Biology

Support vector machine

Binary classification

Theoretical computer science

Set (abstract data type)

Computer science

Code (set theory)

Drug

Graph

Pattern recognition (psychology)

Mathematics

Drug response

Pharmacology

Artificial intelligence

Programming language

Deep learning

Artificial neural network

Binary number

Convolutional neural network

Machine learning

Arithmetic

Convolution (computer science)

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Drug response prediction is an important problem in computational personalized medicine. Many machine-learning-based methods, especially deep learning-based ones, have been proposed for this task. However, these methods often represent the drugs as strings, which are not a natural way to depict molecules. Also, interpretation (e.g., what are the mutation or copy number aberration contributing to the drug response) has not been considered thoroughly.In this study, we propose a novel method, GraphDRP, based on graph convolutional network for the problem. In GraphDRP, drugs were represented in molecular graphs directly capturing the bonds among atoms, meanwhile cell lines were depicted as binary vectors of genomic aberrations. Representative features of drugs and cell lines were learned by convolution layers, then combined to represent for each drug-cell line pair. Finally, the response value of each drug-cell line pair was predicted by a fully-connected neural network. Four variants of graph convolutional networks were used for learning the features of drugs.We found that GraphDRP outperforms tCNNS in all performance measures for all experiments. Also, through saliency maps of the resulting GraphDRP models, we discovered the contribution of the genomic aberrations to the responses.Representing drugs as graphs can improve the performance of drug response prediction. Availability of data and materials: Data and source code can be downloaded athttps://github.com/hauldhut/GraphDRP.

Graph Convolutional Networks for Drug Response Prediction