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Prediction of Protein Subcellular Multi-locations with a Min-Max Modular Support Vector Machine

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Advances in Neural Networks - ISNN 2006 (ISNN 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3973))

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Abstract

How to predict subcellular multi-locations of proteins with machine learning techniques is a challenging problem in computational biology community. Regarding the protein multi-location problem as a multi-label pattern classification problem, we propose a new predicting method for dealing with the protein subcellular localization problem in this paper. Two key points of the proposed method are to divide a seriously unbalanced multi-location problem into a number of more balanced two-class subproblems by using the part-versus-part task decomposition approach, and learn all of the subproblems by using the min-max modular support vector machine (M3-SVM). To evaluate the effectiveness of the proposed method, we perform experiments on yeast protein data set by using two kinds of task decomposition strategies and three kinds of feature extraction methods. The experimental results demonstrate that our method achieves the highest prediction accuracy, which is much better than that obtained by the existing approach based on the traditional support vector machine.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Rd., Shanghai, 200240, China

    Yang Yang & Bao-Liang Lu

Authors
  1. Yang Yang
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  2. Bao-Liang Lu
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Editor information

Editors and Affiliations

  1. Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

    Jun Wang

  2. Computational Intelligence Laboratory, School of Computer Science and Engineering, University of Electronic Science and Technology of China, 610054, Chengdu, P.R. China

    Zhang Yi

  3. Department of Electrical Engineering, University of Louisville, 40292, Louisville, KY, U.S.A

    Jacek M. Zurada

  4. Laboratory for Computational Biology, Shanghai Center for Systems Biomedicine, 800 Dong Chuan Rd, 200240, Shanghai, China

    Bao-Liang Lu

  5. School of Electrical and Electronic Engineering, University of Manchester, UK

    Hujun Yin

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© 2006 Springer-Verlag Berlin Heidelberg

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Yang, Y., Lu, BL. (2006). Prediction of Protein Subcellular Multi-locations with a Min-Max Modular Support Vector Machine. In: Wang, J., Yi, Z., Zurada, J.M., Lu, BL., Yin, H. (eds) Advances in Neural Networks - ISNN 2006. ISNN 2006. Lecture Notes in Computer Science, vol 3973. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11760191_98

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  • DOI: https://doi.org/10.1007/11760191_98

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-34482-7

  • Online ISBN: 978-3-540-34483-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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