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Protein Classification Using Random Walk on Graph

  • Xiaohua Xu
  • Lin Lu
  • Ping He
  • Zhoujin Pan
  • Cheng Jing
Part of the Communications in Computer and Information Science book series (CCIS, volume 304)

Abstract

Inspired by the label propagation based on random walk, a basic classifier is proposed for biological computation. We apply this model to predict the localization of proteins, specifically the yeast and gram-negative bacteria protein data. A series of evaluations and comparisons are conducted to prove its excellent performance as an effectively independent classifier.

Keywords

random walk classification protein classification 

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References

  1. 1.
    Lovász, L.: Random Walks on Graphs: A Survey. Combinatorics. In: Paul Erdös is Eighty, vol. 2, pp. 1–46. Keszthely, Hungary (1993)Google Scholar
  2. 2.
    Szummer, M., Jaakkola, T.: Patially Labeled Classification with Markov Random Walk. In: Advances in Neural Information Processing Systems 14, pp. 945–952 (2002)Google Scholar
  3. 3.
    Zhu, X.J., Ghahramani, Z.B., John, L.: Semi-supervised Learning using Gaussian Fields and Harmonic Functions. In: The 20th International Conference on Machine Learning, pp. 912–919 (2003)Google Scholar
  4. 4.
    Zhu, X.J., John, L., Zoubin, G.: Combining Active Learning and Semi-supervised Learning using Gaussian Fields and Harmonic Functions. In: ICML 2003 Workshop on The Continuum from Labeled to Unlabeled Data in Machine Learning and Data Mining, pp. 58–65 (2003)Google Scholar
  5. 5.
    Smriti, B., Graham, C., Muthukrishnan, S.: Node Classification in Social Networks (2011), Arxiv preprint arXiv: 1101. 3291Google Scholar
  6. 6.
    Min, R., Bonner, A., Li, J., Zhang, Z.: Learned Random-Walk Kernels and Empirical-map Kernels for Protein Sequence Classification. J. Comput Biol. 16(3), 457–474 (2009)MathSciNetCrossRefGoogle Scholar
  7. 7.
    Freschi, V.: Protein Function Prediction from Interaction Networks using a Random Walk Ranking Algorithm. In: Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering BIBE 2007, pp. 42–48 (2007)Google Scholar
  8. 8.
    Xu, X.H. (ed.): Random Walk Learning on Graph. Nanjing University of Aeronautics and Astronautics, Nanjing (2008)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Xiaohua Xu
    • 1
  • Lin Lu
    • 1
  • Ping He
    • 1
  • Zhoujin Pan
    • 1
  • Cheng Jing
    • 1
  1. 1.Department of Computer ScienceYangzhou UniversityYangzhouChina

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