Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism

Abstract

Abstract Recent studies have shown that the expression of circRNAs would affect drug sensitivity of cells and thus significantly influence the efficacy of drugs. Traditional biomedical experiments to validate such relationships are time-consuming and costly. Therefore, developing effective computational methods to predict potential associations between circRNAs and drug sensitivity is an important and urgent task. In this study, we propose a novel method, called MNGACDA, to predict possible circRNA–drug sensitivity associations for further biomedical screening. First, MNGACDA uses multiple sources of information from circRNAs and drugs to construct multimodal networks. It then employs node-level attention graph auto-encoders to obtain low-dimensional embeddings for circRNAs and drugs from the multimodal networks. Finally, an inner product decoder is applied to predict the association scores between circRNAs and drug sensitivity based on the embedding representations of circRNAs and drugs. Extensive experimental results based on cross-validations show that MNGACDA outperforms six other state-of-the-art methods. Furthermore, excellent performance in case studies demonstrates that MNGACDA is an effective tool for predicting circRNA–drug sensitivity associations in real situations. These results confirm the reliable prediction ability of MNGACDA in revealing circRNA–drug sensitivity associations.