Title
Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems.
Abstract
We consider the problem of parameter estimation (model calibration) in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector). In order to surmount these difficulties, global optimization (GO) methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochastic-deterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness.We have developed a new procedure based on the scatter search methodology for nonlinear optimization of dynamic models of arbitrary (or even unknown) structure (i.e. black-box models). In this contribution, we describe and apply this novel metaheuristic, inspired by recent developments in the field of operations research, to a set of complex identification problems and we make a critical comparison with respect to the previous (above mentioned) successful methods.Robust and efficient methods for parameter estimation are of key importance in systems biology and related areas. The new metaheuristic presented in this paper aims to ensure the proper solution of these problems by adopting a global optimization approach, while keeping the computational effort under reasonable values. This new metaheuristic was applied to a set of three challenging parameter estimation problems of nonlinear dynamic biological systems, outperforming very significantly all the methods previously used for these benchmark problems.
Year
DOI
Venue
2006
10.1186/1471-2105-7-483
BMC Bioinformatics
Keywords
Field
DocType
nonlinear optimization,computational biology,global optimization,parameter estimation,operations research,stochastic processes,system biology,nonlinear dynamics,algorithms,bioinformatics,biological systems,microarrays,systems biology
Mathematical optimization,Nonlinear system,Global optimization,Computer science,Stochastic process,Algorithm,Robustness (computer science),Local search (optimization),Bioinformatics,Estimation theory,Computation,Metaheuristic
Journal
Volume
Issue
ISSN
7
1
1471-2105
Citations 
PageRank 
References 
89
4.06
15
Authors
3
Name
Order
Citations
PageRank
Maria Rodriguez-Fernandez116211.05
Jose A. Egea230216.76
Julio R. Banga366550.71