4 citations · 8 across the 12 of their papers we have counts for
13 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…
Capturing LLM Capabilities via Evidence-Calibrated Query Clustering
Fangzhou Wu, Sandeep Silwal, Qiuyi Zhang
Query clustering organizes queries into groups that reflect shared latent capability demands, enabling capability-aware LLM evaluation. Existing clustering methods, which primarily…
DynMuon: A Dynamic Spectral Shaping View of Muon
Fangzhou Wu, Rikhav Shah, Sandeep Silwal +1
In recent years, Muon has emerged as the dominant method for training large language models, and transformers more broadly. The essential difference, when compared to standard grad…
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…
GeoCycler: Reward-Aligned 3D Diffusion for Constraint-Conditioned Cyclic Peptide Design
Jingjie Zhang, Hanqun Cao, Haosen Shi +10
Cyclic peptides are attractive therapeutic modalities because their closed-ring topology can improve stability and target specificity. However, de novo cyclic peptide design remain…
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…
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…
Proteo-R1: Reasoning Foundation Models for De Novo Protein Design
Fang Wu, Weihao Xuan, Heli Qi +26
Deep learning in de novo protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries…
AI Scientists for Building Virtual-Cell Models
Xiangru Tang, Zhuoyun Yu, Jiapeng Chen +12
Autonomous agents, from virtual laboratories to biological data-analysis agents and co-scientists, have begun to turn scientific goals into hypotheses. Whether they can go further…
Agent KB: Leveraging Cross-Domain Experience for Agentic Problem Solving
Xiangru Tang, Tianrui Qin, Tianhao Peng +15
AI agent frameworks operate in isolation, forcing agents to rediscover solutions and repeat mistakes across different systems. Despite valuable problem-solving experiences accumula…
MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks
Yanjun Shao, Xiangru Tang, Jiwoong Sohn +10
Complex medical reasoning requires integrating heterogeneous clinical evidence across multiple inference steps. Large language models (LLMs) now approach this through two routes: i…
D-Flow: Multi-modality Flow Matching for D-peptide Design
Fang Wu, Shuting Jin, Xiangru Tang +3
Among these, D-peptides are resistant to proteolysis, exhibit greater in vivo stability, and are easier to synthesize. Despite advances in deep learning for peptide discovery, the…
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation
Xiangru Tang, Howard Dai, Elizabeth Knight +4
Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative mod…