PMDAGS: Predicting miRNA-Disease Associations With Graph Nonlinear Diffusion Convolution Network and Similarities

Many studies have proven that microRNAs (miRNAs) can participate in a wide range of biological processes and can be considered as potential noninvasive biomarkers for disease diagnosis and prognosis. Therefore, many computational methods have been developed to identifying miRNA-disease associations, ultimately enhancing the efficiency of disease diagnosis and treatment. In this study, we also introduced a new computational method called PMDAGS, which predicts miRNA-disease associations by utilizing graph nonlinear diffusion convolution network and similarities. PMDAGS first calculates miRNA similarity and disease similarity based on miRNA-target interactions, disease-gene associations and known miRNA-disease associations, respectively. Next, we construct the initial feature of each miRNA (disease) by concatenating its final similarity vector with its known association vector. Based on the known miRNA-disease association network and the initial feature vector of each node, we further apply nonlinear diffusion graph convolution network model to extract the feature embedding vectors. Finally, we concatenate the feature embedding vectors of miRNA and disease and input them into a multi-layer perceptron to identify potential miRNA-disease associations. We conduct 5-fold cross validation (5CV), 10-fold cross validation (10CV), and global leave-one-out cross validation (GLOOCV) on HMDD v2.0 and HMDD v3.2. PMDAGS achieves AUCs of 0.9222, 0.9228, and 0.9221 under 5CV, 10CV and GLOOCV on HMDD v2.0, respectively. In addition, PMDAGS also achieves AUC values of 0.9366, 0.9377, and 0.9376 under 5CV, 10CV and GLOOCV on HMDD v3.2, respectively. According to the experimental results, we can conclude that PMDAGS outperforms other compared methods and can effectively predict miRNA-disease associations.