6 citations · 25 across the 11 of their papers we have counts for
12 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…
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…