6 citations · 25 across the 11 of their papers we have counts for
15 papers
Learning from Unverified Peers via Shared Residual Distillation
Feiyang Chen, Runze Ma, Zichen Wang +4
A language model can generate several solutions to the same problem, some leading to correct answers and others to incorrect ones. Many post-training methods turn these trajectorie…
ReTerm: Recovery Training for Self-Improving Terminal Agents
Wei Xie, Kaituo Feng, Shiming Fu +3
Terminal agents have shown strong abilities in complex coding tasks. However, they often struggle to recover from errors during long-running execution (e.g., command errors, faulty…
Does Learning Protein Folding Generalize to Broader Reasoning?
Yong Liu, Zhanpeng Shi, Yizhou Dang +4
Large language models rely heavily on human text, which often conveys surface answers rather than the spatial and structural logic behind them. Protein folding is a natural testbed…
Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design
Xiaoliang Shi, Zichen Wang, Runze Ma +2
Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules. Although recent protein language models have enabled progres…
VCWorld: A Biological World Model for Virtual Cell Simulation
Zhijian Wei, Runze Ma, Zichen Wang +3
Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings…
NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction
Zhongmin Li, Runze Ma, Jiahao Tan +2
Nucleotide sequence variation can induce significant shifts in functional fitness. Recent nucleotide foundation models promise to predict such fitness effects directly from sequenc…
ODesign: A World Model for Biomolecular Interaction Design
Odin Zhang, Xujun Zhang, Haitao Lin +34
Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged…
From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery
Jiaqi Wei, Yuejin Yang, Xiang Zhang +24
Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pi…
An Energy-Adaptive Elastic Equivariant Transformer Framework for Protein Structure Representation
Zhongyue Zhang, Runze Ma, Yanjie Huang +1
Structure-informed protein representation learning is essential for effective protein function annotation and \textit{de novo} design. However, the presence of inherent noise in bo…
RiboFlow: Conditional De Novo RNA Co-Design via Synergistic Flow Matching
Runze Ma, Zhongyue Zhang, Zichen Wang +4
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA tha…
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua, Jiarui Lu, Yong Liu +7
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interaction prediction, primarily from a binding…
Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization
Zichen Wang, Yaokun Ji, Jianing Tian +1
Antibodies are essential proteins responsible for immune responses in organisms, capable of specifically recognizing antigen molecules of pathogens. Recent advances in generative m…
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics
Chenqing Hua, Yong Liu, Dinghuai Zhang +6
Enzyme design is a critical area in biotechnology, with applications ranging from drug development to synthetic biology. Traditional methods for enzyme function prediction or prote…
ReactZyme: A Benchmark for Enzyme-Reaction Prediction
Chenqing Hua, Bozitao Zhong, Sitao Luan +4
Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essen…
Effective Protein-Protein Interaction Exploration with PPIretrieval
Chenqing Hua, Connor Coley, Guy Wolf +2
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of mul…