MCCMF: collaborative matrix factorization based on matrix completion for predicting miRNA-disease associations

BMC Bioinformatics

Xiang-Zhen Kong¹  Meng-Meng Yin¹  Tian-Ru Wu¹  Cui-Na Jiao¹  Ying-Lian Gao¹  Jin-Xing Liu¹ 

[1] School of Computer Science, Qufu Normal University, 276826, Rizhao, China;

关键词: MiRNA-disease association prediction;    Matrix completion;    Weight K Nearest Known Neighbors;    Matrix factorization;   

DOI  :  10.1186/s12859-020-03799-6

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (miRNAs) are non-coding RNAs with regulatory functions. Many studies have shown that miRNAs are closely associated with human diseases. Among the methods to explore the relationship between the miRNA and the disease, traditional methods are time-consuming and the accuracy needs to be improved. In view of the shortcoming of previous models, a method, collaborative matrix factorization based on matrix completion (MCCMF) is proposed to predict the unknown miRNA-disease associations.ResultsThe complete matrix of the miRNA and the disease is obtained by matrix completion. Moreover, Gaussian Interaction Profile kernel is added to the miRNA functional similarity matrix and the disease semantic similarity matrix. Then the Weight K Nearest Known Neighbors method is used to pretreat the association matrix, so the model is close to the reality. Finally, collaborative matrix factorization method is applied to obtain the prediction results. Therefore, the MCCMF obtains a satisfactory result in the fivefold cross-validation, with an AUC of 0.9569 (0.0005).ConclusionsThe AUC value of MCCMF is higher than other advanced methods in the fivefold cross validation experiment. In order to comprehensively evaluate the performance of MCCMF, accuracy, precision, recall and f-measure are also added. The final experimental results demonstrate that MCCMF outperforms other methods in predicting miRNA-disease associations. In the end, the effectiveness and practicability of MCCMF are further verified by researching three specific diseases.

【 授权许可】

CC BY