A constraint solving approach to model reduction by tropical equilibration

Abstract : Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing multi-scale models for instance. While singular perturbation theory is a standard mathematical tool to analyze the different time scales of a dynamical system and decompose the system accordingly, tropical methods provide a simple algebraic framework to perform these analyses systematically in polynomial systems. The crux of these methods is in the computation of tropical equilibrations. In this paper we show that constraint-based methods, using reified constraints for expressing the equilibration conditions, make it possible to numerically solve non-linear tropical equilibration problems, out of reach of standard computation methods. We illustrate this approach first with the detailed reduction of a simple biochemical mechanism, the Michaelis-Menten enzymatic reaction model, and second, with large-scale performance figures obtained on the http://biomodels.net repository
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https://hal.inria.fr/hal-01098530
Contributor : Sylvain Soliman <>
Submitted on : Friday, December 26, 2014 - 1:30:40 PM
Last modification on : Monday, September 24, 2018 - 2:00:04 PM

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Sylvain Soliman, François Fages, Ovidiu Radulescu. A constraint solving approach to model reduction by tropical equilibration. Algorithms for Molecular Biology, BioMed Central, 2014, 9 (1), pp.24. ⟨10.1186/s13015-014-0024-2⟩. ⟨hal-01098530⟩

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