title: Parameter optimization by using differential elimination: a general approach for introducing constraints into objective functions.
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.
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. m.nakatsui@aist.go.jp
authors.forename: Masahiko
authors.initials: M
authors.lastname: Nakatsui
authors.forename: Katsuhisa
authors.initials: K
authors.lastname: Horimoto
authors.forename: Masahiro
authors.initials: M
authors.lastname: Okamoto
authors.forename: Yasuhito
authors.initials: Y
authors.lastname: Tokumoto
authors.forename: Jun
authors.initials: J
authors.lastname: Miyake
mesh_terms: D000465:Algorithms; D001686:Biological Phenomena; D019295:Computational Biology / Q000379:methods*; D007700:Kinetics; D008954:Models, Biological; D008956:Models, Chemical; D058615:Synthetic Biology; D049490:Systems Biology