NTSMDA: prediction of miRNA–disease associations by integrating network topological similarity

Recently, accumulating studies have indicated that microRNAs (miRNAs) play an important role in exploring the pathogenesis of various human diseases at the molecular level and may result in the design of specific tools for diagnosis, treatment evaluation and prevention. Experimental identification of disease-related miRNAs is time-consuming and labour-intensive. Hence, there is a stressing need to propose efficient computational methods to detect more potential miRNA–disease associations. Currently, several computational approaches for identifying disease-related miRNAs on the miRNA–disease network have gained much attention by means of integrating miRNA functional similarities and disease semantic similarities. However, these methods rarely consider the network topological similarity of the miRNA–disease association network. Here, in this paper we develop an improved computational method named NTSMDA that is based on known miRNA–disease network topological similarity to exploit more potential disease-related miRNAs. We achieve an AUC of 89.4% by using the leave-one-out cross-validation experiment, demonstrating the excellent predictive performance of NTSMDA. Furthermore, predicted highly ranked miRNA–disease associations of breast neoplasms, lung neoplasms and prostatic neoplasms are manually confirmed by different related databases and literature, providing evidence for the good performance and potential value of the NTSMDA method in inferring miRNA–disease associations. The R code and readme file of NTSMDA can be downloaded from https://github.com/USTC-HIlab/NTSMDA.