Publikation: Reconstructing species-based dynamics from reduced stochastic rule-based models
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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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PETROV, Tatjana, Jerome FERET, Heinz KOEPPL, 2012. Reconstructing species-based dynamics from reduced stochastic rule-based models. 2012 Winter Simulation Conference : WSC 2012. Berlin, Germany, 9. Dez. 2012 - 12. Dez. 2012. In: Proceedings of the 2012 Winter Simulation Conference (WSC 2012). Piscataway, NJ: IEEE, 2012, 225. ISSN 0891-7736. ISBN 978-1-4673-4779-2. Available under: doi: 10.1109/WSC.2012.6465241BibTex
@inproceedings{Petrov2012-12Recon-42189,
year={2012},
doi={10.1109/WSC.2012.6465241},
title={Reconstructing species-based dynamics from reduced stochastic rule-based models},
isbn={978-1-4673-4779-2},
issn={0891-7736},
publisher={IEEE},
address={Piscataway, NJ},
booktitle={Proceedings of the 2012 Winter Simulation Conference (WSC 2012)},
author={Petrov, Tatjana and Feret, Jerome and Koeppl, Heinz},
note={Article Number: 225}
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