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GRASP with Path-Relinking for Data Clustering: A Case Study for Biological Data

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Experimental Algorithms (SEA 2011)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6630))

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Abstract

Cluster analysis has been applied to several domains with numerous applications. In this paper, we propose several GRASP with path-relinking heuristics for data clustering problems using as case study biological datasets. All these variants are based on the construction and local search procedures introduced by Nascimento et. al [22]. We hybridized the GRASP proposed by Nascimento et. al [22] with four alternatives for relinking method: forward, backward, mixed, and randomized. To our knowledge, GRASP with path-relinking has never been applied to cluster biological datasets. Extensive comparative experiments with other algorithms on a large set of test instances, according to different distance metrics (Euclidean, city block, cosine, and Pearson), show that the best of the proposed variants is both effective and efficient.

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References

  1. Aiex, R.: Uma investigação experimental da distribuição de probabilidade de tempo de solução em heurísticas GRASP e sua aplicação na análise de implementações paralelas. Ph.D. thesis, Department of Computer Science, Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil (2002)

    Google Scholar 

  2. Aiex, R., Binato, S., Resende, M.: Parallel GRASP with path-relinking for job shop scheduling. Parallel Computing 29, 393–430 (2003)

    Article  MathSciNet  Google Scholar 

  3. Aiex, R., Resende, M., Pardalos, P., Toraldo, G.: GRASP with path relinking for the three-index assignment problem. INFORMS J. on Computing 17(2), 224–247 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  4. Bennett, K.P., Mangasarian, O.: Robust linear programming discrimination of two linearly inseparable sets. Optimization Methods and Software 1(1), 23–34 (1992)

    Article  Google Scholar 

  5. Binato, S., Faria Jr., H., Resende, M.: Greedy randomized adaptive path relinking. In: Sousa, J. (ed.) Proceedings of the IV Metaheuristics International Conference, pp. 393–397 (2001)

    Google Scholar 

  6. Ding, C., Dubchak, I.: Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 17(4), 349–358 (2001)

    Article  Google Scholar 

  7. Feo, T., Resende, M.: A probabilistic heuristic for a computationally difficult set covering problem. Operations Research Letters 8, 67–71 (1989)

    Article  MathSciNet  MATH  Google Scholar 

  8. Feo, T., Resende, M.: Greedy randomized adaptive search procedures. J. of Global Optimization 6, 109–133 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  9. Festa, P., Resende, M.: GRASP: An annotated bibliography. In: Ribeiro, C., Hansen, P. (eds.) Essays and Surveys on Metaheuristics, pp. 325–367. Kluwer Academic Publishers, Dordrecht (2002)

    Chapter  Google Scholar 

  10. Festa, P., Resende, M.: An annotated bibliography of GRASP – Part I: Algorithms. International Transactions on Operational Research 16, 1–24 (2009)

    Article  MATH  Google Scholar 

  11. Festa, P., Resende, M.: An annotated bibliography of GRASP – Part II: Applications. International Transactions on Operational Research (2009)

    Google Scholar 

  12. Fisher, R., et al.: The use of multiple measurements in taxonomic problems. Annals of Eugenics 7, 179–188 (1936)

    Article  Google Scholar 

  13. Glover, F.: Tabu search and adaptive memory programing – Advances, applications and challenges. In: Barr, R., Helgason, R., Kennington, J. (eds.) Interfaces in Computer Science and Operations Research, pp. 1–75. Kluwer, Dordrecht (1996)

    Google Scholar 

  14. Glover, F.: Multi-start and strategic oscillation methods – Principles to exploit adaptive memory. In: Laguna, M., Gonzáles-Velarde, J. (eds.) Computing Tools for Modeling, Optimization and Simulation: Interfaces in Computer Science and Operations Research, pp. 1–24. Kluwer, Dordrecht (2000)

    Google Scholar 

  15. Glover, F., Laguna, M.: Tabu Search. Kluwer, Dordrecht (1997)

    Book  MATH  Google Scholar 

  16. Glover, F., Laguna, M., Martí, R.: Fundamentals of scatter search and path relinking. Control and Cybernetics 39, 653–684 (2000)

    MathSciNet  MATH  Google Scholar 

  17. Kaufman, L., Rousseeuw, P.: Finding groups in data: an introduction to cluster analysis. WileyBlackwell (2005)

    Google Scholar 

  18. Laguna, M., Martí, R.: GRASP and path relinking for 2-layer straight line crossing minimization. INFORMS Journal on Computing 11, 44–52 (1999)

    Article  MATH  Google Scholar 

  19. Matsumoto, M., Nishimura, T.: Mersenne Twister: A 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Transactions on Modeling and Computer Simulation 8, 3–30 (1998)

    Article  MATH  Google Scholar 

  20. Monti, S., Savage, K., Kutok, J., Feuerhake, F., Kurtin, P., Mihm, M., Wu, B., Pasqualucci, L., Neuberg, D., Aguiar, R., et al.: Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood 105(5), 1851–1861 (2005)

    Article  Google Scholar 

  21. Nakai, K., Kanehisa, M.: Expert system for predicting protein localization sites in gram-negative bacteria. Proteins: Structure, Function, and Bioinformatics 11(2), 95–110 (1991)

    Article  Google Scholar 

  22. Nascimento, M., Toledo, F., de Carvalho, A.: Investigation of a new GRASP-based clustering algorithm applied to biological data. Computers & Operations Research 37(8), 1381–1388 (2010)

    Article  MATH  Google Scholar 

  23. Resende, M., Ribeiro, C.: Greedy randomized adaptive search procedures. In: Glover, F., Kochenberger, G. (eds.) Handbook of Metaheuristics, pp. 219–249. Kluwer Academic Publishers, Dordrecht (2002)

    Google Scholar 

  24. Resende, M., Ribeiro, C.: GRASP with path-relinking: Recent advances and applications. In: Ibaraki, T., Nonobe, K., Yagiura, M. (eds.) Metaheuristics: Progress as Real Problem Solvers, pp. 29–63. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  25. Resende, M., Ribeiro, C.: Greedy randomized adaptive search procedures: Advances and applications. In: Gendreau, M., Potvin, J.Y. (eds.) Handbook of Metaheuristics, 2nd edn., pp. 281–317. Springer Science+Business Media (2010)

    Google Scholar 

  26. Ribeiro, C., Rosseti, I.: Efficient Graph Rewriting and Its Implementation. LNCS 2004, pp. 922–926 (2002)

    Google Scholar 

  27. Ribeiro, C., Uchoa, E., Werneck, R.: A hybrid GRASP with perturbations for the Steiner problem in graphs. INFORMS Journal on Computing 14, 228–246 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  28. Rosenwald, A., Wright, G., Chan, W., Connors, J., Campo, E., Fisher, R., Gascoyne, R., Muller-Hermelink, H., Smeland, E., Staudt, L.: The use of molecular profiling to predict survival after chemotherapy for diffuse Large-B-cell lymphoma. The New England Journal of Medicine 346(25), 1937–1947 (2002)

    Article  Google Scholar 

  29. Rosseti, I.: Heurísticas para o problema de síntese de redes a 2-caminhos. Ph.D. thesis, Department of Computer Science, Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil (July 2003)

    Google Scholar 

  30. Su, A., Cooke, M., Ching, K., Hakak, Y., Walker, J., Wiltshire, T., Orth, A., Vega, R., Sapinoso, L., Moqrich, A., et al.: Large-scale analysis of the human and mouse transcriptomes. Proceedings of the National Academy of Sciences 99(7), 4465–4470 (2002)

    Article  Google Scholar 

  31. Van’t, V., Laura, J., Hongyue, D., Vijver, M.V.D., He, Y., Hart, A., et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871), 530–536 (2002)

    Article  Google Scholar 

  32. West, M., Blanchette, C., Dressman, H., Huang, E., Ishida, S., Spang, R., Zuzan, H., Olson, J., Marks, J., Nevins, J.: Predicting the clinical status of human breast cancer by using gene expression profiles. Proceedings of the National Academy of Sciences of the United States of America 98(20), 11462 (2001)

    Article  Google Scholar 

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Frinhani, R.M.D., Silva, R.M.A., Mateus, G.R., Festa, P., Resende, M.G.C. (2011). GRASP with Path-Relinking for Data Clustering: A Case Study for Biological Data. In: Pardalos, P.M., Rebennack, S. (eds) Experimental Algorithms. SEA 2011. Lecture Notes in Computer Science, vol 6630. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20662-7_35

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  • DOI: https://doi.org/10.1007/978-3-642-20662-7_35

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-20661-0

  • Online ISBN: 978-3-642-20662-7

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