6 papers
Structure-Regularized Interpretable TCR-Epitope Prediction
Jiarui Li, Zixiang Yin, Yunbei Zhang +4
T cell receptor (TCR)-epitope binding prediction is essential for understanding adaptive immunity and developing immunotherapies. Existing sequence- and structure-based models ofte…
APLSuite: An Integrated Suite for CD4+ T Cell Epitope Prediction via Antigen Processing Likelihood
Jiarui Li, Marco K. Carbullido, Jai Bansal +2
Computational epitope prediction is a critical tool for exploring and understanding CD4+ T cell-mediated immune responses, a key aspect of adaptive immunity. While existing computa…
Why Does It Look There? Structured Explanations for Image Classification
Jiarui Li, Zixiang Yin, Samuel J Landry +2
Deep learning models achieve remarkable predictive performance, yet their black-box nature limits transparency and trustworthiness. Although numerous explainable artificial intelli…
TCR-EML: Explainable Model Layers for TCR-pMHC Prediction
Jiarui Li, Zixiang Yin, Zhengming Ding +2
T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is a central component of adaptive immunity, with implications for vaccine design, cancer immunotherapy, and autoi…
Quantifying Cross-Attention Interaction in Transformers for Interpreting TCR-pMHC Binding
Jiarui Li, Zixiang Yin, Haley Smith +3
CD8+ "killer" T cells and CD4+ "helper" T cells play a central role in the adaptive immune system by recognizing antigens presented by Major Histocompatibility Complex (pMHC) molec…
Rational Multi-Modal Transformers for TCR-pMHC Prediction
Jiarui Li, Zixiang Yin, Zhengming Ding +2
T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is fundamental to adaptive immunity and central to the development of T cell-based immunotherapies. While transfor…