Publication detail

Abstraction-based segmental simulation of reaction networks using adaptive memoization

HELFRICH, M. ANDRIUSHCHENKO, R. ČEŠKA, M. KŘETÍNSKÝ, J. MARTIČEK, Š. ŠAFRÁNEK, D.

Original Title

Abstraction-based segmental simulation of reaction networks using adaptive memoization

Type

journal article in Web of Science

Language

English

Original Abstract

Background Stochastic models are commonly employed in the system and synthetic biology to study the effects of stochastic fluctuations emanating from reactions involving species with low copy-numbers. Many important models feature complex dynamics, involving a state-space explosion, stiffness, and multimodality, that complicate the quantitative analysis needed to understand their stochastic behavior. Direct numerical analysis of such models is typically not feasible and generating many simulation runs that adequately approximate the model's dynamics may take a prohibitively long time. Results We propose a new memoization technique that leverages a population-based abstraction and combines previously generated parts of simulations, called segments, to generate new simulations more efficiently while preserving the original system's dynamics and its diversity. Our algorithm adapts online to identify the most important abstract states and thus utilizes the available memory efficiently. Conclusion We demonstrate that in combination with a novel fully automatic and adaptive hybrid simulation scheme, we can speed up the generation of trajectories significantly and correctly predict the transient behavior of complex stochastic systems.

Keywords

Reaction networks, stochastic simulation, population abstraction, memoization

Authors

HELFRICH, M.; ANDRIUSHCHENKO, R.; ČEŠKA, M.; KŘETÍNSKÝ, J.; MARTIČEK, Š.; ŠAFRÁNEK, D.

Released

1. 12. 2024

ISBN

1471-2105

Periodical

BMC BIOINFORMATICS

Year of study

25

Number

1

State

United Kingdom of Great Britain and Northern Ireland

Pages from

1

Pages to

24

Pages count

24

URL

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05966-5

BibTex

@article{BUT193584,
  author="HELFRICH, M. and ANDRIUSHCHENKO, R. and ČEŠKA, M. and KŘETÍNSKÝ, J. and MARTIČEK, Š. and ŠAFRÁNEK, D.",
  title="Abstraction-based segmental simulation of reaction networks using adaptive memoization",
  journal="BMC BIOINFORMATICS",
  year="2024",
  volume="25",
  number="1",
  pages="1--24",
  doi="10.1186/s12859-024-05966-5",
  issn="1471-2105",
  url="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05966-5"
}