Uniformization techniques for stochastic simulation of chemical reaction networks

Published in The Journal of Chemical Physics, 2019

Published journal article / author pre-print

Recommended citation: Casper Beentjes, Ruth Baker, "Uniformization techniques for stochastic simulation of chemical reaction networks." The Journal of Chemical Physics 150 (15), 154107 (2019).

Abstract: This work considers the method of uniformization for continuous-time Markov chains in the context of chemical reaction networks. Previous work in the literature has shown that uniformization can be beneficial in the context of time-inhomogeneous models, such as chemical reaction networks incorporating extrinsic noise. This paper lays focus on the understanding of uniformization from the viewpoint of sample paths of chemical reaction networks. In particular, an efficient pathwise stochastic simulation algorithm for time-homogeneous models is presented which is complexity-wise equal to Gillespie's direct method. This new approach therefore enlarges the class of problems for which the uniformization approach forms a computationally attractive choice. Furthermore, as a new application of the uniformization method, we provide a novel variance reduction method for (raw) moment estimators of chemical reaction networks based upon the combination of stratification and uniformization.