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Reconstructing species-based dynamics from reduced stochastic rule-based models

Author(s):

Tatjana Petrov, Jerome Feret, H. Koeppl
Conference/Journal:

Winter Simulation Conference 2012
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.

Year:

2012
Type of Publication:

(01)Article
Supervisor:



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% Autogenerated BibTeX entry
@InProceedings { PetFer:2012:IFA_4276,
    author={Tatjana Petrov and Jerome Feret and H. Koeppl},
    title={{Reconstructing species-based dynamics from reduced
	  stochastic rule-based models}},
    booktitle={Winter Simulation Conference 2012},
    pages={},
    year={2012},
    address={},
    month=dec,
    url={http://control.ee.ethz.ch/index.cgi?page=publications;action=details;id=4276}
}
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