New Benchmarking Shows Limited Generalization Power of TCR Antigenic Epitope Prediction Models

Yiming Liao; Yiheng Li; Ning Jiang; Bo Li; Keke Chen

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arXiv · 2606.04994

New Benchmarking Shows Limited Generalization Power of TCR Antigenic Epitope Prediction Models

Yiming Liao·Yiheng Li·Ning Jiang·Bo Li·Keke Chen

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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. A major limitation is the absence of rigorously defined, unseen benchmark datasets that allow unbiased evaluation of model performance and generalizability. Here, we describe two complementary classes of datasets that meet this criterion and argue that they provide both a robust framework for model assessment and a foundation for next-generation TCR-antigen prediction algorithm development.

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Yiming Liao, Yiheng Li, Ning Jiang, Bo Li, Keke Chen. 2026-06-03. New Benchmarking Shows Limited Generalization Power of TCR Antigenic Epitope Prediction Models. https://arxiv.org/abs/2606.04994

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