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

Dateien

Zu diesem Dokument gibt es keine Dateien.

Datum

2012

Autor:innen

Petrov, Tatjana

Feret, Jerome

Koeppl, Heinz

DOI (zitierfähiger Link)

https://doi.org/10.1109/WSC.2012.6465241

Sammlungen

Informatik und Informationswissenschaft

Publikationstyp

Beitrag zu einem Konferenzband

Publikationsstatus

Published

Erschienen 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.2012.6465241

Zusammenfassung

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.

Fachgebiet (DDC)

004 Informatik

Konferenz

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

Zitieren

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, 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.2012.6465241

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}
}

RDF

<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/server/rdf/resource/123456789/42189">
    <dcterms:issued>2012-12</dcterms:issued>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-04-26T14:40:47Z</dc:date>
    <dc:contributor>Petrov, Tatjana</dc:contributor>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:language>eng</dc:language>
    <dc:contributor>Feret, Jerome</dc:contributor>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dc:contributor>Koeppl, Heinz</dc:contributor>
    <dc:creator>Feret, Jerome</dc:creator>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dcterms:title>Reconstructing species-based dynamics from reduced stochastic rule-based models</dcterms:title>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/42189"/>
    <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>
    <dc:creator>Koeppl, Heinz</dc:creator>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-04-26T14:40:47Z</dcterms:available>
    <dc:creator>Petrov, Tatjana</dc:creator>
  </rdf:Description>
</rdf:RDF>

Universitätsbibliographie

Nein