DeepEAG: An edge-powered graph neural network using SMILES augmentation for cancer drug response prediction

Abstract Motivation:: The prediction of cancer drug response is a challenging subject in modern personalized cancer therapy due to the uncertainty of drug efficacy and the heterogeneity of patients. It has been shown that the characteristics of the drug itself and the genomic characteristics of the patient can greatly influence the results of cancer drug response. Therefore, accurate, efficient, and comprehensive methods for drug feature extraction and genomics integration are crucial to improve the prediction accuracy. Results:: Accurate prediction of cancer drug response is vital for guiding the design of anticancer drugs. In this study, we propose an end-to-end deep learning model named DeepEAG which is based on a complete-graph update mode to predict IC50. Specifically, we integrate an edge update mechanism on the basis of a hybrid graph convolutional network to comprehensively learn the potential high-dimensional representation of topological structures in drugs, including atomic characteristics and chemical bond information. Additionally, we present a novel approach for enhancing Simplified Molecular Input Line Entry Specification (SMILES) data by employing sequence recombination to eliminate the defect of single sequence representation of drug molecules. Our extensive experiments show that DeepEAG outperforms other existing methods across multiple evaluation parameters in multiple test sets. Furthermore, we identify several potential anticancer agents, including bortezomib, which has proven to be an effective clinical treatment option. Our results highlight the potential value of DeepEAG in guiding the design of specific cancer treatment regimens.