Can neural network constraints in GP provide power to detect genes associated with human disease?

Lecture Notes in Computer Science

Volumn 3449, Issue , 2005, Pages 44-53

  Bush, William S ^a   Motsinger, Alison A ^a   Dudek, Scott M ^a   Ritchie, Marylyn D ^a  

^a VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; DISEASES; GENES; GENETIC ENGINEERING; IDENTIFICATION (CONTROL SYSTEMS);

GENETIC ARCHITECTURE; GENETIC EFFECTS; HUMAN GENETICS; NEURAL NETWORK CONSTRAINTS;

NEURAL NETWORKS;

EID: 24644454835     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/978-3-540-32003-6_5     Document Type: Conference Paper

References (27)

1. Kardia S.L.R.: Context-dependent genetic effects in hypertension. Curr. Hypertens. Reports. 2 (2000) 32-38
2. Moore J.H. and Williams S.M.: New strategies for identifying gene-gene interactions in hypertension. Ann. Med. 34 (2002) 88-95
3. Kooperberg C, Ruczinski I, LeBlanc ML, Hsu L. Sequence Analysis using Logic Regression, Genetic Epidemiology, SI (2001) 626-631.
4. Zhu, J. Classification of gene microarrays by penalized logistic regression. Biostatistics 5 (2003) 427-443.
5. Tahri-Daizadeh N, Tregouet DA, Nicaud V, Manuel N, Cambien F, Tiret L. Automated detection of informative combined effects in genetic association studies of complex traits. Genome Res. 8 (2003) 1952-60.
6. Nelson M, Kardia SLR, Ferrell RE, Sing CF. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 11 (2001) 458-470.
7. Culverhouse R, Klein T, Shannon W. Detecting epistatic interactions contributing to quantitative traits. Genet Epidemiol. 27 (2004) 141-52.
8. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Pari FF, Moore JH. Multifactor dimensionality reduction reveals high-order interactions among estrogen metabolism genes in sporadic breast cancer. Am J Hum Genet 69 (2001) 138-147.
9. Hahn LW, Ritchie MD, Moore JH. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19 (2003) 376-382.
10. Ritchie MD, Hahn LW, Moore JH. Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Gen Epi 24 (2003) 150-157.
11. Marinov M, Weeks D: The complexity of linkage analysis with neural networks. Hum Hered 51 (2001) 169-176
12. Lucek P., Hanke J., Reich J., Solla S.A., Ott, J. Multi-locus nonparametric linkage analysis of complex trait loci with neural networks. Hum Hered 48 (1998), 275-84
13. Koza JR, Rice JP: Genetic generation of both the weights and architecture for a neural network. IEEE Press (1991) Vol II.
14. Gruau FC: Cellular encoding of genetic neural networks. Master's thesis Ecole Normale Supérieure de Lyon (1992) 1-42
15. Ritchie M.D., White B.C., Parker J.S., Hahn L.W., Moore J.H.: Optimization of neural network architecture using genetic programming improves detection of gene-gene interactions in studies of human diseases. BMC Bioinformatics, 4 (2003) 28
16. Moore J.H., Parker J.S., Olsen N.J., Aune T.S.: Symbolic discriminant analysis of microarray data in autoimmune disease. Genet Epidemiol 23 (2002) 57-69
17. Moore J.H, Parker, J.S., Hahn L.W.: Symbolic Discriminant Analysis for Mining Gene Expression Patterns. In: Lecture Notes in Artificial Intelligence Vol. 2167, (2001) 372-381
18. Ritchie M.D, Coffey C.S, Moore J.H.: Genetic Programming Neural Networks: A Bioinformatics Tool for Human Genetics. Lecture Notes in Computer Science, Vol. 3102 (2004) 438-448
19. Mitchell M.: An Introduction to Genetic Algorithms. MIT Press, Cambridge (1996)
20. Moore J.H.: Cross validation consistency for the assessment of genetic programming results in microarray studies. In: Lecture Notes in Computer Science Vol 2611 ed. by: Raidl, G, et al. Springer-Verlag, Berlin (2003) 99-106
21. 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. Am. J. Hum. Genet. 69 (2001) 138-147
22. Koza JR: Genetic Programming: On the programming of computers by means of natural selection. MIT Press, Cambridge (1993)
23. Koza JR: Genetic Programming II: Automatic discovery of reusable programs. MIT Press, Cambridge (1998)
24. Koza JR, Bennett FH, Andre D, Keane, MA: Genetic Programming III: Automatic programming and automatic circuit synthesis. MIT Press, Cambridge (1999)
25. Culverhouse R., Suarez B.K., Lin J., Reich T.: A Perspective on Epistasis: Limits of Models Displaying No Main Effect. Am J Hum Genet 70 (2002) 461-471
26. Moore, J.H., Hahn L.W., Ritchie M.D., Thornton T.A., White B.C.: Application of genetic algorithms to the discovery of complex genetic models for simulations studies in human genetics. In: Proceedings of the Genetic and Evolutionary Algorithm Conference ed. by W.B. Langdon, et al. Morgan Kaufman Publishers San Francisco (2002) 1150-1155
27. Ott J.: Neural networks and disease association. Am. J. Med. Genet. 105 (2001) 60-61