Abstraction-Based Segmental Simulation of Chemical Reaction Networks

conference paper

English

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.

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

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

17. 6. 2022

Springer Verlag

Bucharest

978-3-031-15033-3

International Conference on Computational Methods in Systems Biology

Lecture Notes in Bioinformatics

41

60

20