IDEAS home Printed from https://ideas.repec.org/a/spr/stmapp/v31y2022i2d10.1007_s10260-021-00600-7.html
   My bibliography  Save this article

Discussion to: Bayesian graphical models for modern biological applications by Y. Ni, V. Baladandayuthapani, M. Vannucci and F.C. Stingo

Author

Listed:
  • Michael Schweinberger

    (University of Missouri)

Abstract

It is a pleasure to congratulate Ni et al. (Stat Methods Appl 490:1–32, 2021) on the recent advances in Bayesian graphical models reviewed in Ni et al. (Stat Methods Appl 490:1–32, 2021). The authors have given considerable thought to the construction and estimation of Bayesian graphical models that capture salient features of biological networks. My discussion focuses on computational challenges and opportunities along with priors, pointing out limitations of the Markov random field priors reviewed in Ni et al. (Stat Methods Appl 490:1–32, 2021) and exploring possible generalizations that capture additional features of conditional independence graphs, such as hub structure and clustering. I conclude with a short discussion of the intersection of graphical models and random graph models.

Suggested Citation

  • Michael Schweinberger, 2022. "Discussion to: Bayesian graphical models for modern biological applications by Y. Ni, V. Baladandayuthapani, M. Vannucci and F.C. Stingo," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 31(2), pages 253-260, June.
    • Handle: RePEc:spr:stmapp:v:31:y:2022:i:2:d:10.1007_s10260-021-00600-7
    DOI: 10.1007/s10260-021-00600-7
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s10260-021-00600-7
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1007/s10260-021-00600-7?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Sundberg,Rolf, 2019. "Statistical Modelling by Exponential Families," Cambridge Books, Cambridge University Press, number 9781108701112.
    2. Sundberg,Rolf, 2019. "Statistical Modelling by Exponential Families," Cambridge Books, Cambridge University Press, number 9781108476591.
    3. Christine Peterson & Francesco C. Stingo & Marina Vannucci, 2015. "Bayesian Inference of Multiple Gaussian Graphical Models," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(509), pages 159-174, March.
    4. Steffen Lauritzen & Alessandro Rinaldo & Kayvan Sadeghi, 2018. "Random networks, graphical models and exchangeability," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 80(3), pages 481-508, June.
    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. Park, Jaewoo & Jin, Ick Hoon & Schweinberger, Michael, 2022. "Bayesian model selection for high-dimensional Ising models, with applications to educational data," Computational Statistics & Data Analysis, Elsevier, vol. 165(C).
    2. Bodnar, Olha & Bodnar, Taras, 2024. "Gibbs sampler approach for objective Bayesian inference in elliptical multivariate meta-analysis random effects model," Computational Statistics & Data Analysis, Elsevier, vol. 197(C).
    3. Whiteley, Nick, 2021. "Dimension-free Wasserstein contraction of nonlinear filters," Stochastic Processes and their Applications, Elsevier, vol. 135(C), pages 31-50.
    4. Vassilios Bazinas & Bent Nielsen, 2022. "Causal Transmission in Reduced-Form Models," Econometrics, MDPI, vol. 10(2), pages 1-25, March.
    5. Frank Kwasniok, 2021. "Semiparametric maximum likelihood probability density estimation," PLOS ONE, Public Library of Science, vol. 16(11), pages 1-33, November.
    6. Aris Spanos, 2022. "Frequentist Model-based Statistical Induction and the Replication Crisis," Journal of Quantitative Economics, Springer;The Indian Econometric Society (TIES), vol. 20(1), pages 133-159, September.
    7. Paci, Lucia & Consonni, Guido, 2020. "Structural learning of contemporaneous dependencies in graphical VAR models," Computational Statistics & Data Analysis, Elsevier, vol. 144(C).
    8. Kayvan Sadeghi & Alessandro Rinaldo, 2020. "Hierarchical models for independence structures of networks," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 74(3), pages 439-457, August.
    9. Mehran Aflakparast & Mathisca de Gunst & Wessel van Wieringen, 2020. "Analysis of Twitter data with the Bayesian fused graphical lasso," PLOS ONE, Public Library of Science, vol. 15(7), pages 1-28, July.
    10. Wessel N. van Wieringen & Carel F. W. Peeters & Renee X. de Menezes & Mark A. van de Wiel, 2018. "Testing for pathway (in)activation by using Gaussian graphical models," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 67(5), pages 1419-1436, November.
    11. Anindya Bhadra, 2022. "Discussion to: Bayesian graphical models for modern biological applications by Y. Ni, V. Baladandayuthapani, M. Vannucci and F.C. Stingo," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 31(2), pages 235-239, June.
    12. van Wieringen, Wessel N. & Stam, Koen A. & Peeters, Carel F.W. & van de Wiel, Mark A., 2020. "Updating of the Gaussian graphical model through targeted penalized estimation," Journal of Multivariate Analysis, Elsevier, vol. 178(C).
    13. Yang Ni & Peter Müller & Yitan Zhu & Yuan Ji, 2018. "Heterogeneous reciprocal graphical models," Biometrics, The International Biometric Society, vol. 74(2), pages 606-615, June.
    14. Federico Castelletti & Guido Consonni, 2021. "Bayesian inference of causal effects from observational data in Gaussian graphical models," Biometrics, The International Biometric Society, vol. 77(1), pages 136-149, March.
    15. Thierry Chekouo & Francesco C. Stingo & James D. Doecke & Kim-Anh Do, 2017. "A Bayesian integrative approach for multi-platform genomic data: A kidney cancer case study," Biometrics, The International Biometric Society, vol. 73(2), pages 615-624, June.
    16. Lin Zhang & Andrew DiLernia & Karina Quevedo & Jazmin Camchong & Kelvin Lim & Wei Pan, 2021. "A random covariance model for bi‐level graphical modeling with application to resting‐state fMRI data," Biometrics, The International Biometric Society, vol. 77(4), pages 1385-1396, December.
    17. Christine B. Peterson & Nathan Osborne & Francesco C. Stingo & Pierrick Bourgeat & James D. Doecke & Marina Vannucci, 2020. "Bayesian modeling of multiple structural connectivity networks during the progression of Alzheimer's disease," Biometrics, The International Biometric Society, vol. 76(4), pages 1120-1132, December.
    18. Castelletti, Federico & Peluso, Stefano, 2021. "Equivalence class selection of categorical graphical models," Computational Statistics & Data Analysis, Elsevier, vol. 164(C).
    19. Yang Ni & Francesco C. Stingo & Veerabhadran Baladandayuthapani, 2015. "Bayesian nonlinear model selection for gene regulatory networks," Biometrics, The International Biometric Society, vol. 71(3), pages 585-595, September.
    20. Zhixiang Lin & Tao Wang & Can Yang & Hongyu Zhao, 2017. "On joint estimation of Gaussian graphical models for spatial and temporal data," Biometrics, The International Biometric Society, vol. 73(3), pages 769-779, September.

    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:spr:stmapp:v:31:y:2022:i:2:d:10.1007_s10260-021-00600-7. 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: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    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.