DANE-MDA: Predicting microRNA-disease associations via deep attributed network embedding

Abstract

Summary Predicting the microRNA-disease associations by using computational methods is conductive to the efficiency of costly and laborious traditional bio-experiments. In this study, we propose a computational machine learning-based method (DANE-MDA) that preserves integrated structure and attribute features via deep attributed network embedding to predict potential miRNA-disease associations. Specifically, the integrated features are extracted by using deep stacked auto-encoder on the diverse orders of matrixes containing structure and attribute information and are then trained by using random forest classifier. Under 5-fold cross-validation experiments, DANE-MDA yielded average accuracy, sensitivity, and AUC at 85.59%, 84.23%, and 0.9264 in term of HMDD v3.0 dataset, and 83.21%, 80.39%, and 0.9113 in term of HMDD v2.0 dataset, respectively. Additionally, case studies on breast, colon, and lung neoplasms related disease show that 47, 47, and 46 of the top 50 miRNAs can be predicted and retrieved in the other database.