Publication detail

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

HELFRICH, M. ČEŠKA, M. KŘETÍNSKÝ, J. MARTIČEK, Š.

Original Title

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

Type

conference paper

Language

English

Original 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.

Keywords

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

Authors

HELFRICH, M.; ČEŠKA, M.; KŘETÍNSKÝ, J.; MARTIČEK, Š.

Released

17. 6. 2022

Publisher

Springer Verlag

Location

Bucharest

ISBN

978-3-031-15033-3

Book

International Conference on Computational Methods in Systems Biology

Edition

Lecture Notes in Bioinformatics

Pages from

41

Pages to

60

Pages count

20

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"
}