title: Model selection in systems biology depends on experimental design.
abstract: Experimental design attempts to maximise the information available for modelling tasks. An optimal experiment allows the inferred models or parameters to be chosen with the highest expected degree of confidence. If the true system is faithfully reproduced by one of the models, the merit of this approach is clear - we simply wish to identify it and the true parameters with the most certainty. However, in the more realistic situation where all models are incorrect or incomplete, the interpretation of model selection outcomes and the role of experimental design needs to be examined more carefully. Using a novel experimental design and model selection framework for stochastic state-space models, we perform high-throughput in-silico analyses on families of gene regulatory cascade models, to show that the selected model can depend on the experiment performed. We observe that experimental design thus makes confidence a criterion for model choice, but that this does not necessarily correlate with a model's predictive power or correctness. Finally, in the special case of linear ordinary differential equation (ODE) models, we explore how wrong a model has to be before it influences the conclusions of a model selection analysis.
authors.affiliation: Centre for Integrative Systems Biology at Imperial College London, London, United Kingdom.
authors.forename: Daniel
authors.initials: D
authors.lastname: Silk
authors.affiliation: Centre for Integrative Systems Biology at Imperial College London, London, United Kingdom.
authors.forename: Paul D W
authors.initials: PD
authors.lastname: Kirk
authors.affiliation: Centre for Integrative Systems Biology at Imperial College London, London, United Kingdom.
authors.forename: Chris P
authors.initials: CP
authors.lastname: Barnes
authors.affiliation: Centre for Integrative Systems Biology at Imperial College London, London, United Kingdom.
authors.forename: Tina
authors.initials: T
authors.lastname: Toni
authors.affiliation: Centre for Integrative Systems Biology at Imperial College London, London, United Kingdom.
authors.forename: Michael P H
authors.initials: MP
authors.lastname: Stumpf
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D055641:Mathematical Concepts; D008954:Models, Biological; D009010:Monte Carlo Method; D015398:Signal Transduction; D049490:Systems Biology