Explainability from Training with Applications to TCR-Epitope Prediction

Deep learning models have achieved strong performance in artificial intelligence for science, yet their black-box nature limits our understanding of how they learn scientific tasks. Existing methods for interpretability provide limited insight into how models organize evidence and evolve during learning. We introduce explainability from training (EFT), a model-agnostic paradigm that traces model interpretation during training to explain why models rely on specific features and how they organize these features as predictive evidence. We apply EFT to four state-of-the-art T cell receptor (TCR)-epitope prediction models, TCR-SRIM, TULIP, MixTCRpred, and NetTCR-2.2, spanning post-hoc and interpret-by-design approaches as well as transformers and CNNs. To investigate how structural information affects model explanations, we introduce a benchmark, TCR-XAI2, containing 388 unique experimentally resolved TCR-epitope structures, complemented by structures predicted using AlphaFold3, Boltz-2, TCRModel2, tFold-TCR, and OpenFold3. Using \ModelName[abbr] with TCR-XAI2, we demonstrate that (1) CNN and transformer models exhibit distinct learning trajectories; (2) TCR $\alpha$ and $\beta$ evidence can conflict during learning, limiting the benefits of jointly modeling both chains, while MHC information mitigates this; and (3) real versus predicted structural data for TCR-epitope prediction exhibits distinct TCR and peptide feature preferences as well as differing trajectories of model certainty.