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Published online before print October 14, 2003, 10.1101/gr.1262503
Genome Res. 13:2467-2474, 2003
©2003 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/03 $5.00
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Methods

Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods

Carmen G. Moles1, Pedro Mendes2 and Julio R. Banga1,3

1 Process Engineering Group, Instituto de Investigaciones Marinas (CSIC), 36208 Vigo, Spain 2 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA

Here we address the problem of parameter estimation (inverse problem)of nonlinear dynamic biochemical pathways. This problem is stated as a nonlinear programming (NLP)problem subject to nonlinear differential-algebraic constraints. These problems are known to be frequently ill-conditioned and multimodal. Thus, traditional (gradient-based)local optimization methods fail to arrive at satisfactory solutions. To surmount this limitation, the use of several state-of-the-art deterministic and stochastic global optimization methods is explored. A case study considering the estimation of 36 parameters of a nonlinear biochemical dynamic model is taken as a benchmark. Only a certain type of stochastic algorithm, evolution strategies (ES), is able to solve this problem successfully. Although these stochastic methods cannot guarantee global optimality with certainty, their robustness, plus the fact that in inverse problems they have a known lower bound for the cost function, make them the best available candidates.

3 Corresponding author.
E-MAIL julio{at}iim.csic.es; FAX 34-986292762.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1262503. Article published online before print in October 2003.


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