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Constraint Identification Using Modified Hoare Logic on Hybrid Models of Gene Networks

Authors: Jonathan Behaegel, Jean-Paul Comet, and Maxime Folschette

Published in: LIPIcs, Volume 90, 24th International Symposium on Temporal Representation and Reasoning (TIME 2017)


Abstract
We present a new hybrid Hoare logic dedicated for a class of linear hybrid automata well suited to model gene regulatory networks. These automata rely on Thomas' discrete framework in which qualitative parameters have been replaced by continuous parameters called celerities. The identification of these parameters remains one of the keypoints of the modelling process, and is difficult especially because the modelling framework is based on a continuous time. We introduce Hoare triples which handle biological traces and pre/post-conditions. Observed chronometrical biological traces play the role of an imperative program for classical Hoare logic and our hybrid Hoare logic, defined by inference rules, is proved to be sound. Furthermore, we present a weakest precondition calculus (a la Dijkstra) which leads to constraints on dynamical parameters. Finally, we illustrate our "constraints generator" with a simplified circadian clock model describing the rhythmicity of cells in mammals on a 24-hour period.

Cite as

Jonathan Behaegel, Jean-Paul Comet, and Maxime Folschette. Constraint Identification Using Modified Hoare Logic on Hybrid Models of Gene Networks. In 24th International Symposium on Temporal Representation and Reasoning (TIME 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 90, pp. 5:1-5:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)


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@InProceedings{behaegel_et_al:LIPIcs.TIME.2017.5,
  author =	{Behaegel, Jonathan and Comet, Jean-Paul and Folschette, Maxime},
  title =	{{Constraint Identification Using Modified Hoare Logic on Hybrid Models of Gene Networks}},
  booktitle =	{24th International Symposium on Temporal Representation and Reasoning (TIME 2017)},
  pages =	{5:1--5:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-052-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{90},
  editor =	{Schewe, Sven and Schneider, Thomas and Wijsen, Jef},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2017.5},
  URN =		{urn:nbn:de:0030-drops-79203},
  doi =		{10.4230/LIPIcs.TIME.2017.5},
  annote =	{Keywords: Hoare logic, weakest precondition, linear hybrid automata, constraint synthesis, gene networks}
}
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