HMM-GDAN: Hybrid multi-view and multi-scale graph duplex-attention networks for drug response prediction in cancer

Abstract

Precision medicine is devoted to discovering personalized therapy for complex and difficult diseases like cancer. Many machine learning approaches have been developed for drug response prediction towards precision medicine. Notwithstanding, genetic profiles based multi-view graph learning schemes have not yet been explored for drug response prediction in previous works. Furthermore, multi-scale latent feature fusion is not considered sufficiently in the existing frameworks of graph neural networks (GNNs). Previous works on drug response prediction mainly depend on sequence data or single-view graph data. In this paper, we propose to construct multi-view graph by means of multi-omics data and STRING protein–protein association data, and develop a new architecture of GNNs for drug response prediction in cancer. Specifically, we propose hybrid multi-view and multi-scale graph duplex-attention networks (HMM-GDAN), in which both multi-view self-attention mechanism and view-level attention mechanism are devised to capture the complementary information of views and emphasize on the importance of each view collaboratively, and rich multi-scale features are constructed and integrated to further form high-level representations for better prediction. Experiments on GDSC2 dataset verify the superiority of the proposed HMM-GDAN when compared with state-of-the-art baselines. The effectiveness of multi-view and multi-scale strategies is demonstrated by the ablation study.