Abstraction-Based Segmental Simulation of Chemical Reaction
Networks

D 2022

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

HELFRICH, Martin; Milan ČEŠKA; Jan KŘETÍNSKÝ a Stefan MARTICEK

Základní údaje

Originální název

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

Autoři

HELFRICH, Martin; Milan ČEŠKA; Jan KŘETÍNSKÝ a Stefan MARTICEK

Vydání

Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Bucharest, Romania, September 14-16, 2022, Proceedings, od s. 41-60, 20 s. 2022

Nakladatel

Springer

Další údaje

Typ výsledku

Stať ve sborníku

Označené pro přenos do RIV

Organizační jednotka

Fakulta informatiky

ISBN

9783031150333

ISSN

DOI

https://doi.org/10.1007/978-3-031-15034-0_3

Změněno: 17. 3. 2025 14:43, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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 system’s 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.

Citovat

HELFRICH, Martin; Milan ČEŠKA; Jan KŘETÍNSKÝ a Stefan MARTICEK. Abstraction-Based Segmental Simulation of Chemical Reaction Networks. In Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Bucharest, Romania, September 14-16, 2022, Proceedings. Springer, 2022, s. 41-60. ISBN 9783031150333. Dostupné z: https://doi.org/10.1007/978-3-031-15034-0_3.

@inproceedings{2484775,
   author = {Helfrich, Martin and Češka, Milan and Křetínský, Jan and Marticek, Stefan},
   booktitle = {Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Bucharest, Romania, September 14-16, 2022, Proceedings},
   doi = {https://doi.org/10.1007/978-3-031-15034-0_3},
   isbn = {9783031150333},
   pages = {41-60},
   publisher = {Springer},
   title = {Abstraction-Based Segmental Simulation of Chemical Reaction Networks},
   year = {2022}
}

TY  - CONF
ID  - 2484775
AU  - Helfrich, Martin - Češka, Milan - Křetínský, Jan - Marticek, Stefan
PY  - 2022
TI  - Abstraction-Based Segmental Simulation of Chemical Reaction Networks
PB  - Springer
SN  - 9783031150333
N2  - 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 system’s 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.
ER  -

HELFRICH, Martin; Milan ČEŠKA; Jan KŘETÍNSKÝ a Stefan MARTICEK. Abstraction-Based Segmental Simulation of Chemical Reaction Networks. In \textit{Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Bucharest, Romania, September 14-16, 2022, Proceedings}. Springer, 2022, s.~41-60. ISBN~9783031150333. Dostupné z: https://doi.org/10.1007/978-3-031-15034-0\_{}3.

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