Predicting Disease Related microRNA Based on Similarity and Topology

• Main Authors: Zhihua Chen, Xinke Wang, Peng Gao, Hongju Liu, Bosheng Song
• Format: Article
• Language: English
• Published: MDPI AG 2019-11-01
• Series: Cells
• Subjects: mirna; network embedding; heterogeneous network; link prediction; topology information; machine learning
• Online Access: https://www.mdpi.com/2073-4409/8/11/1405

It is known that many diseases are caused by mutations or abnormalities in microRNA (miRNA). The usual method to predict miRNA disease relationships is to build a high-quality similarity network of diseases and miRNAs. All unobserved associations are ranked by their similarity scores, such that a higher score indicates a greater probability of a potential connection. However, this approach does not utilize information within the network. Therefore, in this study, we propose a machine learning method, called STIM, which uses network topology information to predict disease−miRNA associations. In contrast to the conventional approach, STIM constructs features according to information on similarity and topology in networks and then uses a machine learning model to predict potential associations. To verify the reliability and accuracy of our method, we compared STIM to other classical algorithms. The results of fivefold cross validation demonstrated that STIM outperforms many existing methods, particularly in terms of the area under the curve. In addition, the top 30 candidate miRNAs recommended by STIM in a case study of lung neoplasm have been confirmed in previous experiments, which proved the validity of the method.