Artifact for CMSB22 paper "Abstraction-Based Segmental Simulation of Chemical Reaction Networks"

Helfrich, Martin; Ceska, Milan; Kretinsky, Jan; Martiček, Štefan

doi:10.5281/zenodo.6658925

2022

DOI: 10.5281/zenodo.6658925

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Artifact for CMSB22 paper "Abstraction-Based Segmental Simulation of Chemical Reaction Networks"

Martin Helfrich,

Milan Ceska,

Jan Kretinsky

et al.

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Abstraction-Based Segmental Simulation of Chemical Reaction Networks

Helfrich¹,

Češka²,

Křetínský³

et al. 2022

Preprint

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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.

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Abstraction-Based Segmental Simulation of Chemical Reaction Networks

Helfrich¹,

Češka²,

Křetínský³

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

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Artifact for CMSB22 paper "Abstraction-Based Segmental Simulation of Chemical Reaction Networks"

Cited by 1 publication

References 1 publication

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

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