Attentive Variational Information Bottleneck for TCR–peptide interaction prediction
Filippo Grazioli, Pierre Machart, Anja Mösch, Kai Li, Leonardo V. Castorina, Nico Pfeifer, Martin Renqiang Min
Abstract
MOTIVATION: We present a multi-sequence generalization of Variational Information Bottleneck and call the resulting model Attentive Variational Information Bottleneck (AVIB). Our AVIB model leverages multi-head self-attention to implicitly approximate a posterior distribution over latent encodings conditioned on multiple input sequences. We apply AVIB to a fundamental immuno-oncology problem: predicting the interactions between T-cell receptors (TCRs) and peptides. RESULTS: Experimental results on various datasets show that AVIB significantly outperforms state-of-the-art methods for TCR-peptide interaction prediction. Additionally, we show that the latent posterior distribution learned by AVIB is particularly effective for the unsupervised detection of out-of-distribution amino acid sequences. AVAILABILITY AND IMPLEMENTATION: The code and the data used for this study are publicly available at: https://github.com/nec-research/vibtcr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.