CUED Publications database

Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach

Pan, W and Yuan, Y and Goncalves, J and Stan, G-B (2012) Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach. Proceedings of the IEEE Conference on Decision and Control. pp. 2334-2339. ISSN 0191-2216

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Abstract

Reconstruction of biochemical reaction networks (BRN) and genetic regulatory networks (GRN) in particular is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and rational functions are typically used to model biochemical reaction networks. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data quite difficult. In this paper, we present a network reconstruction algorithm that can deal with ODE model descriptions containing polynomial and rational functions. Rather than identifying the parameters of linear or nonlinear ODEs characterised by pre-defined equation structures, our methodology allows us to determine the nonlinear ODEs structure together with their associated parameters. To solve the network reconstruction problem, we cast it as a compressive sensing (CS) problem and use sparse Bayesian learning (SBL) algorithms as a computationally efficient and robust way to obtain its solution. © 2012 IEEE.

Item Type: Article
Subjects: UNSPECIFIED
Divisions: Div F > Control
Depositing User: Cron Job
Date Deposited: 07 Mar 2014 11:51
Last Modified: 16 Dec 2014 19:07
DOI: 10.1109/CDC.2012.6426216