Precise Parameter Synthesis for Stochastic Biochemical Systems

D 2014

Precise Parameter Synthesis for Stochastic Biochemical Systems

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

Základní údaje

Originální název

Precise Parameter Synthesis for Stochastic Biochemical Systems

Autoři

ČEŠKA, Milan (203 Česká republika, garant, domácí), Frits DANNENBERG (528 Nizozemské království), Marta KWIATKOWSKA (826 Velká Británie a Severní Irsko) a Nicola PAOLETTI (380 Itálie)

Vydání

Switzerland, Computational Methods in Systems Biology, od s. 86-98, 13 s. 2014

Nakladatel

Springer International Publishing

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Impakt faktor

Impact factor: 0.402 v roce 2005

Kód RIV

RIV/00216224:14330/14:00077017

Organizační jednotka

Fakulta informatiky

ISBN

978-3-319-12981-5

ISSN

DOI

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

Klíčová slova anglicky

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

Štítky

firank_B

Změněno: 27. 4. 2015 06:02, RNDr. Pavel Šmerk, Ph.D.

Anotace

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 a Nicola PAOLETTI. Precise Parameter Synthesis for Stochastic Biochemical Systems. In Computational Methods in Systems Biology. Switzerland: Springer International Publishing, 2014, s. 86-98. ISBN 978-3-319-12981-5. Dostupné z: 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 a Nicola PAOLETTI. Precise Parameter Synthesis for Stochastic Biochemical Systems. In \textit{Computational Methods in Systems Biology}. Switzerland: Springer International Publishing, 2014, s.~86-98. ISBN~978-3-319-12981-5. Dostupné z: https://dx.doi.org/10.1007/978-3-319-12982-2\_{}7.

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