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

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ID: 321856
2026
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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 to 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available online at Bioinformatics.
Reference Key
openalex_W7170072121 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Xiangzheng Fu, Xi Zhang, Linlin Zhuo, Yuehua Chen, Dongsheng Cao, Q C Zou
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Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag544
URL
https://doi.org/10.1093/bioinformatics/btag544
Keywords Keywords not found

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