title: Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Process Engineering Group, Instituto de Investigaciones Marinas (C.S.I.C.), Spanish Council for Scientific Research, Vigo, Spain. mrodriguez@iim.csic.es <mrodriguez@iim.csic.es>
authors.forename: Maria
authors.initials: M
authors.lastname: Rodriguez-Fernandez
authors.forename: Jose A
authors.initials: JA
authors.lastname: Egea
authors.forename: Julio R
authors.initials: JR
authors.lastname: Banga
mesh_terms: D000465:Algorithms; D000081008:Bicyclic Monoterpenes; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D017320:HIV Protease Inhibitors / Q000494:pharmacology; D008956:Models, Chemical; D015233:Models, Statistical; D008962:Models, Theoretical; D039821:Monoterpenes / Q000737:chemistry; D017711:Nonlinear Dynamics; D009716:Numerical Analysis, Computer-Assisted; D012984:Software; D013269:Stochastic Processes; D049490:Systems Biology
chemical_list: D000081008:Bicyclic Monoterpenes; D017320:HIV Protease Inhibitors; D039821:Monoterpenes; C005451:alpha-pinene