Drug Sensitivity Prediction Based on Multi-stage Multi-modal Drug Representation Learning.

Abstract

Accurate prediction of anticancer drug responses is essential for developing personalized treatment plans in order to improve cancer patient survival rates and reduce healthcare costs. To this end, we propose a drug sensitivity prediction model based on multi-stage multi-modal drug representations (ModDRDSP) to reflect the properties of drugs more comprehensively, and to better model the complex interactions between cells and drugs. Specifically, we adopt the SMILES representation learning method based on the deep hierarchical bi-directional GRU network (DSBiGRU) and the molecular graph representation learning method based on the deep message-crossing network (DMCN) for the multi-modal information of drugs. Additionally, we integrate the multi-omics information of cell lines based on a convolutional neural network (CNN). Finally, we use an ensemble deep forest algorithm for the prediction of drug sensitivity. After validation, the ModDRDSP shows impressive performance which outperforms the four current industry-leading models. More importantly, ablation experiments demonstrate the validity of each module of the proposed model, and case studies show the good results of ModDRDSP for predicting drug sensitivity, further establishing the superiority of ModDRDSP in terms of performance.