Literature DB >> 26274260

Higher-order Lie symmetries in identifiability and predictability analysis of dynamic models.

Benjamin Merkt1, Jens Timmer1,2,3, Daniel Kaschek1.   

Abstract

Parameter estimation in ordinary differential equations (ODEs) has manifold applications not only in physics but also in the life sciences. When estimating the ODE parameters from experimentally observed data, the modeler is frequently concerned with the question of parameter identifiability. The source of parameter nonidentifiability is tightly related to Lie group symmetries. In the present work, we establish a direct search algorithm for the determination of admitted Lie group symmetries. We clarify the relationship between admitted symmetries and parameter nonidentifiability. The proposed algorithm is applied to illustrative toy models as well as a data-based ODE model of the NFκB signaling pathway. We find that besides translations and scaling transformations also higher-order transformations play a role. Enabled by the knowledge about the explicit underlying symmetry transformations, we show how models with nonidentifiable parameters can still be employed to make reliable predictions.

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Year:  2015        PMID: 26274260     DOI: 10.1103/PhysRevE.92.012920

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  9 in total

1.  A protocol for dynamic model calibration.

Authors:  Alejandro F Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R Banga
Journal:  Brief Bioinform       Date:  2022-01-17       Impact factor: 11.622

2.  Dynamic modeling of Nrf2 pathway activation in liver cells after toxicant exposure.

Authors:  Steven Hiemstra; Mirjam Fehling-Kaschek; Isoude A Kuijper; Bob van de Water; Daniel Kaschek; Luc J M Bischoff; Lukas S Wijaya; Marcus Rosenblatt; Jeroen Esselink; Allard van Egmond; Jornt Mos; Joost B Beltman; Jens Timmer
Journal:  Sci Rep       Date:  2022-05-05       Impact factor: 4.996

3.  Driving the Model to Its Limit: Profile Likelihood Based Model Reduction.

Authors:  Tim Maiwald; Helge Hass; Bernhard Steiert; Joep Vanlier; Raphael Engesser; Andreas Raue; Friederike Kipkeew; Hans H Bock; Daniel Kaschek; Clemens Kreutz; Jens Timmer
Journal:  PLoS One       Date:  2016-09-02       Impact factor: 3.240

4.  Estimation and Identifiability of Model Parameters in Human Nociceptive Processing Using Yes-No Detection Responses to Electrocutaneous Stimulation.

Authors:  Huan Yang; Hil G E Meijer; Jan R Buitenweg; Stephan A van Gils
Journal:  Front Psychol       Date:  2016-12-05

5.  Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

Authors:  Alejandro F Villaverde; Julio R Banga
Journal:  PLoS Comput Biol       Date:  2017-11-29       Impact factor: 4.475

6.  Testing structural identifiability by a simple scaling method.

Authors:  Mario Castro; Rob J de Boer
Journal:  PLoS Comput Biol       Date:  2020-11-03       Impact factor: 4.475

7.  On testing structural identifiability by a simple scaling method: Relying on scaling symmetries can be misleading.

Authors:  Alejandro F Villaverde; Gemma Massonis
Journal:  PLoS Comput Biol       Date:  2021-10-14       Impact factor: 4.475

8.  Occam's razor gets a new edge: the use of symmetries in model selection.

Authors:  Johannes G Borgqvist; Sam Palmer
Journal:  J R Soc Interface       Date:  2022-08-24       Impact factor: 4.293

9.  Model-based identification of TNFα-induced IKKβ-mediated and IκBα-mediated regulation of NFκB signal transduction as a tool to quantify the impact of drug-induced liver injury compounds.

Authors:  Angela Oppelt; Daniel Kaschek; Suzanna Huppelschoten; Rowena Sison-Young; Fang Zhang; Marie Buck-Wiese; Franziska Herrmann; Sebastian Malkusch; Carmen L Krüger; Mara Meub; Benjamin Merkt; Lea Zimmermann; Amy Schofield; Robert P Jones; Hassan Malik; Marcel Schilling; Mike Heilemann; Bob van de Water; Christopher E Goldring; B Kevin Park; Jens Timmer; Ursula Klingmüller
Journal:  NPJ Syst Biol Appl       Date:  2018-06-11
  9 in total

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