Effective parameter estimation for S-system models using LPMs and evolutionary algorithms

2010 IEEE World Congress on Computational Intelligence, WCCI 2010 - 2010 IEEE Congress on Evolutionary Computation, CEC 2010

Volumn , Issue , 2010, Pages

  Kimura, Shuhei ^a   Amano, Yusuke ^a   Matsumura, Koki ^a   Okada Hatakeyama, Mariko ^b  

^a TOTTORI UNIVERSITY   (Japan)

^b Institute of Physical and Chemical Research   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL GENETIC NETWORK; DIMENSION REDUCTION; DIMENSIONAL FUNCTIONS; DIMENSIONAL PROBLEMS; FUNCTION OPTIMIZATION; GENETIC NETWORKS; IDEAL MODEL; LINEAR PROGRAMMING PROBLEM; NUMERICAL EXPERIMENTS; PROBLEM DECOMPOSITION; S-SYSTEMS; SEARCH DIMENSIONS; SUB-PROBLEMS;

EVOLUTIONARY ALGORITHMS; GENES; GENETIC PROGRAMMING; LINEAR PROGRAMMING; OPTIMIZATION; PROBLEM SOLVING;

PARAMETER ESTIMATION;

EID: 79959382451     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2010.5586248     Document Type: Conference Paper

References (29)

1. T. Akutsu, S. Miyano and S. Kuhara, "Inferring Qualitative Relations in Genetic Networks and Metabolic Pathways," Bioinformatics, vol. 16, pp. 727-734, 2000.
2. I.C. Chou, H. Martens and E.O. Voit, "Parameter Estimation in Biochemical Systems Models with Alternating Regression," Theoretical Biology and Medical Modelling, vol. 3: 25, 2006.
3. I.C. Chou and E.O. Voit, "Recent Developments in Parameter Estimation and Structure Identification of Biochemical and Genomic Systems," Mathematical Biosciences, vol. 219, pp. 57-83, 2009.
4. W.S. Cleveland, "Robust Locally Weight Regression and Smoothing Scatterplots," J. of American Statistical Association, vol. 79, pp. 829-836, 1979.
5. P. D'haeseleer, S. Liang and R. Somogyi, "Genetic Network Inference: From Co-expression Clustering to Reverse Engineering," Bioinformatics, vol. 16, pp. 707-726, 2000.
6. O.R. Gonzalez, C. Küper, K. Jung, P.C. Naval Jr. and E. Mendoza, "Parameter Estimation using Simulated Annealing for S-system Models of Biochemical Networks," Bioinformatics, vol. 23, pp. 480-486, 2007.
7. T. Graepel, R. Herbrich, B. Schölkopf, A. Smola, P. Bartlett, K.R. Müller, K. Obermayer and R. Williamson, "Classification on Proximity Data with LP-Machines," Proc. of International Conference on Artificial Neural Networks'99, pp. 304-309, 1999.
8. S. Kikuchi, D. Tominaga, M. Arita, K. Takahashi and M. Tomita, "Dynamic Modeling of Genetic Networks using Genetic Algorithm and S-system," Bioinformatics, vol. 19, pp. 643-650, 2003.
9. S. Kimura, I. Ono, H. Kita and S. Kobayashi, "An Extension of UNDX based on Guidelines for Designing Crossover Operators: Proposition and Evaluation of ENDX," Trans. of the Society of Instrument and Control Engineers, vol. 36, pp. 1162-1171, 2000 (in Japanese).
10. S. Kimura and A. Konagaya, "High Dimensional Function Optimization using a New Genetic Local Search suitable for Parallel Computers," Proc. of 2003 Conference on Systems, Man & Cybernetics, pp. 335-342, 2003.
11. S. Kimura, M. Hatakeyama and A. Konagaya, "Inference of S-system Models of Genetic Networks from Noisy Time-series Data," Chem-Bio Informatics J., vol. 4, pp. 1-14, 2004.
12. S. Kimura, K. Ide, A. Kashihara, M. Kano, M. Hatakeyama, R. Masui, N. Nakagawa, S. Yokoyama, S. Kuramitsu and A. Konagaya, "Inference of S-system Models of Genetic Networks using a Cooperative Coevolutionary Algorithm," Bioinformatics, vol. 21, pp. 1154-1163, 2005.
13. S. Kimura, K. Sonoda, S. Yamane, H. Maeda, K. Matsumura and M. Hatakeyama, "Function Approximation Approach to the Inference of Reduced NGnet Models of Genetic Networks," BMC Bioinformatics, vol. 9:23, 2008.
14. S. Kimura, S. Nakayama and M. Hatakeyama, "Genetic Network Inference as a Series of Discrimination Tasks," Bioinformatics, vol. 25, pp. 918-925, 2009.
15. S. Kimura, Y. Shiraishi and M. Hatakeyama, "Inference of Genetic Networks using Linear Programming Machines: Application of A Priori Knowledge," Proc. of 2009 International Joint Conference on Neural Networks, pp. 1617-1624, 2009.
16. S. Kimura, Y. Shiraishi and M. Okada, "Inference of Genetic Networks using LPMs: Assessment of Confidence Values of Regulations," J. of Bioinformatics and Computational Biology, in press.
17. Y. Maki, T. Ueda, M. Okamoto, N. Uematsu, Y. Inamura and Y. Eguchi, "Inference of Genetic Network Using the Expression Profile Time Course Data of Mouse P19 Cells," Genome Informatics, vol. 13, pp. 382-383, 2002.
18. A.A. Margolin, I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. Dalla-Favera and A. Califano, "ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context," BMC Bioinformatics, vol. 7: S7, 2006.
19. T. Nakakuki, N. Yumoto, T. Naka, M. Shirouzu, S. Yokoyama and M. Hatakeyama, "Topological Analysis of MAPK Cascade for Kinetic ErbB Signaling," PLoS ONE, vol. 3: e1782, 2008.
20. W.H. Press, S.A. Teukolsky, W.T. Vetterling and B.P. Flannery, Numerical Recipes in C 2nd Edition, Cambridge: Cambridge University Press, 1995.
21. H. Satoh, M. Yamamura and S. Kobayashi, "Minimal Generation Gap Model for GAs considering Both Exploration and Exploitation," Proc. of International Conference on Soft Computing (IIZUKA'96), pp. 494-497, 1996.
22. D. Thieffry, A.M. Huerta, E. Pérez-Rueda and J. Collado-Vides, "From Specific Gene Regulation to Genomic Networks: a Global Analysis of Transcriptional Regulation in Escherichia coli," BioEssays, vol. 20, pp. 433-440, 1998.
23. K.Y. Tsai and F.S. Wang, "Evolutionary Optimization with Data Collocation for Reverse Engineering of Biological Networks," Bioinformatics, vol. 21, pp. 1180-1188, 2005.
24. S.R. Veflingstad, J. Almeida and E.O. Voit, "Priming Nonlinear Searches for Pathway Identification," Theoretical Biology and Medical Modelling, vol. 1: 8, 2004.
25. M. Vilela, C.C.H. Borges, S. Vinga, A.T.R. Vanconcelos, H. Santos, E.O. Voit and J.S. Almeida, "Automated Smoother for the Numerical Decoupling of Dynamics Models," BMC Bioinformatics, vol. 8:305, 2007.
26. E.O. Voit, Computational Analysis of Biochemical Systems, Cambridge: Cambridge University Press, 2000.
27. E.O. Voit and J. Almeida, "Decoupling Dynamical Systems for Pathway Identification from Metabolic Profiles," Bioinformatics, vol. 20, pp. 1670-1681, 2004.
28. M.K.S. Yeung, J. Tegnér and J.J. Collins, "Reverse Engineering Gene Networks using Singular Value Decomposition and Robust Regression," Proc. of National Academy of Sciences of USA, vol. 99, pp. 6163-6168, 2002.
29. J. Yu, V.A. Smith, P.P. Wang, A.J. Hartemink and E.D. Jarvis, "Advances to Bayesian Network Inference for Generating Causal Networks from Observational Biological Data," Bioinformatics, vol. 20, pp. 3594-3603, 2004.