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Reconstructing Species-Based Dynamics from Reduced Stochastic Rule-Based Models.

Tatjana Petrov 1 Jérôme Feret 2 Heinz Koeppl 1
1 BISON
IFA - Institut für Automatik - Automatic Control Laboratory
2 ABSTRACTION - Abstract Interpretation and Static Analysis
DI-ENS - Département d'informatique de l'École normale supérieure, Inria Paris-Rocquencourt, CNRS - Centre National de la Recherche Scientifique : UMR 8548
Abstract : Many bio-molecular reactions inside the cell are characterized by complex-formation and mutual modification of a few constituent molecules that give rise to a combinatorial number of reachable complexes or species. For such cases rule-based models (or site-graph-rewrite rules), offer a compact model description, by enumerating only the necessary context of interacting molecules. Such a model specification induces symmetries in the underlying Markov chain, which we have recently exploited for model reduction, based on a backward Markovian bisimulation. Interestingly, the method showed a theoretical possibility of reconstructing the high-dimensional species-based dynamics from the aggregate state. In this paper, we present a procedure for reconstructing the high-dimensional species-based dynamics from the aggregate state, and we provide an algorithm for computing such de-aggregation functions explicitly. The algorithm involves counting the automorphisms of a connected site-graph, and has a quadratic time complexity in the number of molecules which constitute the site-graphs of interest. We provide illustrating case studies.
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https://hal.inria.fr/hal-00734483
Contributor : Jérôme Feret <>
Submitted on : Saturday, September 22, 2012 - 8:50:20 AM
Last modification on : Thursday, July 1, 2021 - 5:58:03 PM

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  • HAL Id : hal-00734483, version 1

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Tatjana Petrov, Jérôme Feret, Heinz Koeppl. Reconstructing Species-Based Dynamics from Reduced Stochastic Rule-Based Models.. WSC - Winter Simulation Conference - 2012, Dec 2012, Berlin, Germany. ⟨hal-00734483⟩

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