Stochastic kinetic models: dynamic independence, modularity and graphs

DOI10.1214/09-AOS779zbMATH Open1203.92033arXiv1010.3916WikidataQ42199708 ScholiaQ42199708MaRDI QIDQ988005FDOQ988005

Authors: Clive Bowsher 

Publication date: 24 August 2010

Published in: The Annals of Statistics (Search for Journal in Brave)

Abstract: The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular systems. We identify SKM subprocesses with the corresponding counting processes and propose a directed, cyclic graph (the kinetic independence graph or KIG) that encodes the local independence structure of their conditional intensities. Given a partition $[A,D,B]$ of the vertices, the graphical separation $AperpB|D$ in the undirected KIG has an intuitive chemical interpretation and implies that $A$ is locally independent of $B$ given $AcupD$. It is proved that this separation also results in global independence of the internal histories of $A$ and $B$ conditional on a history of the jumps in $D$ which, under conditions we derive, corresponds to the internal history of $D$. The results enable mathematical definition of a modularization of an SKM using its implied dynamics. Graphical decomposition methods are developed for the identification and efficient computation of nested modularizations. Application to an SKM of the red blood cell advances understanding of this biochemical system.

Full work available at URL: https://arxiv.org/abs/1010.3916

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zbMATH Keywords

systems biologyreaction networksstochastic kinetic modelcounting and point processesdynamic and local independencegraphical decompositionkinetic independence graph

Mathematics Subject Classification ID

Applications of graph theory (05C90) Point processes (e.g., Poisson, Cox, Hawkes processes) (60G55) Directed graphs (digraphs), tournaments (05C20) Dynamical systems in biology (37N25) Systems biology, networks (92C42) Cell biology (92C37) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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• The dynamics of stochastic mono-molecular reaction systems in stochastic environments
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• Nonparametric likelihood based estimation of linear filters for point processes
• Graphs, random sums, and sojourn time distributions, with application to ion-channel modeling

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