Fast adaptive uniformization of the chemical master equation

F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, IET Systems Biology 4 (2010) 441–452.

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Journal Article | Published | English

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Author
Didier, Frédéric; Henzinger, Thomas AIST Austria ; Mateescu, Maria; Wolf, Verena
Department
Abstract
Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). The uniformization technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this paper we present an on-the-fly variant of uniformization, where we improve the original algorithm at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks.
Publishing Year
Date Published
2010-11-15
Journal Title
IET Systems Biology
Volume
4
Issue
6
Page
441 - 452
IST-REx-ID

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Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. IET Systems Biology. 2010;4(6):441-452. doi:10.1049/iet-syb.2010.0005
Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). Fast adaptive uniformization of the chemical master equation. IET Systems Biology, 4(6), 441–452. https://doi.org/10.1049/iet-syb.2010.0005
Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems Biology 4, no. 6 (2010): 441–52. https://doi.org/10.1049/iet-syb.2010.0005.
F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” IET Systems Biology, vol. 4, no. 6, pp. 441–452, 2010.
Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization of the chemical master equation. IET Systems Biology. 4(6), 441–452.
Didier, Frédéric, et al. “Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems Biology, vol. 4, no. 6, Institution of Engineering and Technology, 2010, pp. 441–52, doi:10.1049/iet-syb.2010.0005.
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