7 papers
Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization
Xinwu Ye, He Cao, Hao Li +5
Biomolecular generators are often adapted with reward feedback to improve task-specific utility, but pushing utility alone can concentrate generation on a narrow family of candidat…
ReactBench: A Benchmark for Topological Reasoning in MLLMs on Chemical Reaction Diagrams
Qiang Xu, Shengyuan Bai, Yu Wang +6
Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological str…
Mozi: Governed Autonomy for Drug Discovery LLM Agents
He Cao, Siyu Liu, Fan Zhang +7
Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlene…
A Novel 4-D Dataset Paradigm for Studying Complete Ligand-Protein Dissociation Dynamics
Maodong Li, Jiying Zhang, Zhe Wang +7
The kinetics and dynamics of drug-protein binding and dissociation are crucial to understanding drug absorption and metabolism. Despite advances in artificial intelligence (AI) too…
Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis
Hao Li, He Cao, Shenyao Peng +7
Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle betwee…
BioMD: All-atom Generative Model for Biomolecular Dynamics Simulation
Bin Feng, Jiying Zhang, Xinni Zhang +2
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their uti…