10 papers
Adversarial Attacks on Deep OCR Systems
Wenbo Sun, Hongzong LI, Yanyun Wang +5
Deep-OCR (DeepSeek-OCR) advances document recognition by treating the visual modality as an optical compression medium, enabling long-context OCR at low token cost. However, its in…
SynLeaF: A Dual-Stage Multimodal Fusion Framework for Synthetic Lethality Prediction Across Pan- and Single-Cancer Contexts
Zheming Xing, Siyuan Zhou, Ruinan Wang +9
Accurate prediction of synthetic lethality (SL) is important for guiding the development of cancer drugs and therapies. SL prediction faces significant challenges in the effective…
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…
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…
Comparative Analysis of Machine Learning Algorithms for Predicting On-Target and Off-Target Effects of CRISPR-Cas13d for gene editing
Jingze Liu, Jiahao Ma
CRISPR-Cas13 is a system that utilizes single stranded RNAs for RNA editing. Prediction of on-target and off-target effects for the CRISPR-Cas13d dependency enables us to design sp…