KOPS - The Institutional Repository of the University of Konstanz

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

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

Cite This

Files in this item

Files Size Format View

There are no files associated with this item.

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

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

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/42189"> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/36"/> <dcterms:abstract xml:lang="eng">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.</dcterms:abstract> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dc:contributor>Koeppl, Heinz</dc:contributor> <dc:creator>Feret, Jerome</dc:creator> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-04-26T14:40:47Z</dc:date> <dcterms:issued>2012-12</dcterms:issued> <dcterms:title>Reconstructing species-based dynamics from reduced stochastic rule-based models</dcterms:title> <dc:language>eng</dc:language> <dc:contributor>Feret, Jerome</dc:contributor> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-04-26T14:40:47Z</dcterms:available> <dc:creator>Koeppl, Heinz</dc:creator> <dc:creator>Petrov, Tatjana</dc:creator> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/42189"/> <dc:contributor>Petrov, Tatjana</dc:contributor> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/36"/> </rdf:Description> </rdf:RDF>

This item appears in the following Collection(s)

Search KOPS


Browse

My Account