8 papers
Physicochemically Informed Dual-Conditioned Generative Model of T-Cell Receptor Variable Regions for Cellular Therapy
Jiahao Ma, Hongzong Li, Ye-Fan Hu +1
Physicochemically informed biological sequence generation has the potential to accelerate computer-aided cellular therapy, yet current models fail to \emph{jointly} ensure novelty,…
ABConformer: Physics-inspired Sliding Attention for Antibody-Antigen Interface Prediction
Zhang-Yu You, Jiahao Ma, Hongzong Li +2
Accurate prediction of antibody-antigen (Ab-Ag) interfaces is critical for vaccine design, immunodiagnostics, and therapeutic antibody development. However, achieving reliable pred…
CAME-AB: Cross-Modality Attention with Mixture-of-Experts for Antibody Binding Site Prediction
Hongzong Li, Jiahao Ma, Zhanpeng Shi +5
Antibody binding site prediction plays a pivotal role in computational immunology and therapeutic antibody design. Existing sequence or structure methods rely on single-view featur…
The Matthew Effect of AI Programming Assistants: A Hidden Bias in Software Evolution
Fei Gu, Zi Liang, Jiahao MA +1
AI-assisted programming is rapidly reshaping software development, with large language models (LLMs) enabling new paradigms such as vibe coding and agentic coding. While prior work…
TopoBind: Multi-Modal Prediction of Antibody-Antigen Binding Free Energy via Sequence Embeddings and Structural Topology
Ciyuan Yu, Hongzong Li, Jiahao Ma +3
Predicting the binding free energy between antibodies and antigens is a key challenge in structure-aware biomolecular modeling, with direct implications for antibody design. Most e…
BConformeR: A Conformer Based on Mutual Sampling for Unified Prediction of Continuous and Discontinuous Antibody Binding Sites
Zhangyu You, Jiahao Ma, Hongzong Li +2
Accurate prediction of antibody-binding sites (epitopes) on antigens is crucial for vaccine design, immunodiagnostics, therapeutic antibody development, antibody engineering, resea…
Catch Causal Signals from Edges for Label Imbalance in Graph Classification
Fengrui Zhang, Yujia Yin, Hongzong Li +2
Despite significant advancements in causal research on graphs and its application to cracking label imbalance, the role of edge features in detecting the causal effects within grap…
Remodeling Peptide-MHC-TCR Triad Binding as Sequence Fusion for Immunogenicity Prediction
Jiahao Ma, Hongzong Li, Jian-Dong Huang +2
The complex nature of tripartite peptide-MHC-TCR interactions is a critical yet underexplored area in immunogenicity prediction. Traditional studies on TCR-antigen binding have not…