Parameter optimization by using differential elimination: A general approach for introducing constraints into objective functions

Masahiko Nakatsui, Katsuhisa Horimoto, Masahiro Okamoto, Yasuhito Tokumoto, Jun Miyake

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Background: The investigation of network dynamics is a major issue in systems and synthetic biology. One of the essential steps in a dynamics investigation is the parameter estimation in the model that expresses biological phenomena. Indeed, various techniques for parameter optimization have been devised and implemented in both free and commercial software. While the computational time for parameter estimation has been greatly reduced, due to improvements in calculation algorithms and the advent of high performance computers, the accuracy of parameter estimation has not been addressed. . Results: We propose a new approach for parameter optimization by using differential elimination, to estimate kinetic parameter values with a high degree of accuracy. First, we utilize differential elimination, which is an algebraic approach for rewriting a system of differential equations into another equivalent system, to derive the constraints between kinetic parameters from differential equations. Second, we estimate the kinetic parameters introducing these constraints into an objective function, in addition to the error function of the square difference between the measured and estimated data, in the standard parameter optimization method. To evaluate the ability of our method, we performed a simulation study by using the objective function with and without the newly developed constraints: the parameters in two models of linear and non-linear equations, under the assumption that only one molecule in each model can be measured, were estimated by using a genetic algorithm (GA) and particle swarm optimization (PSO). As a result, the introduction of new constraints was dramatically effective: the GA and PSO with new constraints could successfully estimate the kinetic parameters in the simulated models, with a high degree of accuracy, while the conventional GA and PSO methods without them frequently failed.Conclusions: The introduction of new constraints in an objective function by using differential elimination resulted in the drastic improvement of the estimation accuracy in parameter optimization methods. The performance of our approach was illustrated by simulations of the parameter optimization for two models of linear and non-linear equations, which included unmeasured molecules, by two types of optimization techniques. As a result, our method is a promising development in parameter optimization. .

Original languageEnglish
Article number9
JournalBMC systems biology
Volume4
Issue numberSUPPL. 2
DOIs
Publication statusPublished - Sep 13 2010

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Parameter Optimization
Elimination
Objective function
Kinetic parameters
Kinetics
Particle Swarm Optimization
Optimization Methods
Parameter Estimation
Statistical Models
Parameter estimation
Particle swarm optimization (PSO)
Genetic Algorithm
Genetic algorithms
Synthetic Biology
Nonlinear equations
Nonlinear Equations
Biological Phenomena
Molecules
Systems Biology
Estimate

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Modelling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Parameter optimization by using differential elimination : A general approach for introducing constraints into objective functions. / Nakatsui, Masahiko; Horimoto, Katsuhisa; Okamoto, Masahiro; Tokumoto, Yasuhito; Miyake, Jun.

In: BMC systems biology, Vol. 4, No. SUPPL. 2, 9, 13.09.2010.

Research output: Contribution to journalArticle

Nakatsui, Masahiko ; Horimoto, Katsuhisa ; Okamoto, Masahiro ; Tokumoto, Yasuhito ; Miyake, Jun. / Parameter optimization by using differential elimination : A general approach for introducing constraints into objective functions. In: BMC systems biology. 2010 ; Vol. 4, No. SUPPL. 2.
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