Publication Details

Semi-quantitative Abstraction and Analysis of Chemical Reaction Networks (Extended Abstract)

ČEŠKA Milan and KŘETÍNSKÝ Jan. Semi-quantitative Abstraction and Analysis of Chemical Reaction Networks (Extended Abstract). In: Proceedings of the 17th International Conference on Computational Methods in Systems Biology. Lecture Notes in Bioinformatics. Trieste: Springer International Publishing, 2019, pp. 337-341. ISBN 978-3-030-31303-6.
Czech title
Semikvantitativní analýza chemických reakčních sítí (rozšířený abstrakt)
Type
conference paper
Language
english
Authors
Češka Milan, doc. 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
337-341
Proceedings
Proceedings of the 17th International Conference on Computational Methods in Systems Biology
Series
Lecture Notes in Bioinformatics
Conference
17th International Conference on Computational Methods in Systems Biology, Trieste, IT
ISBN
978-3-030-31303-6
Publisher
Springer International Publishing
Place
Trieste, IT
DOI
UT WoS
000557875100022
EID Scopus
BibTeX
@INPROCEEDINGS{FITPUB12151,
   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 (Extended Abstract)",
   pages = "337--341",
   booktitle = "Proceedings of the 17th International Conference on Computational Methods in Systems Biology",
   series = "Lecture Notes in Bioinformatics",
   year = 2019,
   location = "Trieste, IT",
   publisher = "Springer International Publishing",
   ISBN = "978-3-030-31303-6",
   doi = "10.1007/978-3-030-31304-3\_22",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/12151"
}
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