title: miRBoost: boosting support vector machines for microRNA precursor classification.
abstract: Identification of microRNAs (miRNAs) is an important step toward understanding post-transcriptional gene regulation and miRNA-related pathology. Difficulties in identifying miRNAs through experimental techniques combined with the huge amount of data from new sequencing technologies have made in silico discrimination of bona fide miRNA precursors from non-miRNA hairpin-like structures an important topic in bioinformatics. Among various techniques developed for this classification problem, machine learning approaches have proved to be the most promising. However these approaches require the use of training data, which is problematic due to an imbalance in the number of miRNAs (positive data) and non-miRNAs (negative data), which leads to a degradation of their performance. In order to address this issue, we present an ensemble method that uses a boosting technique with support vector machine components to deal with imbalanced training data. Classification is performed following a feature selection on 187 novel and existing features. The algorithm, miRBoost, performed better in comparison with state-of-the-art methods on imbalanced human and cross-species data. It also showed the highest ability among the tested methods for discovering novel miRNA precursors. In addition, miRBoost was over 1400 times faster than the second most accurate tool tested and was significantly faster than most of the other tools. miRBoost thus provides a good compromise between prediction efficiency and execution time, making it highly suitable for use in genome-wide miRNA precursor prediction. The software miRBoost is available on our web server http://EvryRNA.ibisc.univ-evry.fr.
authors: IBISC - IBGBI, University of Evry, 91037 Evry CEDEX, France Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors: Van Du T
authors: Vdu T
authors: Tran
authors: IBISC - IBGBI, University of Evry, 91037 Evry CEDEX, France LCB, CNRS UMR 7283, 13009 Marseille, France.
authors: Sebastien
authors: S
authors: Tempel
authors: IBISC - IBGBI, University of Evry, 91037 Evry CEDEX, France.
authors: Benjamin
authors: B
authors: Zerath
authors: IBISC - IBGBI, University of Evry, 91037 Evry CEDEX, France.
authors: Farida
authors: F
authors: Zehraoui
authors: IBISC - IBGBI, University of Evry, 91037 Evry CEDEX, France tahi@ibisc.univ-evry.fr.
authors: Fariza
authors: F
authors: Tahi
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D035683:MicroRNAs / Q000145:classification* / Q000235:genetics; D012322:RNA Precursors / Q000145:classification* / Q000235:genetics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D012984:Software; D060388:Support Vector Machine
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors
keywords: boosting; classification; imbalanced data; microRNA prediction; support vector machine (SVM)