Metaheuristics in combinatorial optimization: Overview and conceptual comparison
ACM Computing Surveys (CSUR)
Stochastic Local Search: Foundations & Applications
Stochastic Local Search: Foundations & Applications
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
Automatic algorithm configuration based on local search
AAAI'07 Proceedings of the 22nd national conference on Artificial intelligence - Volume 2
A computational framework for modelling multicellular biochemistry
CEC'09 Proceedings of the Eleventh conference on Congress on Evolutionary Computation
A graphical representation for biological processes in the stochastic pi-calculus
Transactions on Computational Systems Biology VII
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In this paper we address the problem of tuning parameters of a biological model, in particular a simulator of stochastic processes. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. We tackle the problem with a metaheuristic algorithm for continuous variables, Particle swarm optimisation, and show the effectiveness of the method in a prominent case-study, namely the mitogen-activated protein kinase cascade.