Publication Details
Abstraction-Based Segmental Simulation of Chemical Reaction Networks
chemical reaction networks, population models, stochastic simulation algorithm,
model abstraction
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.
@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"
}