Benchmarking optimization methods for parameter estimation in large kinetic models

Bioinformatics
Alejandro F VillaverdeJulio R Banga

Abstract

Kinetic models contain unknown parameters that are estimated by optimizing the fit to experimental data. This task can be computationally challenging due to the presence of local optima and ill-conditioning. While a variety of optimization methods have been suggested to surmount these issues, it is difficult to choose the best one for a given problem a priori. A systematic comparison of parameter estimation methods for problems with tens to hundreds of optimization variables is currently missing, and smaller studies provided contradictory findings. We use a collection of benchmarks to evaluate the performance of two families of optimization methods: (i) multi-starts of deterministic local searches and (ii) stochastic global optimization metaheuristics; the latter may be combined with deterministic local searches, leading to hybrid methods. A fair comparison is ensured through a collaborative evaluation and a consideration of multiple performance metrics. We discuss possible evaluation criteria to assess the trade-off between computational efficiency and robustness. Our results show that, thanks to recent advances in the calculation of parametric sensitivities, a multi-start of gradient-based local methods is often a successful ...Continue Reading

References

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Nov 4, 2006·BMC Bioinformatics·Maria Rodriguez-FernandezJulio R Banga
Jun 27, 2007·Biotechnology and Bioengineering·Christophe ChassagnoleMatthias Reuss
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Sep 3, 2010·Genes & Development·William W ChenPeter K Sorger
Jun 26, 2012·BMC Systems Biology·Alejandro F VillaverdeJulio R Banga
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Apr 17, 2015·BMC Systems Biology·Alejandro F VillaverdeJulio R Banga
Sep 4, 2015·Biotechnology Journal·Shyam SrinivasanRadhakrishnan Mahadevan
Oct 31, 2015·BMC Systems Biology·Attila Gábor, Julio R Banga
Jan 24, 2017·PLoS Computational Biology·Fabian FröhlichJan Hasenauer
Aug 5, 2017·Journal of the Royal Society, Interface·Ann C Babtie, Michael P H Stumpf
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Oct 14, 2017·Biotechnology Journal·Sarantos KyriakopoulosDong-Yup Lee
Dec 6, 2017·Bioinformatics·Thomas S LigonJan Hasenauer

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Citations

Jul 28, 2019·Bioinformatics·Leonard SchmiesterDaniel Weindl
Jul 23, 2020·Journal of Mathematical Biology·Leonard SchmiesterJan Hasenauer
Jan 10, 2019·Bioinformatics·Helge HassClemens Kreutz
Nov 19, 2020·PLoS Computational Biology·Alireza YazdaniGeorge Em Karniadakis
Mar 6, 2021·Frontiers in Bioengineering and Biotechnology·Natal A W van RielAlbert K Groen
Sep 16, 2019·IScience·Eshan D MitraWilliam S Hlavacek
Oct 8, 2021·Briefings in Bioinformatics·Alejandro F VillaverdeJulio R Banga
Jan 1, 2022·WIREs Mechanisms of Disease·Yu ZhangAleksander S Popel

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Software Mentioned

MATLAB
SYNBIOCONTROL
FMINCON MATLAB Optimization Toolbox
eSS
SUNDIALS
NL2SOL
MEIGO toolbox
AMICI
FWD
NOLOC

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