7 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…
MIND: Insightful Multi-subject Invariant Neural Decoding
Zixiang Yin, Jiarui Li, Zhengming Ding
Decoding visual signals holds the tantalizing potential to unravel the complexities of cognition and perception. While recent studies have focused on reconstructing visual stimuli…