Oncotarget

Research Papers:

SSCMDA: spy and super cluster strategy for MiRNA-disease association prediction

Qi Zhao _, Di Xie, Hongsheng Liu, Fan Wang, Gui-Ying Yan and Xing Chen

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Oncotarget. 2018; 9:1826-1842. https://doi.org/10.18632/oncotarget.22812

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Abstract

Qi Zhao1,2, Di Xie1, Hongsheng Liu2,3, Fan Wang4,5, Gui-Ying Yan6 and Xing Chen7

1School of Mathematics, Liaoning University, Shenyang, China

2Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang, China

3School of Life Science, Liaoning University, Shenyang, China

4School of Mechatronic Engineering, China University of Mining and Technology, Xuzhou, China

5Jiangsu Key Laboratory of Mine Mechanical and Electrical Equipment, China University of Mining and Technology, Xuzhou, China

6Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China

7School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China

Correspondence to:

Qi Zhao, email: zhaoqi@lnu.edu.cn

Xing Chen, email: xingchen@amss.ac.cn

Keywords: microRNA; disease; association prediction; spy strategy; super cluster strategy

Received: July 18, 2017     Accepted: October 30, 2017     Published: December 01, 2017

ABSTRACT

In the biological field, the identification of the associations between microRNAs (miRNAs) and diseases has been paid increasing attention as an extremely meaningful study for the clinical medicine. However, it is expensive and time-consuming to confirm miRNA-disease associations by experimental methods. Therefore, in recent years, several effective computational models for predicting the potential miRNA-disease associations have been developed. In this paper, we proposed the Spy and Super Cluster strategy for MiRNA-Disease Association prediction (SSCMDA) based on known miRNA-disease associations, integrated disease similarity and integrated miRNA similarity. For problems of mixed unknown miRNA-disease pairs containing both potential associations and real negative associations, which will lead to inaccurate prediction, spy strategy is adopted by SSCMDA to identify reliable negative samples from the unknown miRNA-disease pairs. Moreover, the super-cluster strategy could gather as many positive samples as possible to improve the accuracy of the prediction by overcoming the shortage of lacking sufficient positive training samples. As a result, the AUCs of global leave-one-out cross validation (LOOCV), local LOOCV and 5-fold cross validation were 0.9007, 0.8747 and 0.8806+/-0.0025, respectively. According to the AUC results, SSCMDA has shown a significant improvement compared with some previous models. We further carried out case studies based on various version of HMDD database to test the prediction performance robustness of SSCMDA. We also implemented case study to examine whether SSCMDA was effective for new diseases without any known associated miRNAs. As a result, a large proportion of the predicted miRNAs have been verified by experimental reports.


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