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

Petrov, Tatjana; Feret, Jerome; Koeppl, Heinz

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

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Date

2012

Authors

Petrov, Tatjana

Feret, Jerome

Koeppl, Heinz

DOI (citable link)

10.1109/WSC.2012.6465241

Collections

Informatik und Informationswissenschaft

Publication type

Contribution to a conference collection

Publication status

Published

Published in

Proceedings of the 2012 Winter Simulation Conference (WSC 2012). - Piscataway, NJ : IEEE, 2012. - 225. - ISSN 0891-7736. - ISBN 978-1-4673-4779-2

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.

Subject (DDC)

004 Computer Science

Conference

2012 Winter Simulation Conference : WSC 2012, Dec 9, 2012 - Dec 12, 2012, Berlin, Germany

Cite This

ISO 690

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, Dec 9, 2012 - Dec 12, 2012. In: Proceedings of the 2012 Winter Simulation Conference (WSC 2012). Piscataway, NJ:IEEE, 225. ISSN 0891-7736. ISBN 978-1-4673-4779-2. Available under: doi: 10.1109/WSC.2012.6465241

BibTex

@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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