Publication Details

Precise parameter synthesis for stochastic biochemical systems

ČEŠKA Milan, DANNENBERG Frits, KWIATKOWSKA Marta, PAOLETTI Nicola and BRIM Luboš. Precise parameter synthesis for stochastic biochemical systems. Acta Informatica, vol. 54, no. 6, 2016, pp. 589-623. ISSN 0001-5903. Available from: http://link.springer.com/article/10.1007/s00236-016-0265-2
Czech title
Přesná syntéza parametrů pro stochastické biochemické systémy
Type
journal article
Language
english
Authors
Češka Milan, doc. RNDr., Ph.D. (DITS FIT BUT)
Dannenberg Frits (UOx)
Kwiatkowska Marta (UOx)
Paoletti Nicola (UOx)
Brim Luboš, prof. RNDr., CSc. (FI MUNI)
URL
Keywords

parameter synthesis, stochastic biochemical models, continuous-time Markov Chains, continuous stochastic logic 

Abstract

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 or minimised. Our method is based on extending CSL model checking and standard uniformisation to parametric models, in order to compute safe bounds on the satisfaction probability of the property. We develop synthesis algorithms that yield answers that are precise to within an arbitrarily small tolerance value. The algorithms combine the computation of probability bounds with the refinement and sampling of the parameter space. Our methods are precise and efficient, and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for three biologically motivated case studies: infection control for a SIR epidemic model; reliability analysis of molecular computation by a DNA walker; and bistability in the gene regulation of the mammalian cell cycle.

Published
2016
Pages
589-623
Journal
Acta Informatica, vol. 54, no. 6, ISSN 0001-5903
Publisher
Springer Verlag
DOI
UT WoS
000407713300003
EID Scopus
BibTeX
@ARTICLE{FITPUB11210,
   author = "Milan \v{C}e\v{s}ka and Frits Dannenberg and Marta Kwiatkowska and Nicola Paoletti and Lubo\v{s} Brim",
   title = "Precise parameter synthesis for stochastic biochemical systems",
   pages = "589--623",
   journal = "Acta Informatica",
   volume = 54,
   number = 6,
   year = 2016,
   ISSN = "0001-5903",
   doi = "10.1007/s00236-016-0265-2",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/11210"
}
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