Literature DB >> 33505318

Searching for Errors in Models of Complex Dynamic Systems.

Dominik Kahl1, Maik Kschischo1.   

Abstract

Mathematical modeling is seen as a key step to understand, predict, and control the temporal dynamics of interacting systems in such diverse areas like physics, biology, medicine, and economics. However, for large and complex systems we usually have only partial knowledge about the network, the coupling functions, and the interactions with the environment governing the dynamic behavior. This incomplete knowledge induces structural model errors which can in turn be the cause of erroneous model predictions or misguided interpretations. Uncovering the location of such structural model errors in large networks can be a daunting task for a modeler. Here, we present a data driven method to search for structural model errors and to confine their position in large and complex dynamic networks. We introduce a coherence measure for pairs of network nodes, which indicates, how difficult it is to distinguish these nodes as sources of an error. By clustering network nodes into coherence groups and inferring the cluster inputs we can decide, which cluster is affected by an error. We demonstrate the utility of our method for the C. elegans neural network, for a signal transduction model for UV-B light induced morphogenesis and for synthetic examples.
Copyright © 2021 Kahl and Kschischo.

Entities:  

Keywords:  complex systems; error localization; fault detection; input reconstruction; open systems

Year:  2021        PMID: 33505318      PMCID: PMC7830364          DOI: 10.3389/fphys.2020.612590

Source DB:  PubMed          Journal:  Front Physiol        ISSN: 1664-042X            Impact factor:   4.566


  11 in total

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Authors:  Areti Tsigkinopoulou; Syed Murtuza Baker; Rainer Breitling
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2.  Discovering governing equations from data by sparse identification of nonlinear dynamical systems.

Authors:  Steven L Brunton; Joshua L Proctor; J Nathan Kutz
Journal:  Proc Natl Acad Sci U S A       Date:  2016-03-28       Impact factor: 11.205

3.  SEEDS: data driven inference of structural model errors and unknown inputs for dynamic systems biology.

Authors:  Tobias Newmiwaka; Benjamin Engelhardt; Philipp Wendland; Dominik Kahl; Holger Fröhlich; Maik Kschischo
Journal:  Bioinformatics       Date:  2021-06-09       Impact factor: 6.937

4.  Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling.

Authors:  Xinhao Ouyang; Xi Huang; Xiao Jin; Zheng Chen; Panyu Yang; Hao Ge; Shigui Li; Xing Wang Deng
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-21       Impact factor: 11.205

Review 5.  A Transparent window into biology: A primer on Caenorhabditis elegans.

Authors:  Ann K Corsi; Bruce Wightman; Martin Chalfie
Journal:  WormBook       Date:  2015-06-18

6.  Structural properties of the Caenorhabditis elegans neuronal network.

Authors:  Lav R Varshney; Beth L Chen; Eric Paniagua; David H Hall; Dmitri B Chklovskii
Journal:  PLoS Comput Biol       Date:  2011-02-03       Impact factor: 4.475

7.  Learning (from) the errors of a systems biology model.

Authors:  Benjamin Engelhardt; Holger Frőhlich; Maik Kschischo
Journal:  Sci Rep       Date:  2016-02-11       Impact factor: 4.379

8.  Network control principles predict neuron function in the Caenorhabditis elegans connectome.

Authors:  Gang Yan; Petra E Vértes; Emma K Towlson; Yee Lian Chew; Denise S Walker; William R Schafer; Albert-László Barabási
Journal:  Nature       Date:  2017-10-18       Impact factor: 49.962

9.  Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models.

Authors:  Alejandro F Villaverde; Nikolaos Tsiantis; Julio R Banga
Journal:  J R Soc Interface       Date:  2019-07-03       Impact factor: 4.118

10.  Dimensionality and dynamics in the behavior of C. elegans.

Authors:  Greg J Stephens; Bethany Johnson-Kerner; William Bialek; William S Ryu
Journal:  PLoS Comput Biol       Date:  2008-04-25       Impact factor: 4.475

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