DynaTCR: dynamic hard-negative ensemble graph learning improves TCR-epitope binding prediction

Abstract

Abstract Motivation T-cell receptors (TCRs) recognize antigenic peptides presented by major histocompatibility complex (MHC) molecules and are central to adaptive immunity. Computational prediction of TCR–epitope binding (TEB) can accelerate immunotherapy development, yet remains hampered by limited labeled data, false-negative noise in unobserved pairs, and over-smoothing in graph-based models. Results We present DynaTCR, a dynamic graph ensemble learning framework for TEB prediction. DynaTCR encodes TCR and epitope sequences with protein language model embeddings and organizes them into a bipartite interaction graph. A graph regularization-variance-preserving aggregation (GR-VPA) encoder stabilizes message propagation and alleviates over-smoothing, while a global attention layer captures long-range dependencies. Multiple base learners are trained with iteratively updated hard-negative samples to reduce false-negative predictions. Under the StrictTCR evaluation protocol on four public datasets, DynaTCR achieves AUC improvements of 4.0–8.2 percentage points over the strongest existing method and up to 15.8 percentage points in AUPR. On the most stringently curated dataset, DynaTCR attains an AUC of 95.1%. Furthermore, on an independent structure-derived test set, DynaTCR achieves the highest AUC (72.6%) among all compared methods, demonstrating its robustness and effectiveness for TEB prediction and candidate prioritization. Availability Source code and data can be downloaded from: https://github.com/2014402680/TEB/.