Structured Projection-Based Model Reduction With Application to Stochastic Biochemical Networks

DOI10.1109/TAC.2017.2691315MaRDI QIDQ4566912zbMATH OpenOpenAlexWikidataFDO

Authors

Publication date 27 June 2018

Published in IEEE Transactions on Automatic Control (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1510.05784

Mathematics Subject Classification ID

Numerical solutions to stochastic differential and integral equations (65C30) Systems biology, networks (92C42) Medical applications (general) (92C50) System structure simplification (93B11)

Abstract: The Chemical Master Equation (CME) is well known to provide the highest resolution models of a biochemical reaction network. Unfortunately, even simulating the CME can be a challenging task. For this reason more simple approximations to the CME have been proposed. In this work we focus on one such model, the Linear Noise Approximation. Specifically, we consider implications of a recently proposed LNA time-scale separation method. We show that the reduced order LNA converges to the full order model in the mean square sense. Using this as motivation we derive a network structure preserving reduction algorithm based on structured projections. We present convex optimisation algorithms that describe how such projections can be computed and we discuss when structured solutions exits. We also show that for a certain class of systems, structured projections can be found using basic linear algebra and no optimisation is necessary. The algorithms are then applied to a linearised stochastic LNA model of the yeast glycolysis pathway.

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(2)

• Balanced truncation for model reduction of biological oscillators
• A geometric method for model reduction of biochemical networks with polynomial rate functions

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