Predicting Anti-Cancer Drug Response Based on Hypergraph Representation Learning

Accurate prediction of drug responses is critical for advancing personalized cancer therapies. Although current graph neural network (GNN)-based approaches predominantly focus on pairwise interactions between cell lines and drugs, they often neglect the potential of higher-order interactions. In this study, we present HRLCDR, a novel computational framework that utilizes Hypergraph Representation Learning to predict Cancer Drug Responses. HRLCDR begins by constructing hypergraphs for both cell lines and drugs and then processes through low-pass and high-pass hypergraph convolutions, allowing the model to extract both common and different features from the complex higher-order interactions between cell lines and drugs. After that, HRLCDR constructs a heterogeneous graph using known cell line responses to drugs. Parallel heterogeneous graph convolution operations are then employed to extract primary interaction features between cell lines and drugs from these associations. Finally, HRLCDR integrates the features learned from both the hypergraphs and the heterogeneous graph, predicting drug response via Classifiers. We evaluated HRLCDR's performance on two major cancer drug response datasets: the Cancer Drug Sensitivity Data (GDSC) and the Cancer Cell Line Encyclopedia (CCLE). The results demonstrate that HRLCDR outperforms current state-of-the-art methods, underscoring its potential to enhance the accuracy and reliability of cancer drug response predictions.