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Register a new userStructured Projection-Based Model Reduction with Application to Stochastic Biochemical Networks
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Added by
Aivar Sootla
Publication date
2015
fields
Informatics Engineering
and research's language is
English
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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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In this paper, we consider the problem of model order reduction of stochastic biochemical networks. In particular, we reduce the order of (the number of equations in) the Linear Noise Approximation of the Chemical Master Equation, which is often used to describe biochemical networks. In contrast to other biochemical network reduction methods, the presented one is projection-based. Projection-based methods are powerful tools, but the cost of their use is the loss of physical interpretation of the nodes in the network. In order alleviate this drawback, we employ structured projectors, which means that some nodes in the network will keep their physical interpretation. For many models in engineering, finding structured projectors is not always feasible; however, in the context of biochemical networks it is much more likely as the networks are often (almost) monotonic. To summarise, the method can serve as a trade-off between approximation quality and physical interpretation, which is illustrated on numerical examples.
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This paper presents a model reduction method for the class of linear quantum stochastic systems often encountered in quantum optics and their related fields. The approach is proposed on the basis of an interpolatory projection ensuring that specific input-output responses of the original and the reduced-order systems are matched at multiple selected points (or frequencies). Importantly, the physical realizability property of the original quantum system imposed by the law of quantum mechanics is preserved under our tangential interpolatory projection. An error bound is established for the proposed model reduction method and an avenue to select interpolation points is proposed. A passivity preserving model reduction method is also presented. Examples of both active and passive systems are provided to illustrate the merits of our proposed approach.
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