11 papers
Molecular LLM Agents: From Architectural Design to Scientific Autonomy
Jiatong Li, Wengyu Zhang, Weida Wang +8
Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or web environments, molecular LLM a…
Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad
Jiatong Li, Yuxuan Ren, Weida Wang +2
Chemical reasoning language models are expected to derive molecular answers through faithful chain-of-thought (CoT). However, across four reasoning model families and twelve chemis…
Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis
Jiatong Li, Weida Wang, Changmeng Zheng +4
Large Language Models (LLMs) have recently shown promise in molecular discovery, yet a gap remains between their probabilistic nature over discrete sequential tokens and the rigid…
Energy-Guided Generative Modeling for Low-Energy Molecular Structure Discovery
Guikun Xu, Xiaohan Yi, Ziqiao Meng +2
Exploring molecular energy landscapes and identifying ground-state conformations are central challenges in computational chemistry. However, generating diverse low-energy conformer…
MolViBench: Evaluating LLMs on Molecular Vibe Coding
Jiatong Li, Yuxuan Ren, Weida Wang +4
Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents wi…
Question-Adaptive Graph Learning for Multi-hop Retrieval Augmented Generation
Yuchen Yan, Peiyan Zhang, Zhihua Liu +4
Retrieval-augmented generation (RAG) has demonstrated its ability to enhance Large Language Models (LLMs) by integrating external knowledge sources. However, multi-hop questions, w…