Accurate computational prediction of T cell receptor (TCR) antigen specificity would transform the study of T cell biology and enable scalable immune engineering, yet existing models lack sufficient sensitivity and specificity for broad applications. A major limitation is the absence of rigorously defined, unseen benchmark datasets that allow unbiased evaluation of model performance and generalizability.
arXiv:2606. 04994v1 Announce Type: new Abstract: Accurate computational prediction of T cell receptor (TCR) antigen specificity would transform the study of T cell biology and enable scalable immune engineering, yet existing models lack sufficient sensitivity and specificity for broad applications.
arXiv:2606. 30902v1 Announce Type: cross Abstract: T cell receptor (TCR)-epitope binding prediction is essential for understanding adaptive immunity and developing immunotherapies.
arXiv:2606. 28659v1 Announce Type: cross Abstract: High-fidelity molecular docking simulations can produce biologically relevant estimates of epitope-receptor binding affinity but are computationally expensive and therefore limit the number of candidates that can be screened for vaccine design.
arXiv:2603. 13431v3 Announce Type: replace-cross Abstract: Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development.
arXiv:2602. 01051v5 Announce Type: replace Abstract: Repertoire-level analysis of T cell receptors offers a biologically grounded signal for disease detection and immune monitoring, yet practical deployment is impeded by label sparsity, cohort heterogeneity, and the computational burden of adapting large encoders to new tasks.
arXiv:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.
arXiv:2602. 17330v5 Announce Type: replace-cross Abstract: Comparative analysis of adaptive immune repertoires at population scale is hampered by two practical bottlenecks: the near-quadratic cost of pairwise affinity evaluations and dataset imbalances that obscure clinically important minority clonotypes.
arXiv:2605. 21610v2 Announce Type: replace Abstract: Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they largely ignore the antigen input.
arXiv:2607. 20057v1 Announce Type: cross Abstract: Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules.
arXiv:2607. 17244v1 Announce Type: new Abstract: Longitudinal T cell receptor repertoires contain signals of clonal expansion, contraction, disappearance, and reappearance after immune perturbation.
arXiv:2605. 21600v2 Announce Type: replace Abstract: Computational antibody CDR design methods condition on antigen structure to generate binding loops.
Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules. Although recent protein language models have enabled progress in single-chain protein modeling and generation, they often fall short in antigen-specific antibody design, where effective modeling requires explicit pairing between antibody and antigen, particularly at the epitope level.