Publication Details

Semi-Quantitative Abstraction and Analysis of Chemical Reaction Networks

ČEŠKA Milan and KŘETÍNSKÝ Jan. Semi-Quantitative Abstraction and Analysis of Chemical Reaction Networks. In: Proceedings of the 31th International Conference on Computer Aided Verification (CAV'19). Lecture Notes of Computer Science, vol. 11561. New York: Springer International Publishing, 2019, pp. 475-496. ISBN 978-3-030-25540-4.
Type
conference paper
Language
english
Authors
Češka Milan, RNDr., Ph.D. (DITS FIT BUT)
Křetínský Jan (TUM)
Keywords

chemical reaction networks, continuous-time Markov chains, population level abstraction, semiquantitative reasoning 

Abstract

Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of biochemical systems. Many relevant CRNs are particularly challenging for existing techniques due to complex dynamics including stochasticity, stiffness or multimodal population distributions. We propose a novel approach allowing not only to predict, but also to explain both the transient and steady-state behaviour. It focuses on qualitative description of the behaviour and aims at quantitative precision only in orders of magnitude. First we build a compact understandable model, which we then crudely analyse. As demonstrated on complex CRNs from literature, our approach reproduces the known results, but in contrast to the state-of-the-art methods, it runs with virtually no computational cost and thus offers unprecedented scalability.

Published
2019
Pages
475-496
Proceedings
Proceedings of the 31th International Conference on Computer Aided Verification (CAV'19)
Series
Lecture Notes of Computer Science
Volume
11561
Conference
31th International Conference on Computer Aided Verification, New York, US
ISBN
978-3-030-25540-4
Publisher
Springer International Publishing
Place
New York, US
DOI
UT WoS
000491468000028
EID Scopus
BibTeX
@INPROCEEDINGS{FITPUB11965,
   author = "Milan \v{C}e\v{s}ka and Jan K\v{r}et\'{i}nsk\'{y}",
   title = "Semi-Quantitative Abstraction and Analysis of Chemical Reaction Networks",
   pages = "475--496",
   booktitle = "Proceedings of the 31th International Conference on Computer Aided Verification (CAV'19)",
   series = "Lecture Notes of Computer Science",
   volume = 11561,
   year = 2019,
   location = "New York, US",
   publisher = "Springer International Publishing",
   ISBN = "978-3-030-25540-4",
   doi = "10.1007/978-3-030-25540-4\_28",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/11965"
}
Back to top