10 papers
AgentFold: Closed-Loop Agentic Search for Protein Folding Model Design
Mingquan Liu, Jiangyu Chen, Hanqun Cao +9
Scientific LLM agents have shown promise in literature reasoning, tool use, and experiment planning, but it remains unclear whether they can autonomously improve large, tightly cou…
SurfDesign: Effective Protein Design on Molecular Surfaces
Fang Wu, Shuting Jin, Xiangru Tang +5
Protein function is largely determined by molecular surface geometry and physicochemical complementarity, yet most protein design methods condition only on backbone structure. We i…
Latent Action Reparameterization for Efficient Agent Inference
Wenhao Huang, Qingwen Zeng, Qiyue Chen +11
Large language model (LLM) agents often rely on long sequences of low-level textual actions, resulting in large effective decision horizons and high inference cost. While prior wor…
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…
Hypergraph Pattern Machine: Compositional Tokenization for Higher-Order Interactions
Kyrie Zhao, Zehong Wang, Tianyi Ma +5
Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise…
NoiseRater: Meta-Learned Noise Valuation for Diffusion Model Training
Fang Wu, Haokai Zhao, Da Xing +17
Diffusion models have achieved remarkable success across a wide range of generative tasks, yet their training paradigm largely treats injected noise as uniformly informative. In th…