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A combination of feature extraction methods with an ensemble of different classifiers for protein structural class prediction problem

Dehzangi, A. and Paliwal, K.K. and Sharma, Alokanand and Dehzangi, O. and Sattar, A. (2013) A combination of feature extraction methods with an ensemble of different classifiers for protein structural class prediction problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, N/A . p. 1. ISSN 1557-9964

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    Abstract

    Better understanding of structural class of a given protein reveals important information about its overall folding type and its domain. It can also be directly used to provide critical information on general tertiary structure of a protein which has a profound impact on protein function determination and drug design. Despite tremendous enhancements made by pattern recognition-based approaches to solve this problem, it still remains as an unsolved issue for bioinformatics which demands more attention and exploration. In this study, we propose a novel feature extraction model which incorporates physicochemical and evolutionary-based information simultaneously. We also propose overlapped segmented distribution and autocorrelation based feature extraction methods to provide more local and global discriminatory information. The proposed feature extraction methods are explored for 15 most promising attributes that are selected from a wide range of physicochemical-based attributes. Finally, by applying an ensemble of different classifiers namely, Adaboost.M1, LogitBoost, Naive Bayes, Multi-Layer Perceptron (MLP), and Support Vector Machine (SVM) we show enhancement of the protein structural class prediction accuracy for four popular benchmarks.

    Item Type: Journal Article
    Additional Information: This article has been published online. The print version has yet to be released.
    Subjects: T Technology > T Technology (General)
    Divisions: Faculty of Science, Technology and Environment (FSTE) > School of Engineering and Physics
    Depositing User: Alokanand Sharma
    Date Deposited: 06 Nov 2013 10:36
    Last Modified: 15 Jun 2016 14:44
    URI: http://repository.usp.ac.fj/id/eprint/6996
    UNSPECIFIED

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