Multilevel hybrid split-step implicit tau-leap
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Monte Carlo methods (65C05) Biochemistry, molecular biology (92C40) Interacting random processes; statistical mechanics type models; percolation theory (60K35) Continuous-time Markov processes on discrete state spaces (60J27) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Algorithms with automatic result verification (65G20)
Abstract: In biochemically reactive systems with small copy numbers of one or more reactant molecules, the dynamics is dominated by stochastic effects. To approximate those systems, discrete state-space and stochastic simulation approaches have been shown to be more relevant than continuous state-space and deterministic ones. In systems characterized by having simultaneously fast and slow timescales, existing discrete space-state stochastic path simulation methods, such as the stochastic simulation algorithm (SSA) and the explicit tau-leap (Explicit-TL) method, can be very slow. Implicit approximations have been developed to improve numerical stability and provide efficient simulation algorithms for those systems. Here, we propose an efficient Multilevel Monte Carlo (MLMC) method in the spirit of the work by Anderson and Higham (2012). This method uses split-step implicit tau-leap (SSI-TL) at levels where the SSI-TL method is not applicable due to numerical stability issues. We present numerical examples that illustrate the performance of the proposed method.
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Cited in
(9)- Robustly simulating biochemical reaction kinetics using multi-level Monte Carlo approaches
- Learning-based importance sampling via stochastic optimal control for stochastic reaction networks
- Data-driven method for efficient characterization of rare event probabilities in biochemical systems
- Optimal explicit stabilized postprocessed \(\tau\)-leap method for the simulation of chemical kinetics
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- A multilevel adaptive reaction-splitting simulation method for stochastic reaction networks
- Automated importance sampling via optimal control for stochastic reaction networks: a Markovian projection-based approach
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