Algorithms and Applications pp 130-146

Part of the Lecture Notes in Computer Science book series (LNCS, volume 6060) | Cite as

Clustering the Normalized Compression Distance for Influenza Virus Data

  • Kimihito Ito
  • Thomas Zeugmann
  • Yu Zhu

Abstract

The present paper analyzes the usefulness of the normalized compression distance for the problem to cluster the hemagglutinin (HA) sequences of influenza virus data for the HA gene in dependence on the available compressors. Using the CompLearn Toolkit, the built-in compressors zlib and bzip2 are compared.

Moreover, a comparison is made with respect to hierarchical and spectral clustering. For the hierarchical clustering, hclust from the R package is used, and the spectral clustering is done via the kLine algorithm proposed by Fischer and Poland (2004).

Our results are very promising and show that one can obtain an (almost) perfect clustering. It turned out that the zlib compressor allowed for better results than the bzip2 compressor and, if all data are concerned, then hierarchical clustering is a bit better than spectral clustering via kLines.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Kimihito Ito
    • 1
  • Thomas Zeugmann
    • 2
  • Yu Zhu
    • 2
  1. 1.Research Center for Zoonosis ControlHokkaido UniversitySapporoJapan
  2. 2.Division of Computer ScienceHokkaido UniversityJapan

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