Gene selection in cancer classification using PSO/SVM and GA/SVM hybrid algorithms

2007 IEEE Congress on Evolutionary Computation, CEC 2007

Volumn , Issue , 2007, Pages 284-290

  Alba, Enrique ^a   García Nieto, José ^a   Jourdan, Laetitia ^b   Talbi, El Ghazali ^b  

^a UNIVERSITY OF MÁLAGA   (Spain)

^b INRIA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER CLASSIFICATION; GENE SELECTION;

EVOLUTIONARY ALGORITHMS; IMAGE CLASSIFICATION; ONCOLOGY; PARTICLE SWARM OPTIMIZATION (PSO);

GENETIC ENGINEERING;

EID: 63149139219     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2007.4424483     Document Type: Conference Paper

References (32)

1. A. Pease, D. Solas, E. Sullivan, M. Cronin, C. P. Holmes, and S. Fodor, "Light-generated oligonucleotide arrays for rapid dna sequence analysis," in Proc. Natl. Acad. Sci., vol. 96, USA, 1994, pp. 5022-5026.
2. R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, and E. S. Lander, "Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring," Science, vol. 286, pp. 531-537, 1999.
3. Alon, N. Barkai, D. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine, "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays," Proc. Natl. Acad. Sci, vol. 96, pp. 6745-6750, 1999.
4. L. J. van 't Veer, H. Dai, M. J. van de Vijver, Y. D. He, A. A. M. Hart, M. Mao, H. L. Peterse, K. van der Kooy, M. J. Marton, A. T. Witteveen, G. J. Schreiber, R. M. Kerkhoven, C. Roberts, P. S. Linsley, R. Bernards, and S. H. Friend, "Gene expression profiling predicts clinical outcome of breast cancer," Nature, vol. 415, pp. 530-536, 2002.
5. Juliusdottir, D. Corne, E. Keedwell, and A. Narayanan, "Two-phase EA/K-NN for feature selection and classification in cancer microarray datasets," in CIBCB, 2005, pp. 1-8.
6. I. Guyon, J. Weston, S. Barnhill, and V. Vapnik, "Gene selection for cancer classification using support vector machines," Machine Learning, vol. 46, no. 1-3, pp. 389-422, 2002. [Online]. Available: citeseer.ist.psu.edu/ guyon02gene.html
7. J. Kohavi and G. H. John, "The wrapper approach," in Feature Selection for Knowledge Discovery and Data Mining, 1998, pp. 33-50. [Online]. Available: citeseer.ist.psu.edu/article/kohavi97wrapper.html
8. Fix and J. L. Hodges, "Discriminatory analysis. nonparametric discrimination: Consistency properties," 4, US Air Force School of Aviation Medicine, Randolph Field, TX, Tech. Rep., 1951.
9. C. Cortes and V. Vapnik, "Support-vector networks," Machine Learning, vol. 20, no. 3, pp. 273-297, 1995.
10. M. Narendra and K. Fukunaga, "A branch and bound algorithm for feature subset selection," IEEE Trans. on Computer, vol. 26, pp. 917-922, 1977.
11. J. Yang and V. Honavar, Feature Extraction, Construction and Selection: A Data Mining Perspective, 1998, ch. Feature Subset Selection Using a Genetic Algorithm, pp. 177-136.
12. E. B. Huerta, B. Duval, and J.-K. Hao, "A Hybrid GASVM Approach for Gene Selection and Classification of Microarray Data," in Lecture Notes in Computer Science of EvoWorkshops, F. Rothlauf, J. Branke, S. Cagnoni, E. Costa, C. Cotta, R. Drechsler, E. Lutton, P. Machado, J. H. Moore, J. Romero, G. D. Smith, G. Squillero, and H. Takagi, Eds., vol. 3907. Springer, 2006, pp. 34-44.
13. J. Kennedy and R. Eberhart, "Particle Swarm Optimization," in Proc. of the IEEE International Conference on Neural Networks, vol. 4, 1995, pp. 1942-1948.
14. A. Moraglio, C. D. Chio, and R. Poli, "Geometric Particle Swarm Optimization," in 10th European conference on Genetic Programming (EuroGP 2007), ser. Lecture Notes in Computer Science, vol. 4445. Springer, Abril 2007.
15. L. Jourdan, C. Dhaenens, and E.-G. Talbi, "A genetic algorithm for feature selection in data-mining for genetics," in Proceedings of the 4th Metaheuristics International ConferencePorto (MIC'2001), Porto, Portugal, 2001, pp. 29-34.
16. E. F. Petricoin, A. M. Ardekani, B. A. Hitt, P. J. Levine, V. A. Fusaro, S. M. Steinberg, G. B. Mills, C. Simone, D. A. Fishman, E. C. Kohn, and L. A. Liotta, "Use of proteomic patterns in serum to identify ovarian cancer," The Lancet, vol. 359, pp. 572-577, 2002.
17. D. Singh, P. Febbo, K. Ross, D. Jackson, J. Manola, C. Ladd, P. Tamayo, A. Renshaw, A. D'Amico, and J. Richie, "Gene expression correlates of clinical prostate cancer behavior," Cancer Cell, vol. 1, pp. 203-209, 2002.
18. G. J. Gordon, R. V. Jensen, L.-L. Hsiao, S. R. Gullans, J. E. Blumenstock, S. Ramaswamy, W. G. Richards, D. J. Sugarbaker, and R. Bueno, "Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma," Cancer Res, vol. 62, pp. 4963-4967, 2002.
19. S. Mukherjee, Classifying Microarray data using Support Vector Machines, Boston, MA, 2003, ch. 9, pp. 166-185.
20. T. Furey, N. Cristianini, N. Duffy, D. W. Bednarski, M. Schummer, and D. Haussler, "Support vector machines classification and validation of cancer tissue samples using microarray expression data," Bioinformatics, vol. 16, no. 10, pp. 906-914, 2000.
21. J. Kennedy and R. Eberhart, "A Discrete Binary Version of the Particle Swarm Algorithm," in Proceedings of the IEEE International Conference on Systems, Man and Cybernetics, vol. 5, 1997, pp. 4104-4109.
22. M. Clerc, "Binary Particle Swarm Optimisers: Toolbox, Derivations, and Mathematical Insights," 2005. [Online]. Available: http://clerc. maurice.free.fr/pso/
23. A. Moraglio and J. Togelius, "Geometric particle swarm optimization for the sudoku puzzle," in Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2007). London, UK: ACM Press, July 2007.
24. E. Alba and M. Group, "Mallba: A Library of Skeletons for Combinatorial Optimisation," in Proceedings of the Euro-Par, B. Monien and R. Feldmann, Eds., vol. LNCS 2400, 2002, pp. 927-932.
25. S. Cahon, E.-G. Talbi, and N. Melab, "Paradiseo: A framework for parallel and distributed metaheuristics," in Proc. of Internationa the Parallel and Distributed Processing Symposium, 2003, pp. 144-155.
26. C.-C. Chang and C.-J. Lin, "LIBSVM: A library for support vector machines," Software available at URL http://www.csie.ntu.edu.tw/ cjlin/libsvm, 2002.
27. K. Deb and A. R. Reddy, "Classification of two-class cancer data reliably using evolutionary algorithms," KanGAL Report No. 2003001, Tech. Rep., 2003.
28. L. Yu and H. Liu, "Redundancy based feature selection for microarry data," in Proceedings of International Conference on Knowledge Discovery and Data Mining, Seattle, Washington, 2004, pp. 22-25.
29. B. Liu, Q. Cui, T. Jiang, and S. Ma, "A combinational feature selection and ensemble neural network method for classification of gene expression data," BMC Bioinformatics, vol. 5, pp. 136-148, 2004.
30. Q. Shen, W. M. Shi, W. Kong, and B. X. Ye, "A combination of modified particle swarm optimization algorithm and support vector machine for gene selection and classification," Talanta, 2006.
31. R. T. Silver, "Anagrelide is effective in treating patients with hydroxyurea-resistant thrombocytosis in patients with chronic myeloid leukemia," Leukemia, vol. 19, no. 3, p. 3943, 2005. [Online]. Available: http://dx.doi.org/10.1038/sj.leu.2403556
32. C. L. Loprinzi, "Venlafaxine in management of hot flashes in survivors of breast cancer: a randomised controlled trial," The Lancet, vol. 356, no. 9247, pp. 2059-2063, 2000.