Adaptive hybrid simulations for multiscale stochastic reaction networks

The Journal of Chemical Physics ◽

10.1063/1.4905196 ◽

2015 ◽

Vol 142 (3) ◽

pp. 034118 ◽

Author(s):

Benjamin Hepp ◽

Ankit Gupta ◽

Mustafa Khammash

Keyword(s):

Reaction Networks ◽

Stochastic Reaction ◽

Stochastic Reaction Networks ◽

Hybrid Simulations

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State and parameter estimation from exact partial state observation in stochastic reaction networks

The Journal of Chemical Physics ◽

10.1063/5.0032539 ◽

2021 ◽

Vol 154 (3) ◽

pp. 034103

Author(s):

Muruhan Rathinam ◽

Mingkai Yu

Keyword(s):

Parameter Estimation ◽

Reaction Networks ◽

State Observation ◽

Partial State ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series

PLoS Computational Biology ◽

10.1371/journal.pcbi.1005234 ◽

2016 ◽

Vol 12 (12) ◽

pp. e1005234 ◽

Author(s):

Anna Klimovskaia ◽

Stefan Ganscha ◽

Manfred Claassen

Keyword(s):

Time Series ◽

Single Cell ◽

Structure Learning ◽

Reaction Networks ◽

Sparse Regression ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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Accelerated Sensitivity Analysis in High-Dimensional Stochastic Reaction Networks

PLoS ONE ◽

10.1371/journal.pone.0130825 ◽

2015 ◽

Vol 10 (7) ◽

pp. e0130825 ◽

Author(s):

Georgios Arampatzis ◽

Markos A. Katsoulakis ◽

Yannis Pantazis

Keyword(s):

Sensitivity Analysis ◽

Reaction Networks ◽

High Dimensional ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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StochNetV2: A Tool for Automated Deep Abstractions for Stochastic Reaction Networks

Quantitative Evaluation of Systems - Lecture Notes in Computer Science ◽

10.1007/978-3-030-59854-9_4 ◽

2020 ◽

pp. 27-32

Author(s):

Denis Repin ◽

Nhat-Huy Phung ◽

Tatjana Petrov

Keyword(s):

Reaction Networks ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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Ergodicity, Output-Controllability, and Antithetic Integral Control of Uncertain Stochastic Reaction Networks

IEEE Transactions on Automatic Control ◽

10.1109/tac.2020.3005188 ◽

2020 ◽

pp. 1-1

Author(s):

Corentin Briat ◽

Mustafa H. Khammash

Keyword(s):

Reaction Networks ◽

Integral Control ◽

Output Controllability ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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Quantification of loading effects in interconnections of stochastic reaction networks

2019 18th European Control Conference (ECC) ◽

10.23919/ecc.2019.8796155 ◽

2019 ◽

Author(s):

Ankit Gupta ◽

Patrik Durrenberger ◽

Mustafa Khammash

Keyword(s):

Reaction Networks ◽

Loading Effects ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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Ergodicity Analysis and Antithetic Integral Control of a Class of Stochastic Reaction Networks with Delays

SIAM Journal on Applied Dynamical Systems ◽

10.1137/19m1286219 ◽

2020 ◽

Vol 19 (3) ◽

pp. 1575-1608

Author(s):

Corentin Briat ◽

Mustafa Khammash

Keyword(s):

Reaction Networks ◽

Integral Control ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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Constrained approximation of effective generators for multiscale stochastic reaction networks and application to conditioned path sampling

Journal of Computational Physics ◽

10.1016/j.jcp.2016.07.035 ◽

2016 ◽

Vol 323 ◽

pp. 265-282 ◽

Author(s):

Simon L. Cotter

Keyword(s):

Reaction Networks ◽

Path Sampling ◽

Constrained Approximation ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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A moment closure method for stochastic reaction networks

The Journal of Chemical Physics ◽

10.1063/1.3103264 ◽

2009 ◽

Vol 130 (13) ◽

pp. 134107 ◽

Author(s):

Chang Hyeong Lee ◽

Kyeong-Hun Kim ◽

Pilwon Kim

Keyword(s):

Moment Closure ◽

Reaction Networks ◽

Stochastic Reaction ◽

Closure Method ◽

Stochastic Reaction Networks

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An efficient forward–reverse expectation-maximization algorithm for statistical inference in stochastic reaction networks

Stochastic Analysis and Applications ◽

10.1080/07362994.2015.1116396 ◽

2016 ◽

Vol 34 (2) ◽

pp. 193-231 ◽

Author(s):

Christian Bayer ◽

Alvaro Moraes ◽

Raul Tempone ◽

Pedro Vilanova

Keyword(s):

Statistical Inference ◽

Expectation Maximization ◽

Expectation Maximization Algorithm ◽

Reaction Networks ◽

Stochastic Reaction ◽

Stochastic Reaction Networks

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