Publication Details

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

HELFRICH, M.; ČEŠKA, M.; KŘETÍNSKÝ, J.; MARTIČEK, Š. Abstraction-Based Segmental Simulation of Chemical Reaction Networks. In International Conference on Computational Methods in Systems Biology. Lecture Notes in Bioinformatics. Bucharest: Springer Verlag, 2022. p. 41-60. ISBN: 978-3-031-15033-3.
Czech title
Segmentační simulace chemických reakčních sítí
Type
conference paper
Language
English
Authors
Helfrich Martin
Češka Milan, doc. RNDr., Ph.D. (DITS)
KŘETÍNSKÝ, J.
Martiček Štefan, Ing.
Keywords

chemical reaction networks, population models, stochastic simulation algorithm, model abstraction

Abstract

Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of simulation runs. On the one hand, this speeds up the simulation process to obtain multiple runs since we can reuse the segments. On the other hand, questions on diversity and genuineness of our runs arise. However, we ensure that we generate runs close to their true distribution by generating an appropriate abstraction of the original system and utilizing it in the simulation process. Interestingly, as a by-product, we also obtain a yet more efficient simulation scheme, yielding runs over the systems abstraction. These provide a very faithful approximation of concrete runs on the desired level of granularity, at a low cost. Our experiments demonstrate the speedups in the simulations while preserving key dynamical as well as quantitative properties.

Published
2022
Pages
41–60
Proceedings
International Conference on Computational Methods in Systems Biology
Series
Lecture Notes in Bioinformatics
ISBN
978-3-031-15033-3
Publisher
Springer Verlag
Place
Bucharest
DOI
EID Scopus
BibTeX
@inproceedings{BUT179390,
  author="HELFRICH, M. and ČEŠKA, M. and KŘETÍNSKÝ, J. and MARTIČEK, Š.",
  title="Abstraction-Based Segmental Simulation of Chemical Reaction Networks",
  booktitle="International Conference on Computational Methods in Systems Biology",
  year="2022",
  series="Lecture Notes in Bioinformatics",
  pages="41--60",
  publisher="Springer Verlag",
  address="Bucharest",
  doi="10.1007/978-3-031-15034-0\{_}3",
  isbn="978-3-031-15033-3"
}
Back to top