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

  • Aurélien Rizk
  • Grégory Batt
  • François Fages
  • Sylvain Soliman
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5307)

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.

Keywords

Model Check Temporal Logic System Biology Markup Language Covariance Matrix Adaptation Evolution Strategy Numerical Trace 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Aurélien Rizk
    • 1
  • Grégory Batt
    • 1
  • François Fages
    • 1
  • Sylvain Soliman
    • 1
  1. 1.Projet Contraintes, INRIA RocquencourtLe Chesnay CedexFrance

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