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Human Papillomavirus Risk Type Classification from Protein Sequences Using Support Vector Machines

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Applications of Evolutionary Computing (EvoWorkshops 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3907))

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Abstract

Infection by the human papillomavirus (HPV) is associated with the development of cervical cancer. HPV can be classified to high- and low-risk type according to its malignant potential, and detection of the risk type is important to understand the mechanisms and diagnose potential patients. In this paper, we classify the HPV protein sequences by support vector machines. A string kernel is introduced to discriminate HPV protein sequences. The kernel emphasizes amino acids pairs with a distance. In the experiments, our approach is compared with previous methods in accuracy and F1-score, and it has showed better performance. Also, the prediction results for unknown HPV types are presented.

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Author information

Authors and Affiliations

  1. Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, 151-744, South Korea

    Sun Kim & Byoung-Tak Zhang

Authors
  1. Sun Kim
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  2. Byoung-Tak Zhang
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Editor information

Editors and Affiliations

  1. Johannes Gutenberg University, Mainz, Germany

    Franz Rothlauf

  2. Institute AIFB, University of Karlsruhe, 76128, Karlsruhe, Germany

    Jürgen Branke

  3. Dipartimento di Ingegneria dell’Informazione, Università di Parma,  

    Stefano Cagnoni

  4. Centre of Informatics and Systems of the University of Coimbra,  

    Ernesto Costa

  5. Dept. LCC, Universidad de Málaga, Spain

    Carlos Cotta

  6. Institute of Computer Science, University of Bremen, 28359, Bremen, Germany

    Rolf Drechsler

  7. INRIA Saclay - Ile-de-France, Parc Orsay Université, 4, rue Jacques Monod, 91893, ORSAY Cedex, France

    Evelyne Lutton

  8. CISUC, Department of Informatics Engineering, University of Coimbra, Polo II of the University of Coimbra, 3030, Coimbra, Portugal

    Penousal Machado

  9. Dartmouth College, Lebanon, NH, USA

    Jason H. Moore

  10. Universidade de A Coruña, CP 15071, A Coruña, Spain

    Juan Romero

  11. School of Computing Sciences, UEA Norwich, University of East Anglia, NR4 7TJ, Norwich, UK

    George D. Smith

  12. Dipartimento di Automatica e Informatica, Politecnico di Torino, Italy

    Giovanni Squillero

  13. Kyushu University, Japan

    Hideyuki Takagi

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© 2006 Springer-Verlag Berlin Heidelberg

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Kim, S., Zhang, BT. (2006). Human Papillomavirus Risk Type Classification from Protein Sequences Using Support Vector Machines. In: Rothlauf, F., et al. Applications of Evolutionary Computing. EvoWorkshops 2006. Lecture Notes in Computer Science, vol 3907. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11732242_6

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  • DOI: https://doi.org/10.1007/11732242_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-33237-4

  • Online ISBN: 978-3-540-33238-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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