GNNDRP: Graph Neural Network With Multi-Task Learning for Drug Response Prediction

Congzhi Song, Xuan Liu, Zhankun Xiong, Luotao Liu, Wen Zhang

Abstract: Using computational methods to personalize drug response prediction holds great promise to improve cancer therapy. Most existing methods use either biochemical information or response-related networks to predict drug response, nevertheless, the information they considered is not comprehensive. In this study, we present a novel end-to-end deep learning-based method Graph Neural Network with multi-task learning for Drug Response Prediction (GNNDRP). It leverages biochemical features as well as the hidden features from the heterogeneous network which incorporates the known drug-cell line responses, drug similarities, and cell line similarities, to complete the drug response prediction task. Moreover, GNNDRP designs a self-supervised task to enhance the representation capacity from the response network and further improve the model prediction performance. Extensive experiments show that GNNDRP outperforms existing state-of-the-art prediction methods under various experimental settings. The ablation analysis reveals that the biochemical characteristics, response-related network, and our self-supervised strategy can boost the predictive power. Additionally, case studies further validate the effectiveness of GNNDRP in identifying novel drug-cell line responses.

External IDs:doi:10.1109/tcbbio.2025.3548692