Abstract:Binding prediction models accelerate therapeutic antibody and TCR discovery, but their performance on new datasets is unpredictable, often leading to low discovery rates. Density-ratio methods (PAPE, M-CBPE) provide label-free performance estimation for binary classification, but their assumptions and aggregate-only outputs limit binding prediction on neoepitopes, antigen variants and chemical scaffolds. Here we present CaliPPer (Calibration and Prediction of Performance), a post-hoc framework pairing a multi-chain Sample-to-Domain Distance (S2DD) with distance-aware Bayesian recalibration, operating at three resolutions: generalisability score, aggregate performance prediction, and per-sample confidence. Across ten models, eight architectures and two immune-receptor domains, CaliPPer attains distance--performance correlations $|r|=0.80\text{--}0.92$, predicts AUROC/AP/F1 with mean absolute errors $0.008\text{--}0.070$, and improves AUROC by up to $+0.20$ on unseen epitopes/variants. Applied retrospectively to five published TCR, BCR, MHC--peptide and small-molecule studies, CaliPPer raises true discovery rates in all five (e.g.\ $0/5 \to 3/5$ confirmed neoantigens), providing a triage layer between computational prediction and experimental validation.
From: Jian-Qing Zheng [view email]
[v1]
Fri, 5 Jun 2026 13:34:47 UTC (10,226 KB)