Detail publikace

Precise parameter synthesis for stochastic biochemical systems

ČEŠKA, M. DANNENBERG, F. KWIATKOWSKA, M. PAOLETTI, N. BRIM, L.

Originální název

Precise parameter synthesis for stochastic biochemical systems

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

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.

Klíčová slova

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

Autoři

ČEŠKA, M.; DANNENBERG, F.; KWIATKOWSKA, M.; PAOLETTI, N.; BRIM, L.

Vydáno

28. 3. 2016

ISSN

0001-5903

Periodikum

Acta Informatica

Ročník

54

Číslo

6

Stát

Spolková republika Německo

Strany od

589

Strany do

623

Strany počet

35

URL

BibTex

@article{BUT130998,
  author="Milan {Češka} and Frits {Dannenberg} and Marta {Kwiatkowska} and Nicola {Paoletti} and Luboš {Brim}",
  title="Precise parameter synthesis for stochastic biochemical systems",
  journal="Acta Informatica",
  year="2016",
  volume="54",
  number="6",
  pages="589--623",
  doi="10.1007/s00236-016-0265-2",
  issn="0001-5903",
  url="http://link.springer.com/article/10.1007/s00236-016-0265-2"
}