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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" }