Kernel design for RNA classification using Support Vector Machines

Jason T.L. Wang, Xiaoming Wu

Research output: Contribution to journalArticlepeer-review

33 Scopus citations

Abstract

Support Vector Machines (SVMs) are a state-of-the-art machine learning tool widely used in speech recognition, image processing and biological sequence analysis. An essential step in SVMs is to devise a kernel function to compute the similarity between two data points. In this paper we review recent advances of using SVMs for RNA classification. In particular we present a new kernel that takes advantage of both global and local structural information in RNAs and uses the information together to classify RNAs. Experimental results demonstrate the good performance of the new kernel and show that it outperforms existing kernels when applied to classifying non-coding RNA sequences.

Original languageEnglish (US)
Pages (from-to)57-76
Number of pages20
JournalInternational Journal of Data Mining and Bioinformatics
Volume1
Issue number1
DOIs
StatePublished - Jan 1 2006

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Library and Information Sciences

Keywords

  • RNA sequence and structure
  • Support Vector Machines (SVMs)
  • bioinformatics
  • data mining
  • kernel methods

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