On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology

  • Authors:

  • Aurélien Rizk;Grégory Batt;François Fages;Sylvain Soliman

  • Affiliations:

  • Projet Contraintes, INRIA Rocquencourt, Le Chesnay Cedex, France 78153;Projet Contraintes, INRIA Rocquencourt, Le Chesnay Cedex, France 78153;Projet Contraintes, INRIA Rocquencourt, Le Chesnay Cedex, France 78153;Projet Contraintes, INRIA Rocquencourt, Le Chesnay Cedex, France 78153

  • Venue:
  • CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
  • Year:
  • 2008

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Abstract

Finding mathematical models satisfying a specification built from the formalization of biological experiments, is a common task of the modeller that techniques like model-checking help solving, in the qualitative but also in the quantitative case. In this article we propose to go one step further by defining a continuous degree of satisfaction of a temporal logic formula with constraints. We show how such a satisfaction measure can be used as a fitness function with state-of-the-art search methods in order to find biochemical kinetic parameter values satisfying a set of biological properties formalized in temporal logic. We also show how it can be used to define a measure of robustness of a biological model with respect to some specification. These methods are evaluated on models of the cell cycle and of the MAPK signalling cascade.