8 papers
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…
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…
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…