Sensible initialization using expert knowledge for genome-wide analysis of epistasis using genetic programming

2009 IEEE Congress on Evolutionary Computation, CEC 2009

Volumn , Issue , 2009, Pages 1289-1296

  Greene, Casey S ^a   White, Bill C ^a   Moore, Jason H ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATTRIBUTE INTERACTIONS; BIOLOGICAL COMPONENTS; BLADDER CANCERS; DISEASE RISKS; DNA SEQUENCE VARIATIONS; EVOLUTIONARY COMPUTING; EXPERT KNOWLEDGE; HUMAN DISEASE; HUMAN GENOMES; INITIALIZERS; LARGE DATASETS;

BIOLOGY; GENES; NUCLEIC ACIDS;

GENETIC PROGRAMMING;

EID: 69449098752     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2009.4983093     Document Type: Conference Paper

References (41)

1. Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research: , R. Saxena, B. F. Voight, V. Lyssenko, N. P. Burtt, P. I. W. de Bakker, H. Chen, J. J. Roix, S. Kathiresan, J. N. Hirschhorn, M. J. Daly, T. E. Hughes, L. Groop, D. Altshuler, P. Almgren, J. C. Florez, J. Meyer, K. Ardlie, K. B. Bostrom, B. Isomaa, G. Lettre, U. Lindblad, H. N. Lyon, O. Melander, C. Newton-Cheh, P. Nilsson, M. Orho-Melander, L. Rastam, E. K. Speliotes, M.-R. Taskinen, T. Tuomi, C. Guiducci, A. Berglund, J. Carlson, L. Gianniny, R. Hackett, L. Hall, J. Holmkvist, E. Laurila, M. Sjogren, M. Sterner, A. Surti, M. Svensson, M. Svensson, R. Tewhey, B. Blumenstiel, M. Parkin, M. DeFelice, R. Barry, W. Brodeur, J. Camarata, N. Chia, M. Fava, J. Gibbons, B. Handsaker, C. Healy, K. Nguyen, C. Gates, C. Sougnez, D. Gage, M. Nizzari, S. B. Gabriel, G.-W. Chirn, Q. Ma, H. Parikh, D. Richardson, D. Ricke, and S. Purcell, "Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels, " Science, vol.316, no.5829, pp. 1331-1336, Jun. 2007.
2. The Wellcome Trust Case Control Consortium , "Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls, " Nature, vol.447, no.7145, pp. 661-678, Jun. 2007.
3. The International HapMap Consortium, "A haplotype map of the human genome, " Nature, vol.437, no.7063, pp. 1299-1320, Oct 2005.
4. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. W. de Bakker, M. J. Daly, and P. C. Sham, "Plink: a tool set for whole-genome association and population-based linkage analyses, " American Journal of Human Genetics, vol.81, no.3, pp. 559-575, Sep. 2007.
5. J. N. Hirschhorn, K. Lohmueller, E. Byrne, and K. Hirschhorn, "A comprehensive review of genetic association studies, " Genet Med, vol.4, pp. 45-61, 2002.
6. M. Skipper, "Total interconnectedness of everything, " Nat Rev Genet, vol.4, no.10, p. 760, Oct. 2003.
7. A. Hintze and C. Adami, "Evolution of complex modular biological networks, " PLoS Computational Biology, vol.4, no.2, p. e23, Feb. 2008.
8. J. H. Moore, "The ubiquitous nature of epistasis in determining susceptibility to common human diseases, " Human Heredity, vol.56, pp. 73-82, 2003.
9. R. L. Nagel, "Epistasis and the genetics of human diseases, " Comptes Rendus Biologies, vol.328, no.7, pp. 606-615, Jul. 2005.
10. D. E. Goldberg, The Design of Innovation: Lessons from and for Competent Genetic Algorithms. Norwell, MA, USA: Kluwer Academic Publishers, 2002.
11. M. Yeager, N. Orr, R. B. Hayes, K. B. Jacobs, P. Kraft, S. Wacholder, M. J. Minichiello, P. Fearnhead, K. Yu, N. Chatterjee, Z. Wang, R. Welch, B. J. Staats, E. E. Calle, H. S. Feigelson, M. J. Thun, C. Rodriguez, D. Albanes, J. Virtamo, S. Weinstein, F. R. Schumacher, E. Giovannucci, W. C. Willett, G. Cancel-Tassin, O. Cussenot, A. Valeri, G. L. Andriole, E. P. Gelmann, M. Tucker, D. S. Gerhard, J. F. Fraumeni, R. Hoover, D. J. Hunter, S. J. Chanock, and G. Thomas, "Genome-wide association study of prostate cancer identifies a second risk locus at 8q24, " Nat Genet, vol.39, no.5, pp. 645-649, May 2007. (Pubitemid 46676108)
12. I. Tomlinson, E. Webb, L. Carvajal-Carmona, P. Broderick, Z. Kemp, S. Spain, S. Penegar, I. Chandler, M. Gorman, W. Wood, E. Barclay, S. Lubbe, L. Martin, G. Sellick, E. Jaeger, R. Hubner, R. Wild, A. Rowan, S. Fielding, K. Howarth, A. Silver, W. Atkin, K. Muir, R. Logan, D. Kerr, E. Johnstone, O. Sieber, R. Gray, H. Thomas, J. Peto, J.-B. Cazier, and R. Houlston, "A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21, " Nature Genetics, vol.39, no.8, pp. 984-988, Aug. 2007.
13. A. E. Baum, N. Akula, M. Cabanero, I. Cardona, W. Corona, B. Klemens, T. G. Schulze, S. Cichon, M. Rietschel, M. M. Nthen, A. Georgi, J. Schumacher, M. Schwarz, R. A. Jamra, S. Hfels, P. Propping, J. Satagopan, S. D. Detera-Wadleigh, J. Hardy, and F. J. McMahon, "A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder, " Molecular Psychiatry, vol.13, no.2, pp. 197-207, Feb. 2008.
14. W. Banzhaf, P. Nordin, R. E. Keller, and F. D. Francone, Genetic programming: an introduction: on the automatic evolution of computer programs and its applications. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc., 1998.
15. J. R. Koza, Genetic programming: on the programming of computers by means of natural selection. Cambridge, MA, USA: MIT Press, 1992.
16. -, Genetic programming II: automatic discovery of reusable programs. Cambridge, MA, USA: MIT Press, 1994.
17. -, Genetic Programming IV: Routine Human-Competitive Machine Intelligence. Norwell, MA, USA: Kluwer Academic Publishers, 2003.
18. J. R. Koza, D. Andre, F. H. Bennett, and M. A. Keane, Genetic Programming III: Darwinian Invention & Problem Solving. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc., 1999.
19. W. B. Langdon and R. Poli, Foundations of Genetic Programming. Springer-Verlag, 2002. [Online]. Available: http: //www.cs.ucl.ac.uk/staff/W. Langdon/FOGP/
20. W. B. Langdon and J. R. Koza, Genetic Programming and Data Structures: Genetic Programming + Data Structures = Automatic Programming! Norwell, MA, USA: Kluwer Academic Publishers, 1998.
21. A. A. Freitas, Data Mining and Knowledge Discovery with Evolutionary Algorithms. Secaucus, NJ, USA: Springer-Verlag New York, Inc., 2002.
22. G. Fogel and D. Corne, Evolutionary Computation in Bioinformatics. Morgan Kaufmann Publishers, 2003.
23. J. H. Moore and B. C. White, "Genome-wide Genetic Analysis Using Genetic Programming: The Critical Need for Expert Knowledge." Genetic Programming Theory and Practice IV, 2007.
24. B. C. White, J. C. Gilbert, D. M. Reif, and J. H. Moore, "A Statistical Comparison of Grammatical Evolution Strategies in the Domain of Human Genetics, " Proceedings of the IEEE Congress on Evolutionary Computing, pp. 676-682, 2005.
25. J. H. Moore and B. C. White, "Exploiting Expert Knowledge in Genetic Programming for Genome-wide Genetic Analysis." Lecture Notes in Computer Science, vol.4193, pp. 969-977, 2006.
26. C. S. Greene, B. C. White, and J. H. Moore, "An expert knowledgeguided mutation operator for genome-wide genetic analysis using genetic programming, " Lecture Notes in Bioinformatics, vol.4774, pp. 30-40, 2007.
27. B. Snel, G. Lehmann, P. Bork, and M. A. Huynen, "String: a webserver to retrieve and display the repeatedly occurring neighbourhood of a gene, " Nucleic Acids Research, vol.28, no.18, pp. 3442-3444, Sep. 2000.
28. M. Kanehisa and S. Goto, "Kegg: kyoto encyclopedia of genes and genomes, " Nucleic Acids Research, vol.28, no.1, pp. 27-30, 2000.
29. M. García-Arnau, D. Manrique, J. Riós, and A. Rodríguez-Pat ón, "Initialization method for grammar-guided genetic programming, " Know.-Based Syst., vol.20, no.2, pp. 127-133, 2007.
30. S. Luke, "Two fast tree-creation algorithms for genetic programming, " Evolutionary Computation, IEEE Transactions on, vol.4, no.3, pp. 274-283, Sep 2000.
31. S. Luke and L. Panait, "A survey and comparison of tree generation algorithms, " in Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), L. Spector, E. D. Goodman, A. Wu, W. B. Langdon, H.-M. Voigt, M. Gen, S. Sen, M. Dorigo, S. Pezeshk, M. H. Garzon, and E. Burke, Eds. San Francisco, California, USA: Morgan Kaufmann, 7-11 2001, pp. 81-88.
32. M. O'Neill and C. Ryan, Grammatical Evolution: Evolutionary Automatic Programming in an Arbitrary Language. Norwell, MA, USA: Kluwer Academic Publishers, 2003.
33. J. H. Moore, J. S. Parker, N. J. Olsen, and T. Aune, "Symbolic discriminant analysis of microarray data in autoimmune disease, " Genetic Epidemiology, vol.23, pp. 57-69, 2002.
34. J. H. Moore, J. C. Gilbert, C. T. Tsai, F. T. Chiang, T. Holden, N. Barney, and B. C. White, "A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility, " Journal of Theoretical Biology, vol.241, no.2, pp. 252-261, Jul 2006.
35. M. D. Ritchie, L. W. Hahn, N. Roodi, L. R. Bailey, W. D. Dupont, F. F. Parl, and J. H. Moore, "Multifactor dimensionality reduction reveals high-order interactions among estrogen metabolism genes in sporadic breast cancer, " American Journal of Human Genetics, vol.69, pp. 138-147, 2001.
36. R. A. Wilke, D. M. Reif, and J. H. Moore, "Combinatorial pharmacogenetics, " Nature Reviews Drug Discovery, vol.4, pp. 911-918, 2005.
37. K. Kira and L. A. Rendell, "A practical approach to feature selection, " In: Machine Learning: Proceedings of the AAAI'92, 1992.
38. I. Kononenko, "Estimating attributes: Analysis and extension of relief, " Machine Learning: ECML-94, pp. 171-182, 1994.
39. M. Robnik-Sikonja and I. Kononenko, "Theoretical and Empirical Analysis of ReliefF and RReliefF, " Mach. Learn., vol.53, no.1-2, pp. 23-69, 2003.
40. J. H. Moore and B. C. White, "Tuning relieff for genome-wide genetic analysis, " Lecture Notes in Computer Science, vol.4447, pp. 166-175, 2007.
41. J. H. Moore, N. Barney, C. T. Tsai, F. T. Chiang, J. Gui, and B. C. White, "Symbolic modeling of epistasis." Hum Hered, vol.63, no.2, pp. 120-133, Feb 2007.