DNRLMF-MDA:Predicting microRNA-Disease Associations Based on Similarities of microRNAs and Diseases

MicroRNAs (miRNAs) are a class of non-coding RNAs about $\sim$ 22nt nucleotides. Studies have proven that miRNAs play key roles in many human complex diseases. Therefore, discovering miRNA-disease associations is beneficial to understanding disease mechanisms, developing drugs, and treating complex diseases. It is well known that it is a time-consuming and expensive process to discover the miRNA-disease associations via biological experiments. Alternatively, computational models could provide a low-cost and high-efficiency way for predicting miRNA-disease associations. In this study, we propose a method (called DNRLMF-MDA) to predict miRNA-disease associations based on dynamic neighborhood regularized logistic matrix factorization. DNRLMF-MDA integrates known miRNA-disease associations, functional similarity and Gaussian Interaction Profile (GIP) kernel similarity of miRNAs, and functional similarity and GIP kernel similarity of diseases. Especially, positive observations (known miRNA-disease associations) are assigned higher importance levels than negative observations (unknown miRNA-disease associations).DNRLMF-MDA computes the probability that a miRNA would interact with a disease by a logistic matrix factorization method, where latent vectors of miRNAs and diseases represent the properties of miRNAs and diseases, respectively, and further improve prediction performance via dynamic neighborhood regularized. The 5-fold cross validation is adopted to assess the performance of our DNRLMF-MDA, as well as other competing methods for comparison. The computational experiments show that DNRLMF-MDA outperforms the state-of-art method PBMDA. The AUC values of DNRLMF-MDA on three datasets are 0.9357, 0.9411, and 0.9416, respectively, which are superior to the PBMDA's results of 0.9218, 0.9187, and 0.9262. The average computation times per 5-fold cross validation of DNRLMF-MDA on three datasets are 38, 46, and 50 seconds, which are shorter than the PBMDA's average computation times of 10869, 916, and 8448 seconds, respectively. DNRLMF-MDA also can predict potential diseases for new miRNAs. Furthermore, case studies illustrate that DNRLMF-MDA is an effective method to predict miRNA-disease associations.