Records with Subject: System Identification
Incremental Parameter Estimation under Rank-Deficient Measurement Conditions
Kris Villez, Julien Billeter, Dominique Bonvin
May 16, 2019 (v1)
Keywords: extents, graph theory, model identification, observability, optimal clustering, parameter estimation, state decoupling
The computation and modeling of extents has been proposed to handle the complexity of large-scale model identification tasks. Unfortunately, the existing extent-based framework only applies when certain conditions apply. Most typically, it is required that a unique value for each extent can be computed. This severely limits the applicability of this approach. In this work, we propose a novel procedure for parameter estimation inspired by the existing extent-based framework. A key difference with prior work is that the proposed procedure combines structural observability labeling, matrix factorization, and graph-based system partitioning to split the original model parameter estimation problem into parameter estimation problems with the least number of parameters. The value of the proposed method is demonstrated with an extensive simulation study and a study based on a historical data set collected to characterize the isomerization of α -pinene. Most importantly, the obtained resul... [more]
Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design
Nathan Braniff, Matthew Scott, Brian Ingalls
April 15, 2019 (v1)
Keywords: cell physiology, characterization, host-context effects, model fitting, optimal control, optimal experimental design, synthetic biology
Synthetic biology design challenges have driven the use of mathematical models to characterize genetic components and to explore complex design spaces. Traditional approaches to characterization have largely ignored the effect of strain and growth conditions on the dynamics of synthetic genetic circuits, and have thus confounded intrinsic features of the circuit components with cell-level context effects. We present a model that distinguishes an activated gene’s intrinsic kinetics from its physiological context. We then demonstrate an optimal experimental design approach to identify dynamic induction experiments for efficient estimation of the component’s intrinsic parameters. Maximally informative experiments are chosen by formulating the design as an optimal control problem; direct multiple-shooting is used to identify the optimum. Our numerical results suggest that the intrinsic parameters of a genetic component can be more accurately estimated using optimal experimental designs, an... [more]
On-Line Optimal Input Design Increases the Efficiency and Accuracy of the Modelling of an Inducible Synthetic Promoter
Lucia Bandiera, Zhaozheng Hou, Varun B. Kothamachu, Eva Balsa-Canto, Peter S. Swain, Filippo Menolascina
April 8, 2019 (v1)
Keywords: model calibration, model-based optimal experimental design, optimal inputs, synthetic biology, system identification
Synthetic biology seeks to design biological parts and circuits that implement new functions in cells. Major accomplishments have been reported in this field, yet predicting a priori the in vivo behaviour of synthetic gene circuits is major a challenge. Mathematical models offer a means to address this bottleneck. However, in biology, modelling is perceived as an expensive, time-consuming task. Indeed, the quality of predictions depends on the accuracy of parameters, which are traditionally inferred from poorly informative data. How much can parameter accuracy be improved by using model-based optimal experimental design (MBOED)? To tackle this question, we considered an inducible promoter in the yeast S. cerevisiae. Using in vivo data, we re-fit a dynamic model for this component and then compared the performance of standard (e.g., step inputs) and optimally designed experiments for parameter inference. We found that MBOED improves the quality of model calibration by ∼60%. Results furt... [more]
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