DEMLP: DeepWalk Embedding in MLP for miRNA-Disease Association Prediction

Abstract

miRNAs significantly affect multifarious biological processes involving human disease. Biological experiments always need enormous financial support and time cost. Taking expense and difficulty into consideration, to predict the potential miRNA-disease associations, a lot of high-efficiency computational methods by computer have been developed, based on a network generated by miRNA-disease association dataset. However, there exist many challenges. Firstly, the association between miRNAs and diseases is intricate. These methods should consider the influence of the neighborhoods of each node from the network. Secondly, how to measure whether there is an association between two nodes of the network is also an important problem. In our study, we innovatively integrate graph node embedding with a multilayer perceptron and propose a method DEMLP. To begin with, we construct a miRNA-disease network by miRNA-disease adjacency matrix (MDA). Then, low-dimensional embedding representation vectors of nodes are learned from the miRNA-disease network by DeepWalk. Finally, we use these low-dimensional embedding representation vectors as input to train the multilayer perceptron. Experiments show that our proposed method that only utilized the miRNA–disease association information can effectively predict miRNA-disease associations. To evaluate the effectiveness of DEMLP in a miRNA-disease network from HMDD v3.2, we apply fivefold crossvalidation in our study. The ROC-AUC computed result value of DEMLP is 0.943, and the PR-AUC value of DEMLP is 0.937. Compared with other state-of-the-art methods, our method shows good performance using only the miRNA-disease interaction network.