Potential circRNA-disease association prediction using DeepWalk and network consistency projection

• We present a measurement to calculate the similarities for circRNAs and diseases. • A similarity-based model is proposed for excavating circRNA-disease associations. • The method does not need any additional biological features in the prediction process. • The method achieves impressive performance and can effectively predict novel disease circRNAs. A growing body of experimental studies have reported that circular RNAs (circRNAs) are of interest in pathogenicity mechanism research and are becoming new diagnostic biomarkers. As experimental techniques for identifying disease-circRNA interactions are costly and laborious, some computational predictors have been advanced on the basis of the integration of biological features about circRNAs and diseases. However, the existing circRNA-disease relationships are not well exploited. To solve this issue, a novel method named DeepWalk and network consistency projection for circRNA-disease association prediction (DWNCPCDA) is proposed. Specifically, our method first reveals features of nodes learned by the deep learning method DeepWalk based on known circRNA-disease associations to calculate circRNA-circRNA similarity and disease-disease similarity, and then these two similarity networks are further employed to feed to the network consistency projection method to predict unobserved circRNA-disease interactions. As a result, DWNCPCDA shows high-accuracy performances for disease-circRNA interaction prediction: an AUC of 0.9647 with leave-one-out cross validation and an average AUC of 0.9599 with five-fold cross validation. We further perform case studies to prioritize latent circRNAs related to complex human diseases. Overall, this proposed method is able to provide a promising solution for disease-circRNA interaction prediction, and is capable of enhancing existing similarity-based prediction methods.