Component-based construction of bio-pathway models: The parameter estimation problem

Theoretical Computer Science

Volumn 412, Issue 26, 2011, Pages 2840-2853

  Koh, Geoffrey ^a   Hsu, David ^b   Thiagarajan, P S ^b  

^a AGENCY FOR SCIENCE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Belief propagation; Biochemical networks; Components; Composition; Decomposition; Factor graphs; ODEs

Indexed keywords

BELIEF PROPAGATION; BIOCHEMICAL NETWORKS; COMPONENTS; COMPOSITION; FACTOR GRAPHS; ODES;

COMMUNICATION SYSTEMS; ORDINARY DIFFERENTIAL EQUATIONS;

PARAMETER ESTIMATION;

EID: 79955705155     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2011.02.013     Document Type: Conference Paper

References (24)

1. U.S. Bhalla, and R. Iyengar Emergent properties of networks of biological signaling pathways Science 283 5400 1999 381 387
2. E. Klipp, and W. Liebermeister Mathematical modeling of intracellular signaling pathways BMC Neurosci. 7 suppl 1 2006 S10
3. H. Matsuno, Y. Tanaka, H. Aoshima, A. Doi, M. Matsui, and S. Miyano Biopathways representation and simulation on hybrid functional petri net In Silico Biol. 3 3 2003 389 404 (Pubitemid 37493057)
4. D. Koller, and N. Friedman Probabilistic Graphical Models: Principles and Techniques 2009 MIT Press Cambridge
5. G. Koh, H.F.C. Teong, M.-V. Clment, D. Hsu, and P. Thiagarajan A decompositional approach to parameter estimation in pathway modeling Bioinformatics 22 14 2006 e271 e280
6. G. Koh, L. Tucker-Kellogg, D. Hsu, and P.S. Thiagarajan Composing globally consistent pathway parameter estimates through belief propagation WABI'07: Proceedings of the 7th International Workshop on Algorithms in Bioinformatics 2007 Springer-Verlag Berlin, Heidelberg 420 430 (Pubitemid 350271330)
7. C.G. Moles, P. Mendes, and J.R. Banga Parameter estimation in biochemical pathways: a comparison of global optimization methods Genome Res. 13 11 2003 2467 2474 (Pubitemid 37428271)
8. I.-C. Chou, H. Martens, and E.O. Voit Parameter estimation in biochemical systems models with alternating regression Theoret. Biol. Med. Model. 3 25 2006 1 11
9. H. Rohn, B. Ibrahim, T. Lenser, T. Hinze, and P. Dittrich Enhancing parameter estimation of biochemical networks by exponentially scaled search steps EvoBIO'08: Proceedings of the 6th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics 2008 Springer-Verlag Berlin, Heidelberg 177 187
10. O.R. Gonzalez, C. Kper, K. Jung, P.C. Naval, and E. Mendoza Parameter estimation using simulated annealing for s-system models of biochemical networks Bioinformatics 23 4 2007 480 486 (Pubitemid 46323129)
11. R. Donaldson, and D. Gilbert A model checking approach to the parameter estimation of biochemical pathways CMSB'08: Proceedings of the 6th International Conference on Computational Methods in Systems Biology 2008 Springer-Verlag Berlin, Heidelberg 269 287
12. A. Rizk, G. Batt, F. Fages, and S. Soliman On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology CMSB'08: Proceedings of the 6th International Conference on Computational Methods in Systems Biology 2008 Springer-Verlag Berlin, Heidelberg 251 268
13. H. Beyer, and H. Schwefel Evolution strategies a comprehensive introduction Nat. Comput. 1 2002 3 52
14. T.P. Runarsson, and X. Yao Stochastic ranking for constrained evolutionary optimization IEEE Trans. Evol. Comput. 4 3 2000 284 294
15. R. Tarjan Depth-first search and linear graph algorithms SIAM J. Comput. 1 2 1972 146 170
16. G. Koh, D. Hsu, and P.S. Thiagarajan Incremental signaling pathway modeling by data integration Res. in Comput. Mol. Biol RECOMB LNCS vol. 6044 2010 Springer-Verlag 281 296
17. M. Kalos, and P. Whitlock Monte Carlo Methods, vol. 1 1986 John Wiley & Sons New York
18. J. Pearl Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference 1988 Morgen Kaufmann New York
19. R. McEliece, J. MacKay, and J. Cheng Turbo decoding as an instance of pearl's belief propagation algorithm IEEE J. Sel. Areas Commun. 16 1998 140 152 (Pubitemid 128570649)
20. P. Felzenszwalb, and D. Huttenlocher Efficient belief propagation for early vision Int. J. Comput. Vis. 70 2004 41 54
21. A. Rickle, N. Bogdanovic, I. Volkman, B. Winblad, R. Ravid, and R.F. Cowburn Akt activity in alzheimer's disease and other neurodegenerative disorders Neuroreport 15 6 2004 955 959 (Pubitemid 38591242)
22. S. Hardy, and P.N. Robillard Phenomenological and molecular-level petri net modeling and simulation of long-term potentiation Biosystems 82 1 2005 26 38 (Pubitemid 41278601)
23. D. Langford, R. Hurford, M. Hashimoto, M. Digicaylioglu, and E. Masliah Signalling crosstalk in fgf2-mediated protection of endothelial cells from hiv-gp120 BMC Neurosci. 6 2005 8
24. S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer Copasia complex pathway simulator Bioinformatics 22 24 2006 3067 3074