The modelling of biochemical systems requires the knowledge of several quantitative parameters (e.g. reaction rates) which are often hard to measure in laboratory experiments. Furthermore, when the system involves small numbers of molecules, the modelling approach should also take into account the effects of randomness on the system dynamics. In this paper, we tackle the problem of estimating the unknown parameters of stochastic biochemical systems by means of two optimization heuristics, genetic algorithms and particle swarm optimization. Their performances are tested and compared on two basic kinetics schemes: the Michaelis-Menten equation and the Brussellator. The experimental results suggest that particle swarm optimization is a suitable method for this problem. The set of parameters estimated by particle swarm optimization allows us to reliably reconstruct the dynamics of the Michaelis-Menten system and of the Brussellator in the oscillating regime.
A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems / D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini, L. Vanneschi - In: Evolutionary computation, machine learning and data mining in bioinformatics : 7th European Conference, EvoBIO 2009, Tübingen, Germany, April 15 - 17, 2009; proceedings / D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini, L. Vanneschi ; [a cura di] C. Pizzuti, M.D. Ritchie, M. Giacobini. - [s.l] : Springer-Verlag, 2009. - ISBN 978-3-642-01183-2. - pp. 116-127 (( convegno EvoBIO 2009 (7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics) tenutosi a Tubingen, Germany nel 2009 [10.1007/978-3-642-01184-9_11].
A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems
D. BesozziPrimo
;
2009
Abstract
The modelling of biochemical systems requires the knowledge of several quantitative parameters (e.g. reaction rates) which are often hard to measure in laboratory experiments. Furthermore, when the system involves small numbers of molecules, the modelling approach should also take into account the effects of randomness on the system dynamics. In this paper, we tackle the problem of estimating the unknown parameters of stochastic biochemical systems by means of two optimization heuristics, genetic algorithms and particle swarm optimization. Their performances are tested and compared on two basic kinetics schemes: the Michaelis-Menten equation and the Brussellator. The experimental results suggest that particle swarm optimization is a suitable method for this problem. The set of parameters estimated by particle swarm optimization allows us to reliably reconstruct the dynamics of the Michaelis-Menten system and of the Brussellator in the oscillating regime.
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