Effective sample selection for classification of pre-miRNAs

To solve the class imbalance problem in the classification of pre-miRNAs with the ab initio method, we developed a novel sample selection method according to the characteristics of pre-miRNAs. Real/pseudo pre-miRNAs are clustered based on their stem similarity and their distribution in high dimensional sample space, respectively. The training samples are selected according to the sample density of each cluster. Experimental results are validated by the cross-validation and other testing datasets composed of human real/pseudo pre-miRNAs. When compared with the previous method, microPred, our classifier miRNAPred is nearly 12% more accurate. The selected training samples also could be used to train other SVM classifiers, such as tripletSVM, MiPred, miPred, and microPred, to improve their classification performance. The sample selection algorithm is useful for constructing a more efficient classifier for the classification of real pre-miRNAs and pseudo hairpin sequences.