Molecular LLM Agents: From Architectural Design to Scientific Autonomy
Molecular agents, architectural design, and scientific autonomy
Jiatong Li, Wengyu Zhang, Weida Wang, Yuxuan Ren, Wei Liu, Chenyang Mao, Yuqiang Li, Yatao Bian, Changmeng Zheng, Xiaoyong Wei, and Qing Li. (2026). Molecular LLM Agents: From Architectural Design to Scientific Autonomy. arXiv:2608.23104.
About this work
Molecular LLM agents must operate over chemical objects spanning symbolic strings, molecular graphs, 3D conformations, spectra, simulations, and wet-lab measurements. This perspective organizes their design around four components: molecular representation and perception, an LLM-centered agent framework, domain-specific toolboxes, and learning and optimization.
The work also introduces a four-level scientific autonomy ladder, progressing from assistive or fixed workflows to adaptive computational agents, feedback-aware physical experiment agents, and scientific-agenda agents. Together, these views provide a framework for comparing systems, identifying missing capabilities and risks, and guiding future molecular-discovery agents.