A Constraint Solving Approach to Tropical Equilibration and Model Reduction


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 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 tropicalization 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 reduction of simple biochemical mechanisms such as the Michaelis-Menten and Goldbeter-Koshland models, and second, with performance figures obtained on a large scale on the model repository biomodels.net.

In WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013, pages 27–36