MLNGCF: circRNA–disease associations prediction with multilayer attention neural graph-based collaborative filtering

MOTIVATION: CircRNAs play a critical regulatory role in physiological processes, and the abnormal expression of circRNAs can mediate the processes of diseases. Therefore, exploring circRNAs–disease associations is gradually becoming an important area of research. Due to the high cost of validating circRNA–disease associations using traditional wet-lab experiments, novel computational methods based on machine learning are gaining more and more attention in this field. However, current computational methods suffer to insufficient consideration of latent features in circRNA–disease interactions. RESULTS: In this study, a multilayer attention neural graph-based collaborative filtering (MLNGCF) is proposed. MLNGCF first enhances multiple biological information with autoencoder as the initial features of circRNAs and diseases. Then, by constructing a central network of different diseases and circRNAs, a multilayer cooperative attention-based message propagation is performed on the central network to obtain the high-order features of circRNAs and diseases. A neural network-based collaborative filtering is constructed to predict the unknown circRNA–disease associations and update the model parameters. Experiments on the benchmark datasets demonstrate that MLNGCF outperforms state-of-the-art methods, and the prediction results are supported by the literature in the case studies. AVAILABILITY AND IMPLEMENTATION: The source codes and benchmark datasets of MLNGCF are available at https://github.com/ABard0/MLNGCF.