BANDRP: a bilinear attention network for anti-cancer drug response prediction based on fingerprint and multi-omics.

Predicting anti-cancer drug response can help with personalized cancer treatment and is an important topic in modern oncology research. Although some methods have been used for anti-cancer drug response prediction, how to effectively integrate various features related to cancer cell lines, drugs, and their known responses is still affected by the redundant information of input features and the complex interactions between features. In this study, we propose a bilinear attention model, named BANDRP, based on multiple omics data of cancer cell lines and multiple molecular fingerprints of drugs to predict potential anti-cancer drug responses. Compared with existing models, BANDRP uses gene expression data to calculate pathway enrichment scores to enrich the features of cancer cell lines and can automatically learn the interactive information of cancer cell lines and drugs through bilinear attention networks. Benchmarking and independent tests demonstrate that BANDRP surpasses baseline models and exhibits robust generalization performance. Ablation experiments affirm the optimality of the current model architecture and feature selection scheme for our prediction task. Furthermore, analytical experiments and case studies on unknown anti-cancer drug response predictions underscore BANDRP's potential as a potent and reliable framework for predicting anti-cancer drug response.