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Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality

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Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 5808))

Abstract

We present new decomposition heuristics for finding the optimal solution for the maximum-weight connected graph problem, which is known to be NP-hard. Previous optimal algorithms for solving the problem decompose the input graph into subgraphs using heuristics based on node degree. We propose new heuristics based on betweenness centrality measures, and show through computational experiments that our new heuristics tend to reduce the number of subgraphs in the decomposition, and therefore could lead to the reduction in computational time for finding the optimal solution. The method is further applied to analysis of biological pathway data.

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References

  1. Lee, H.F., Dooly, D.R.: Algorithms for the constrained maximum-weight connected graph problem. Naval Research Logistics 43(7), 985–1008 (1996)

    Article  MathSciNet  MATH  Google Scholar 

  2. Lee, H.F., Dooly, D.R.: Decomposition algorithms for the maximum-weight connected graph problem. Naval Research Logistics 45(8), 817–837 (1998)

    Article  MathSciNet  MATH  Google Scholar 

  3. Lee, H.F., Dooly, D.R.: Heuristic algorithms for the fiber optic network expansion problem. Telecommunication Systems 7(4), 355–378 (1997)

    Article  Google Scholar 

  4. Lee, H.F., Dooly, D.R.: The maximum-weight connected graph problem. Technical Report 93-4, Industrial Engineering, Southern Illinois University (1993) (revised November 1995)

    Google Scholar 

  5. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y.: KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480–D484 (2008)

    Article  Google Scholar 

  6. Choi, C., Crass, T., Kel, A., Kel-Margoulis, O., Krull, M., Pistor, S., Potapov, A., Voss, N., Wingender, E.: Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database. Genome Inform. 15(2), 244–254 (2004)

    Google Scholar 

  7. Keseler, I.M., Bonavides-Martínez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T., Peralta-Gil, M., Santos-Zavaleta, A., Shearer, A.G., Karp, P.D.: EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res. 37, D464–D470 (2009)

    Article  Google Scholar 

  8. Vastrik, I., D’Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., Stein, L.: Reactome: a knowledge base of biologic pathways and processes. Genome Biology 8(R39) (2007)

    Google Scholar 

  9. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Edgar, R.: NCBI GEO: mining tens of millions of expression profiles – database and tools update. Nucleic Acids Res. 35, D760–D765 (2007)

    Article  Google Scholar 

  10. Brandes, U.: A faster algorithm for betweenness centrality. Journal of Mathematical Sociology 25(2), 163–177 (2001)

    Article  MATH  Google Scholar 

  11. Gumz, M., Zou, H., Kreinest, P., Childs, A., Belmonte, L., LeGrand, S., Wu, K., Luxon, B., Sinha, M., Parker, A., Sun, L., Ahlquist, D., Wood, C., Copland, J.: Secreted frizzled-related protein 1 loss contributes to tumor phenotype of clear cell renal cell carcinoma. Clin. Cancer Res. 13(16), 4740–4749 (2007)

    Article  Google Scholar 

  12. Edgar, R., Domrachev, M., Lash, A.: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30(1), 207–210 (2002)

    Article  Google Scholar 

  13. Nagasaki, M., Saito, A., Li, C., Jeong, E., Miyano, S.: Systematic reconstruction of TRANSPATH data into cell system markup language. BMC Systems Biology 2(53), (2008)

    Google Scholar 

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© 2009 Springer-Verlag Berlin Heidelberg

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Yamamoto, T., Bannai, H., Nagasaki, M., Miyano, S. (2009). Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality. In: Gama, J., Costa, V.S., Jorge, A.M., Brazdil, P.B. (eds) Discovery Science. DS 2009. Lecture Notes in Computer Science(), vol 5808. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04747-3_40

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  • DOI: https://doi.org/10.1007/978-3-642-04747-3_40

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04746-6

  • Online ISBN: 978-3-642-04747-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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