An LTL Model Checking Approach for Biological Parameter Inference

  • Emmanuelle Gallet
  • Matthieu Manceny
  • Pascale Le Gall
  • Paolo Ballarini
Conference paper

DOI: 10.1007/978-3-319-11737-9_11

Part of the Lecture Notes in Computer Science book series (LNCS, volume 8829)
Cite this paper as:
Gallet E., Manceny M., Le Gall P., Ballarini P. (2014) An LTL Model Checking Approach for Biological Parameter Inference. In: Merz S., Pang J. (eds) Formal Methods and Software Engineering. ICFEM 2014. Lecture Notes in Computer Science, vol 8829. Springer, Cham

Abstract

The identification of biological parameters governing dynamics of Genetic Regulatory Networks (GRN) poses a problem of combinatorial explosion, since the possibilities of parameter instantiation are numerous even for small networks. In this paper, we propose to adapt LTL model checking algorithms to infer biological parameters from biological properties given as LTL formulas. In order to reduce the combinatorial explosion, we represent all the dynamics with one parametric model, so that all GRN dynamics simply result from all eligible parameter instantiations. LTL model checking algorithms are adapted by postponing the parameter instantiation as far as possible. Our approach is implemented within the SPuTNIk tool.

Keywords

LTL Model Checking Parameter Identification Symbolic Execution Genetic Regulatory Network Thomas Discrete Modeling 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Emmanuelle Gallet
    • 1
  • Matthieu Manceny
    • 2
  • Pascale Le Gall
    • 1
  • Paolo Ballarini
    • 1
  1. 1.Laboratoire MASEcole Centrale ParisChâtenay-MalabryFrance
  2. 2.Laboratoire LISITE, ISEPParisFrance

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