Precise Parameter Synthesis for Stochastic Biochemical Systems

D 2014

Precise Parameter Synthesis for Stochastic Biochemical Systems

ČEŠKA, Milan, Frits DANNENBERG, Marta KWIATKOWSKA and Nicola PAOLETTI

Basic information

Original name

Precise Parameter Synthesis for Stochastic Biochemical Systems

Authors

ČEŠKA, Milan (203 Czech Republic, guarantor, belonging to the institution), Frits DANNENBERG (528 Netherlands), Marta KWIATKOWSKA (826 United Kingdom of Great Britain and Northern Ireland) and Nicola PAOLETTI (380 Italy)

Edition

Switzerland, Computational Methods in Systems Biology, p. 86-98, 13 pp. 2014

Publisher

Springer International Publishing

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

Impact factor

Impact factor: 0.402 in 2005

RIV identification code

RIV/00216224:14330/14:00077017

Organization unit

Faculty of Informatics

ISBN

978-3-319-12981-5

ISSN

DOI

http://dx.doi.org/10.1007/978-3-319-12982-2_7

Keywords in English

stochastic biochemical systems; parameter synthesis; continuous time Markov chains; model-checking

Abstract

V originále

We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised/minimised. We develop algorithms based on the computation of lower and upper bounds of the probability, in conjunction with refinement and sampling, which yield answers that are precise to within an arbitrarily small tolerance value. Our methods are efficient and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for two biologically motivated case studies, including the reliability analysis of a DNA walker.

Citovat

ČEŠKA, Milan, Frits DANNENBERG, Marta KWIATKOWSKA and Nicola PAOLETTI. Precise Parameter Synthesis for Stochastic Biochemical Systems. In Computational Methods in Systems Biology. Switzerland: Springer International Publishing, 2014, p. 86-98. ISBN 978-3-319-12981-5. Available from: https://dx.doi.org/10.1007/978-3-319-12982-2_7.

@inproceedings{1204229,
   author = {Češka, Milan and Dannenberg, Frits and Kwiatkowska, Marta and Paoletti, Nicola},
   address = {Switzerland},
   booktitle = {Computational Methods in Systems Biology},
   doi = {http://dx.doi.org/10.1007/978-3-319-12982-2_7},
   keywords = {stochastic biochemical systems; parameter synthesis; continuous time Markov chains; model-checking},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Switzerland},
   isbn = {978-3-319-12981-5},
   pages = {86-98},
   publisher = {Springer International Publishing},
   title = {Precise Parameter Synthesis for Stochastic Biochemical Systems},
   year = {2014}
}

TY  - JOUR
ID  - 1204229
AU  - Češka, Milan - Dannenberg, Frits - Kwiatkowska, Marta - Paoletti, Nicola
PY  - 2014
TI  - Precise Parameter Synthesis for Stochastic Biochemical Systems
PB  - Springer International Publishing
CY  - Switzerland
SN  - 9783319129815
KW  - stochastic biochemical systems
KW  - parameter synthesis
KW  - continuous time Markov chains
KW  - model-checking
N2  - We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised/minimised. We develop algorithms based on the computation of lower and upper bounds of the probability, in conjunction with refinement and sampling, which yield answers that are precise to within an arbitrarily small tolerance value. Our methods are efficient and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for two biologically motivated case studies, including the reliability analysis of a DNA walker.
ER  -

ČEŠKA, Milan, Frits DANNENBERG, Marta KWIATKOWSKA and Nicola PAOLETTI. Precise Parameter Synthesis for Stochastic Biochemical Systems. In \textit{Computational Methods in Systems Biology}. Switzerland: Springer International Publishing, 2014, p.~86-98. ISBN~978-3-319-12981-5. Available from: https://dx.doi.org/10.1007/978-3-319-12982-2\_{}7.

Detailed Information on Publication Record