INTS-MFS:A novel method to predict microRNA-disease associations by integrating network topology similarity and microRNA function similarity

Identifying associations between microRNAs(miRNAs)and diseases is very important to understand the occurrence and development of human diseases.However,these existing methods suffer from the following limitation:first,some disease-related miRNAs are obtained from the miRNA functional similarity networks consisting of heterogeneous data sources,i.e.,disease similarity,protein interaction network,gene expression.Second,little approaches infer disease-related miRNAs depending on the network topological features without the functional similarity of miRNAs.In this paper,we develop a novel model of Integrating Network Topology Similarity and MicroRNA Function Similarity(INTS-MFS).The integrated miRNA similarities are calculated based on miRNA functional similarity and network topological characteristics.INTS-MFS obtained AUC of 0.872 based on five-fold cross-validation and was applied to three common human diseases in case studies.As a results,30 out of top 30 predicted Prostatic Neoplasm-related miRNAs were included in the two databases of dbDEMC and PhenomiR2.0.29 out of top 30 predicted Lung Neoplasm-related miRNAs and Breast Neoplasm-related miRNAs were included in dbDEMC,PhenomiR2.0 and experimental reports.Moreover,INTS-MFS found unknown association with hsa-mir-371a in breast cancer and lung cancer,which have not been reported.It provides biologists new clues for diagnosing breast and lung cancer.

MDA-TOEPGA:A novel method to identify miRNA-disease association based on two-objective evolutionary programming genetic algorithm

The association between miRNA and disease has attracted more and more attention.Until now,existing methods for identifying miRNA related disease mainly rely on top-ranked association model,which may not provide a full landscape of association between miRNA and disease.Hence there is strong need of new computational method to identify the associations from miRNA group view.In this paper,we proposed a framework,MDA-TOEPGA,to identify miRNAdisease association based on two-objective evolutionary programming genetic algorithm,which identifies latent miRNAdisease associations from the view of functional module.To understand the miRNA functional module in diseases,the case study is presented.We have been compared MDA-TOEPGA with several state-of-the-art functional module algorithm.Experimental results showed that our method cannot only outperform classical algorithms,such as K-means,IK-means,MCODE,HC-PIN,and ClusterONE,but can also achieve an ideal overall performance in terms of a composite score consisting of f1,Sensitivity,and Accuracy.Altogether,our study showed that MDA-TOEPGA is a promising method to investigate miRNA-disease association from the landscapes of functional module.