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Genome Research
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Genome Research
Article . 2003 . Peer-reviewed
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Genome Research
Article . 2004
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Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods

Authors: Moles, Carmen G.; Mendes, Pedro; Banga, Julio R.;

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

Abstract

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.

Country
United Kingdom
Keywords

Stochastic Processes, Computational Biology, HIV Protease Inhibitors, Evolution, Molecular, HIV Protease, Models, Chemical, Nonlinear Dynamics, Predictive Value of Tests, Computer Simulation, Genetic Engineering, Molecular Biology, Algorithms, Software

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
677
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