Hybrid extended Luenberger-asymptotic observer for bioprocess state estimation

Hulhoven, Xavier; Wouwer, Alain Vande; Bogaerts, Philippe

doi:10.23919/ecc.2003.7085347

Cited by 3 publications

(1 citation statement)

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“…These algorithms were originally developed for the problem of state estimation, in which one seeks to estimate the time evolution of the unobserved components of the state of a dynamical system. The controls literature on this subject is vast, but in the context of biological or biochemical systems the classically used approaches include Luenberger-like [17] , Kalman filter based, [18] – [20] , and high-gain observers [21] . Other methods have been developed by exploiting the special structure of specific problems [22] .…”

Section: Introductionmentioning

confidence: 99%

Parameter Estimation and Model Selection in Computational Biology

2010

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A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection.

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