success from 79.5% to 87.2%. In a prospective HPK1 study, DrugHarness achieves a more favorable median docking score than Biomni among system-specific candidates. A synthesized compound achieves a cellular IC50 of 14.19 nM, a 2.64-fold potency improvement over the best input reference, with activity competitive with two selected compounds designed by experienced medicinal chemists. These results support conditional skill evolution for scientific agents and demonstrate a workflow connecting computational drug design with experimental validation.

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Yuxing Chen, Zhisheng Zhang, Cheng Tang, Wei Li, Minghui Zhang, Ziyan Huang, Shaocong Wei, Jiawei Chen, Junru Hu, Hongze Zhu, Jianghan Shen, Min Cen, Xinyuan Zhu, Yaxue Zhao, Jubo Wang, Yuqiang Li, Chun-Mei Feng, Zongyuan Ge, Rui Su, Jie Xu, Yirong Chen, Xi Xu, Ming Hu. 2026-10-16. DrugHarness: An Evolvable Agent Harness for Computational Drug Discovery. https://arxiv.org/abs/2610.23791

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