IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1010985.html
   My bibliography  Save this article

Global nonlinear approach for mapping parameters of neural mass models

Author

Listed:
  • Dominic M Dunstan
  • Mark P Richardson
  • Eugenio Abela
  • Ozgur E Akman
  • Marc Goodfellow

Abstract

Neural mass models (NMMs) are important for helping us interpret observations of brain dynamics. They provide a means to understand data in terms of mechanisms such as synaptic interactions between excitatory and inhibitory neuronal populations. To interpret data using NMMs we need to quantitatively compare the output of NMMs with data, and thereby find parameter values for which the model can produce the observed dynamics. Mapping dynamics to NMM parameter values in this way has the potential to improve our understanding of the brain in health and disease.Though abstract, NMMs still comprise of many parameters that are difficult to constrain a priori. This makes it challenging to explore the dynamics of NMMs and elucidate regions of parameter space in which their dynamics best approximate data. Existing approaches to overcome this challenge use a combination of linearising models, constraining the values they can take and exploring restricted subspaces by fixing the values of many parameters a priori. As such, we have little knowledge of the extent to which different regions of parameter space of NMMs can yield dynamics that approximate data, how nonlinearities in models can affect parameter mapping or how best to quantify similarities between model output and data. These issues need to be addressed in order to fully understand the potential and limitations of NMMs, and to aid the development of new models of brain dynamics in the future.To begin to overcome these issues, we present a global nonlinear approach to recovering parameters of NMMs from data. We use global optimisation to explore all parameters of nonlinear NMMs simultaneously, in a minimally constrained way. We do this using multi-objective optimisation (multi-objective evolutionary algorithm, MOEA) so that multiple data features can be quantified. In particular, we use the weighted horizontal visibility graph (wHVG), which is a flexible framework for quantifying different aspects of time series, by converting them into networks.We study EEG alpha activity recorded during the eyes closed resting state from 20 healthy individuals and demonstrate that the MOEA performs favourably compared to single objective approaches. The addition of the wHVG objective allows us to better constrain the model output, which leads to the recovered parameter values being restricted to smaller regions of parameter space, thus improving the practical identifiability of the model. We then use the MOEA to study differences in the alpha rhythm observed in EEG recorded from 20 people with epilepsy. We find that a small number of parameters can explain this difference and that, counterintuitively, the mean excitatory synaptic gain parameter is reduced in people with epilepsy compared to control. In addition, we propose that the MOEA could be used to mine for the presence of pathological rhythms, and demonstrate the application of this to epileptiform spike-wave discharges.Author summary: EEG is a useful tool to study large scale brain activity. Mathematical models have been developed to help improve the understanding of the generation of signals recorded from the EEG during different brain states. The dynamics of these models are dependent on their inputs (or parameters) and hence it is important to explore the parameter combinations that result in model dynamics that approximate data. This allows us to better understand how the data were generated. However, due to the relative complexity of these models, finding the parameter combinations that explain data can be a cumbersome task and hence many studies make simplifications about how model and data are compared. In this study, we introduce methods that do not require these simplifying assumptions. Using these methods we demonstrate that different choices in the way we compare models and data can lead to differences in what we infer about the underlying mechanisms. However, we find that combining different choices into the same algorithm allows us to better approximate features of the data and better constrain model parameters. We apply our method to try to understand differences observed in the resting EEG between patients with epilepsy and controls. We find that the model explains these differences predominately by a reduced excitatory synaptic gain in patients with epilepsy. We also demonstrate the potential of this method to “mine” for different kinds of dynamics in high dimensional models.

Suggested Citation

  • Dominic M Dunstan & Mark P Richardson & Eugenio Abela & Ozgur E Akman & Marc Goodfellow, 2023. "Global nonlinear approach for mapping parameters of neural mass models," PLOS Computational Biology, Public Library of Science, vol. 19(3), pages 1-28, March.
  • Handle: RePEc:plo:pcbi00:1010985
    DOI: 10.1371/journal.pcbi.1010985
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010985
    Download Restriction: no

    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010985&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pcbi.1010985?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Gonçalves, Bruna Amin & Carpi, Laura & Rosso, Osvaldo A. & Ravetti, Martín G., 2016. "Time series characterization via horizontal visibility graph and Information Theory," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 464(C), pages 93-102.
    2. repec:plo:pcbi00:1000092 is not listed on IDEAS
    3. Ryan N Gutenkunst & Joshua J Waterfall & Fergal P Casey & Kevin S Brown & Christopher R Myers & James P Sethna, 2007. "Universally Sloppy Parameter Sensitivities in Systems Biology Models," PLOS Computational Biology, Public Library of Science, vol. 3(10), pages 1-8, October.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Samuel Bandara & Johannes P Schlöder & Roland Eils & Hans Georg Bock & Tobias Meyer, 2009. "Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model," PLOS Computational Biology, Public Library of Science, vol. 5(11), pages 1-12, November.
    2. repec:plo:pcbi00:1007279 is not listed on IDEAS
    3. Adel Dayarian & Madalena Chaves & Eduardo D Sontag & Anirvan M Sengupta, 2009. "Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks," PLOS Computational Biology, Public Library of Science, vol. 5(1), pages 1-12, January.
    4. repec:plo:pgen00:1006132 is not listed on IDEAS
    5. Chen, Yu & Yu, Hui & Liu, Chengjie & Xie, Jin & Han, Jun & Dai, Houde, 2024. "Synergistic fusion of physical modeling and data-driven approaches for parameter inference to enzymatic biodiesel production system," Applied Energy, Elsevier, vol. 373(C).
    6. repec:plo:pone00:0024246 is not listed on IDEAS
    7. Amrita X Sarkar & Eric A Sobie, 2010. "Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells," PLOS Computational Biology, Public Library of Science, vol. 6(9), pages 1-11, September.
    8. Hongwei Shao & Tao Peng & Zhiwei Ji & Jing Su & Xiaobo Zhou, 2013. "Systematically Studying Kinase Inhibitor Induced Signaling Network Signatures by Integrating Both Therapeutic and Side Effects," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-16, December.
    9. Spichak, David & Kupetsky, Audrey & Aragoneses, Andrés, 2021. "Characterizing complexity of non-invertible chaotic maps in the Shannon–Fisher information plane with ordinal patterns," Chaos, Solitons & Fractals, Elsevier, vol. 142(C).
    10. Alireza Yazdani & Lu Lu & Maziar Raissi & George Em Karniadakis, 2020. "Systems biology informed deep learning for inferring parameters and hidden dynamics," PLOS Computational Biology, Public Library of Science, vol. 16(11), pages 1-19, November.
    11. Fridtjof Brauns & Leila Iñigo de la Cruz & Werner K.-G. Daalman & Ilse Bruin & Jacob Halatek & Liedewij Laan & Erwin Frey, 2023. "Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    12. Eberhard O Voit & Harald A Martens & Stig W Omholt, 2015. "150 Years of the Mass Action Law," PLOS Computational Biology, Public Library of Science, vol. 11(1), pages 1-7, January.
    13. Céline Christiansen-Jucht & Kamil Erguler & Chee Yan Shek & María-Gloria Basáñez & Paul E. Parham, 2015. "Modelling Anopheles gambiae s.s. Population Dynamics with Temperature- and Age-Dependent Survival," IJERPH, MDPI, vol. 12(6), pages 1-31, May.
    14. Gabriele Lillacci & Mustafa Khammash, 2010. "Parameter Estimation and Model Selection in Computational Biology," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-17, March.
    15. Andrew White & Malachi Tolman & Howard D Thames & Hubert Rodney Withers & Kathy A Mason & Mark K Transtrum, 2016. "The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems," PLOS Computational Biology, Public Library of Science, vol. 12(12), pages 1-26, December.
    16. Diego Fernández Slezak & Cecilia Suárez & Guillermo A Cecchi & Guillermo Marshall & Gustavo Stolovitzky, 2010. "When the Optimal Is Not the Best: Parameter Estimation in Complex Biological Models," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-10, October.
    17. Elba Raimúndez & Simone Keller & Gwen Zwingenberger & Karolin Ebert & Sabine Hug & Fabian J Theis & Dieter Maier & Birgit Luber & Jan Hasenauer, 2020. "Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines," PLOS Computational Biology, Public Library of Science, vol. 16(3), pages 1-21, March.
    18. Joseph D Taylor & Samuel Winnall & Alain Nogaret, 2020. "Estimation of neuron parameters from imperfect observations," PLOS Computational Biology, Public Library of Science, vol. 16(7), pages 1-22, July.
    19. Xinxian Shao & Andrew Mugler & Justin Kim & Ha Jun Jeong & Bruce R Levin & Ilya Nemenman, 2017. "Growth of bacteria in 3-d colonies," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-19, July.
    20. repec:plo:pcbi00:1003705 is not listed on IDEAS
    21. Maksat Ashyraliyev & Ken Siggens & Hilde Janssens & Joke Blom & Michael Akam & Johannes Jaeger, 2009. "Gene Circuit Analysis of the Terminal Gap Gene huckebein," PLOS Computational Biology, Public Library of Science, vol. 5(10), pages 1-16, October.
    22. Agus Hartoyo & Peter J Cadusch & David T J Liley & Damien G Hicks, 2019. "Parameter estimation and identifiability in a neural population model for electro-cortical activity," PLOS Computational Biology, Public Library of Science, vol. 15(5), pages 1-27, May.
    23. Christian A Tiemann & Joep Vanlier & Maaike H Oosterveer & Albert K Groen & Peter A J Hilbers & Natal A W van Riel, 2013. "Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions," PLOS Computational Biology, Public Library of Science, vol. 9(8), pages 1-15, August.
    24. Li, Sange & Shang, Pengjian, 2021. "Analysis of nonlinear time series using discrete generalized past entropy based on amplitude difference distribution of horizontal visibility graph," Chaos, Solitons & Fractals, Elsevier, vol. 144(C).

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1010985. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.