Literature DB >> 23248992

A finite difference method for estimating second order parameter sensitivities of discrete stochastic chemical reaction networks.

Elizabeth Skubak Wolf1, David F Anderson.   

Abstract

We present an efficient finite difference method for the approximation of second derivatives, with respect to system parameters, of expectations for a class of discrete stochastic chemical reaction networks. The method uses a coupling of the perturbed processes that yields a much lower variance than existing methods, thereby drastically lowering the computational complexity required to solve a given problem. Further, the method is simple to implement and will also prove useful in any setting in which continuous time Markov chains are used to model dynamics, such as population processes. We expect the new method to be useful in the context of optimization algorithms that require knowledge of the Hessian.

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Year:  2012        PMID: 23248992     DOI: 10.1063/1.4770052

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  3 in total

1.  Stochastic representations of ion channel kinetics and exact stochastic simulation of neuronal dynamics.

Authors:  David F Anderson; Bard Ermentrout; Peter J Thomas
Journal:  J Comput Neurosci       Date:  2014-11-19       Impact factor: 1.621

2.  Comparison of finite difference based methods to obtain sensitivities of stochastic chemical kinetic models.

Authors:  Rishi Srivastava; David F Anderson; James B Rawlings
Journal:  J Chem Phys       Date:  2013-02-21       Impact factor: 3.488

3.  Multiplexing information flow through dynamic signalling systems.

Authors:  Giorgos Minas; Dan J Woodcock; Louise Ashall; Claire V Harper; Michael R H White; David A Rand
Journal:  PLoS Comput Biol       Date:  2020-08-03       Impact factor: 4.475

  3 in total

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