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Comparison of methods for the detection of node group membership in bipartite networks

  • E. N. Sawardecker
  • C. A. Amundsen
  • M. Sales-Pardo
  • L. A.N. Amaral
Interdisciplinary Physics

Abstract

Most real-world networks considered in the literature have a modular structure. Analysis of these real-world networks often are performed under the assumption that there is only one type of node. However, social and biochemical systems are often bipartite networks, meaning that there are two exclusive sets of nodes, and that edges run exclusively between nodes belonging to different sets. Here we address the issue of module detection in bipartite networks by comparing the performance of two classes of group identification methods – modularity maximization and clique percolation – on an ensemble of modular random bipartite networks. We find that the modularity maximization methods are able to reliably detect the modular bipartite structure, and that, under some conditions, the simulated annealing method outperforms the spectral decomposition method. We also find that the clique percolation methods are not capable of reliably detecting the modular bipartite structure of the bipartite model networks considered.

Keywords

Simulated Annealing Mutual Information Community Detection Modularity Maximization Team Size 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    M.E.J. Newman, M. Girvan, Phys. Rev. E 69, 026113 (2004)CrossRefADSGoogle Scholar
  2. 2.
    R. Guimerà, L.A.N. Amaral, J. Stat. Mech.: Theor. Exp., P02001 (2005)Google Scholar
  3. 3.
    D.J. Watts, P.S. Dodds, M.E.J. Newman, Science 296, 1302 (2002)Google Scholar
  4. 4.
    L. Donetti, M.A. Muñoz, J. Stat. Mech.: Theor. Exp., P10012 (2004)Google Scholar
  5. 5.
    R. Guimerà, M. Sales-Pardo, L.A.N. Amaral, Phys. Rev. E 70, 025101 (2004)CrossRefADSGoogle Scholar
  6. 6.
    J. Reichardt, S. Bornholdt, Phys. Rev. Lett. 93, 218701 (2004)CrossRefADSGoogle Scholar
  7. 7.
    J. Duch, A. Arenas, Phys. Rev. E 72, 027104 (2005)CrossRefADSGoogle Scholar
  8. 8.
    G. Palla, I. Derényi, I. Farkas, T. Vicsek, Nature 435, 814 (2005)CrossRefADSGoogle Scholar
  9. 9.
    R. Guimerà, S. Mossa, A. Turtschi, L.A.N. Amaral, Proc. Natl. Acad. Sci. USA 102, 7794 (2005)MATHCrossRefMathSciNetADSGoogle Scholar
  10. 10.
    M. Sales-Pardo, R. Guimerà, A.A. Moreira, L.A.N. Amaral, Proc. Natl. Acad. Sci. USA 104, 15224 (2007)CrossRefADSGoogle Scholar
  11. 11.
    R. Guimerà, M. Sales-Pardo, L.A.N. Amaral, Nature Phys. 3, 63 (2007)CrossRefADSGoogle Scholar
  12. 12.
    M.E.J. Newman, Proc. Natl. Acad. Sci. USA 98, 404 (2001)MATHCrossRefMathSciNetADSGoogle Scholar
  13. 13.
    K. Börner, J.T. Maru, R.L. Goldstone, Proc. Natl. Acad. Sci. USA 101, 5266 (2004)CrossRefGoogle Scholar
  14. 14.
    R. Guimerà, B. Uzzi, J. Spiro, L.A.N. Amaral, Science 308, 697 (2005)CrossRefADSGoogle Scholar
  15. 15.
    M.J. Stringer, M. Sales-Pardo, L.A.N. Amaral, PLoS ONE 3, e1683 (2008)CrossRefGoogle Scholar
  16. 16.
    P. Uetz, L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart et al., Nature 403, 623 (2000)CrossRefADSGoogle Scholar
  17. 17.
    H. Jeong, S.P. Mason, A.L. Barabási, Z.N. Oltvai, Nature 411, 41 (2001)CrossRefADSGoogle Scholar
  18. 18.
    S. Maslov, K. Sneppen, Science 296, 910 (2002)CrossRefADSGoogle Scholar
  19. 19.
    S. Li, C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.O. Vidalain, J.D.J. Han, A. Chesneau, T. Hao et al., Science 303, 540 (2004)CrossRefADSGoogle Scholar
  20. 20.
    R. Guimerà, L.A.N. Amaral, Nature 433, 895 (2005)CrossRefADSGoogle Scholar
  21. 21.
    M.J. Barber, Phys. Rev. E 76, 066102 (2007)CrossRefMathSciNetADSGoogle Scholar
  22. 22.
    M.E.J. Newman, Proc. Natl. Acad. Sci. USA 103, 8577 (2006)CrossRefADSGoogle Scholar
  23. 23.
    S. Lehmann, M. Schwartz, L.K. Hansen, Phys. Rev. E 78,016108 (2008)CrossRefMathSciNetADSGoogle Scholar
  24. 24.
    L. Danon, A. Díaz-Guilera, J. Duch, A. Arenas, J. Stat. Mech.: Theor. Exp., P09008 (2005)Google Scholar
  25. 25.
    E.N. Sawardecker, M. Sales-Pardo, L.A.N. Amaral, Eur. Phys. J. B 67, 277 (2009)CrossRefADSGoogle Scholar
  26. 26.
    S. Fortunato, M. Barthélemy, Proc. Natl. Acad. Sci. USA 104, 36 (2007)CrossRefADSGoogle Scholar

Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • E. N. Sawardecker
    • 1
  • C. A. Amundsen
    • 2
  • M. Sales-Pardo
    • 1
    • 3
    • 4
  • L. A.N. Amaral
    • 1
    • 3
    • 5
  1. 1.Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonUSA
  2. 2.Department of Chemical and Biological EngineeringUniversity of Wisconsin – MadisonMadisonUSA
  3. 3.Northwestern Institute on Complex Systems, Northwestern UniversityEvanstonUSA
  4. 4.Northwestern University Clinical and Translational Sciences InstituteChicagoUSA
  5. 5.HHMI, Northwestern UniversityEvanstonUSA

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