GADRP: graph convolutional networks and autoencoders for cancer drug response prediction

Abstract

Drug response prediction in cancer cell lines is of great significance in personalized medicine. In this study, we propose GADRP, a cancer drug response prediction model based on graph convolutional networks (GCNs) and autoencoders (AEs). We first use a stacked deep AE to extract low-dimensional representations from cell line features, and then construct a sparse drug cell line pair (DCP) network incorporating drug, cell line, and DCP similarity information. Later, initial residual and layer attention-based GCN (ILGCN) that can alleviate over-smoothing problem is utilized to learn DCP features. And finally, fully connected network is employed to make prediction. Benchmarking results demonstrate that GADRP can significantly improve prediction performance on all metrics compared with baselines on five datasets. Particularly, experiments of predictions of unknown DCP responses, drug-cancer tissue associations， and drug-pathway associations illustrate the predictive power of GADRP. All results highlight the effectiveness of GADRP in predicting drug responses, and its potential value in guiding anti-cancer drug selection.