Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions

Joel A Paulson, Marc Martin-Casas and Ali Mesbah

PLOS Computational Biology, 2019, vol. 15, issue 8, 1-35

Abstract: We present a novel surrogate modeling method that can be used to accelerate the solution of uncertainty quantification (UQ) problems arising in nonlinear and non-smooth models of biological systems. In particular, we focus on dynamic flux balance analysis (DFBA) models that couple intracellular fluxes, found from the solution of a constrained metabolic network model of the cellular metabolism, to the time-varying nature of the extracellular substrate and product concentrations. DFBA models are generally computationally expensive and present unique challenges to UQ, as they entail dynamic simulations with discrete events that correspond to switches in the active set of the solution of the constrained intracellular model. The proposed non-smooth polynomial chaos expansion (nsPCE) method is an extension of traditional PCE that can effectively capture singularities in the DFBA model response due to the occurrence of these discrete events. The key idea in nsPCE is to use a model of the singularity time to partition the parameter space into two elements on which the model response behaves smoothly. Separate PCE models are then fit in both elements using a basis-adaptive sparse regression approach that is known to scale well with respect to the number of uncertain parameters. We demonstrate the effectiveness of nsPCE on a DFBA model of an E. coli monoculture that consists of 1075 reactions and 761 metabolites. We first illustrate how traditional PCE is unable to handle problems of this level of complexity. We demonstrate that over 800-fold savings in computational cost of uncertainty propagation and Bayesian estimation of parameters in the substrate uptake kinetics can be achieved by using the nsPCE surrogates in place of the full DFBA model simulations. We then investigate the scalability of the nsPCE method by utilizing it for global sensitivity analysis and maximum a posteriori estimation in a synthetic metabolic network problem with a larger number of parameters related to both intracellular and extracellular quantities.Author summary: Construction and validation of mathematical models in biological systems involving genome-scale biomolecular networks is a challenging problem. This article presents a novel surrogate modeling method that can accelerate parameter inference from experimental data and the quantification of uncertainty in the predictions of complex dynamic biological models, with a particular emphasis on nonlinear models with non-smooth behavior. The method is applied to infer extracellular kinetic parameters in a batch fermentation reactor consisting of diauxic growth of E. coli on a glucose/xylose mixed media as well as a larger synthetic metabolic network problem. The proposed approach enables rigorous quantification of parameter uncertainty to determine whether or not available data is sufficient for estimation of all unknown model parameters.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1007308

DOI: 10.1371/journal.pcbi.1007308

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