An expert knowledge-guided mutation operator for genome-wide genetic analysis using genetic programming

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4774 LNBI, Issue , 2007, Pages 30-40

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

^a DARTMOUTH COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DATA ACQUISITION; DATA STRUCTURES; DNA; KNOWLEDGE ACQUISITION;

GENETIC ANALYSIS; KNOWLEDGE GUIDED MUTATION; MUTATION OPERATORS;

GENETIC PROGRAMMING;

EID: 38349045395     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-75286-8_4     Document Type: Conference Paper

References (29)

1. Freitas, A.A.: Understanding the crucial role of attribute interaction in data mining. Artif. Intell. Rev. 16(3), 177-199 (2001)
2. Goldberg, D.E.: The Design of Innovation: Lessons from and for Competent Genetic Algorithms. Kluwer Academic Publishers, Norwell, MA, USA (2002)
3. Consortium, T.I.H.: A haplotype map of the human genome. Nature 437(7063), 1299-1320 (2005)
4. White, B.C., Gilbert, J.C., Reif, D.M., Moore, J.H.: A statistical comparison of grammatical evolution strategies in the domain of human genetics. In: Proceedings of the IEEE Congress on Evolutionary Computing, pp. 676-682. IEEE Computer Society Press, Los Alamitos (2005)
5. Moore, J.H., White, B.C.: Genome-wide genetic analysis using genetic programming: The critical need for expert knowledge. In: Genetic Programming Theory and Practice IV, Springer, Heidelberg (2006)
6. Moore, J., White, B.: Exploiting expert knowledge in genetic programming for genome-wide genetic analysis. In: Runarsson, T.P., Beyer, H.-G., Burke, E., MerelcGuervós, J.J., Whitley, L.D., Yao, X. (eds.) Parallel Problem Solving from Nature - PPSN IX. LNCS, vol. 4193, pp. 969-977. Springer, Heidelberg (2006)
7. Koza, J.R.: Genetic programming: on the programming of computers by means of natural selection. MIT Press, Cambridge, MA, USA (1992)
8. Koza, J.R.: Genetic programming II: automatic discovery of reusable programs. MIT Press, Cambridge, MA, USA (1994)
9. Koza, J.R., Andre, D., Bennett, F.H., Keane, M.A.: Genetic Programming III: Darwinian Invention & Problem Solving. Morgan Kaufmann Publishers Inc., San Francisco, CA, USA (1999)
10. Koza, J.R.: Genetic Programming IV: Routine Human-Competitive Machine Intelligence. Kluwer Academic Publishers, Norwell, MA, USA (2003)
11. Banzhaf, W., Nordin, P., Keller, R.E., Francone, F.D.: Genetic programming: an introduction: on the automatic evolution of computer programs and its applications. Morgan Kaufmann Publishers Inc., San Francisco, CA, USA (1998)
12. Langdon, W.B., Koza, J.R.: Genetic Programming and Data Structures: Genetic Programming + Data Structures = Automatic Programming! Kluwer Academic Publishers, Norwell, MA, USA (1998)
13. Langdon, W.B., Poli, R.: Foundations of Genetic Programming. Springer, Heidelberg (2002)
14. Freitas, A.A.: Data Mining and Knowledge Discovery with Evolutionary Algorithms, Secaucus, NJ, USA. Springer, New York (2002)
15. Fogel, G., Corne, D.: Evolutionary Computation in Bioinformatics. Morgan Kaufmann, San Francisco (2003)
16. Yu, T., Riolo, R., Worzel, B.: Genetic Programming: Theory and Practice (2006) 10.1007/0-387-28111-8.1
17. Luke, S., Spector, L.: A revised comparison of crossover and mutation in genetic programming. In: Koza, J.R., Banzhaf, W., Chellapilla, K., Deb, K., Dorigo, M., Fogel, D.B., Garzon, M.H., Goldberg, D.E., Iba, H., Riolo, R. (eds.) Genetic Programming 1998: Proceedings of the Third Annual Conference, University of Wisconsin, Madison, Wisconsin, USA, pp. 208-213. Morgan Kaufmann, San Francisco (1998)
18. Bearpark, K., Keane, A.: The use of collective memory in genetic programming. In: Jin, Y. (ed.) Knowledge Incorporation in Evolutionary Computation. Studies in Fuzziness and Soft Computing, pp. 15-36. Springer, Heidelberg (2005)
19. Ritchie, M.D., Hahn, L.W., Roodi, N., Bailey, L.R., Dupont, W.D., Pari, F.F., Moore, J.H.: Multifactor dimensionality reduction reveals high-order interactions among estrogen metabolism genes in sporadic breast cancer. American Journal of Human Genetics 69, 138-147 (2001)
20. Moore, J.H.: Computational analysis of gene-gene interactions using multifactor dimensionality reduction. Expert Review of Molecular Diagnostics 4(6), 795-803 (2004)
21. Moore, J.H., Gilbert, J.C., Tsai, C.T., Chiang, F.T., Holden, T., Barney, N., White, B.C.: A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. Journal of Theoretical Biology 241(2), 252-261 (2006)
22. Moore, J.H.: Genome-wide analysis of epistasis using multifactor dimensionality reduction: feature selection and construction in the domain of human genetics. In: Knowledge Discovery and Data Mining: Challenges and Realities with Real World Data. IGI (2007)
23. Wilke, R.A., Reif, D.M., Moore, J.H.: Combinatorial pharmacogenetics. Nature Reviews Drug Discovery 4, 911-918 (2005)
24. Kira, K., Rendell, L.A.: A practical approach to feature selection. In: Machine Learning: Proceedings of the AAAI'92 (1992)
25. Kononenko, I.: Estimating attributes: Analysis and extension of relief. In: Bergadano, F., De Raedt, L. (eds.) ECML 1994. LNCS, vol. 784, pp. 171-182. Springer, Heidelberg (1994)
26. Robnik-Sikonja, M., Kononenko, I.: Theoretical and empirical analysis of relieff and rrelieff. Mach. Learn. 53(1-2), 23-69 (2003)
27. Moore, J.H., White, B.C.: Tuning relieff for genome-wide genetic analysis. LNCS, vol. 4447, pp. 166-175 (2007)
28. Gonzalez, G., Uribe, J.C., Tari, L., Brophy, C., Baral, C.: Mining gene-disease relationships from biomedical literature: Weighting protein-protein interactions and connectivity measures. In: Pacific Symposium on Biocomputing, vol. 12, pp. 28-39 (2007)
29. Moore, J.H., Barney, N., Tsai, C.T., Chiang, F.T., Gui, J., White, B.C.: Symbolic modeling of epistasis. Hum. Hered. 63(2), 120-133 (2007)