Information-theoretic approaches to SVM feature selection for metagenome read classification

Elaine Garbarine, Joseph Depasquale, Vinay Gadia, Robi Polikar, Gail Rosen

    Research output: Contribution to journalArticlepeer-review

    12 Scopus citations

    Abstract

    Analysis of DNA sequences isolated directly from the environment, known as metagenomics, produces a large quantity of genome fragments that need to be classified into specific taxa. Most composition-based classification methods use all features instead of a subset of features that may maximize classifier accuracy. We show that feature selection methods can boost performance of taxonomic classifiers. This work proposes three different filter-based feature selection methods that stem from information theory: (1) a technique that combines Kullback-Leibler, Mutual Information, and distance information, (2) a text mining technique, TF-IDF, and (3) minimum redundancy-maximum-relevance (mRMR). The feature selection methods are compared by how well they improve support vector machine classification of genomic reads. Overall, the 6mer mRMR method performs well, especially on the phyla-level. If the number of total features is very large, feature selection becomes difficult because a small subset of features that captures a majority of the data variance is less likely to exist. Therefore, we conclude that there is a trade-off between feature set size and feature selection method to optimize classification performance. For larger feature set sizes, TF-IDF works better for finer-resolutions while mRMR performs the best out of any method for N = 6 for all taxonomic levels.

    Original languageEnglish (US)
    Pages (from-to)199-209
    Number of pages11
    JournalComputational Biology and Chemistry
    Volume35
    Issue number3
    DOIs
    StatePublished - Jun 2011

    All Science Journal Classification (ASJC) codes

    • Structural Biology
    • Biochemistry
    • Organic Chemistry
    • Computational Mathematics

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