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

Petrov, T. and Feret, J. and Koeppl, H. (2012):
Reconstructing species-based dynamics from reduced stochastic rule-based models.
In: Proceedings of the 2012 Winter Simulation Conference, Winter Simulation Conference, p. 225, [Online-Edition: http://dl.acm.org/citation.cfm?id=2429759.2430062],
[Article]

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.

Item Type: Article
Erschienen: 2012
Creators: Petrov, T. and Feret, J. and Koeppl, H.
Title: Reconstructing species-based dynamics from reduced stochastic rule-based models
Language: English
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.

Journal or Publication Title: Proceedings of the 2012 Winter Simulation Conference
Publisher: Winter Simulation Conference
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Date Deposited: 04 Apr 2014 12:18
Official URL: http://dl.acm.org/citation.cfm?id=2429759.2430062
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