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Conference Papers Year : 2012

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

Tatjana Petrov
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Heinz Koeppl
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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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Dates and versions

hal-00734483 , version 1 (22-09-2012)

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  • HAL Id : hal-00734483 , version 1

Cite

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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