Heterogeneous ensemble approach with discriminative features and modified-SMOTEbagging for pre-miRNA classification

Supatcha Lertampaiporn, Chinae Thammarongtham, Chakarida Nukoolkit, Boonserm Kaewkamnerdpong, Marasri Ruengjitchatchawalya
2012 Nucleic Acids Research  
An ensemble classifier approach for microRNA precursor (pre-miRNA) classification was proposed based upon combining a set of heterogeneous algorithms including support vector machine (SVM), k-nearest neighbors (kNN) and random forest (RF), then aggregating their prediction through a voting system. Additionally, the proposed algorithm, the classification performance was also improved using discriminative features, self-containment and its derivatives, which have shown unique structural
more » ... characteristics of pre-miRNAs. These are applicable across different species. By applying preprocessing methods-both a correlation-based feature selection (CFS) with genetic algorithm (GA) search method and a modified-Synthetic Minority Oversampling Technique (SMOTE) bagging rebalancing method-improvement in the performance of this ensemble was observed. The overall prediction accuracies obtained via 10 runs of 5-fold cross validation (CV) was 96.54%, with sensitivity of 94.8% and specificity of 98.3%-this is better in trade-off sensitivity and specificity values than those of other state-of-the-art methods. The ensemble model was applied to animal, plant and virus pre-miRNA and achieved high accuracy, >93%. Exploiting the discriminative set of selected features also suggests that pre-miRNAs possess high intrinsic structural robustness as compared with other stem loops. Our heterogeneous ensemble method gave a relatively more reliable prediction than those using single classifiers. Our program is available at http://ncrna-pred .com/premiRNA.html.
doi:10.1093/nar/gks878 pmid:23012261 pmcid:PMC3592496 fatcat:ocdrrri7wvbpzioht2wjbk6osy