IDEAS home Printed from
MyIDEAS: Log in (now much improved!) to save this paper

Bayesian Covariance Matrix Estimation using a Mixture of Decomposable Graphical Models

Listed author(s):
  • Helen Armstrong


    (School of Mathematics, University of New South Wales)

  • Christopher K. Carter


    (School of Economics, University of New South Wales)

  • Kevin K. F. Wong

    (Graduate University for Advanced Studies, Tokyo, Japan)

  • Robert Kohn


    (School of Economics, University of New South Wales)

Estimating a covariance matrix efficiently and discovering its structure are important statistical problems with applications in many fields. This article takes a Bayesian approach to estimate the covariance matrix of Gaussian data. We use ideas from Gaussian graphical models and model selection to construct a prior for the covariance matrix that is a mixture over all decomposable graphs, where a graph means the configuration of nonzero offdiagonal elements in the inverse of the covariance matrix. Our prior for the covariance matrix is such that the probability of each graph size is specified by the user and graphs of equal size are assigned equal probability. Most previous approaches assume that all graphs are equally probable. We give empirical results that show the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs, both in identifying the correct decomposable graph and in more efficiently estimating the covariance matrix. The advantage is greatest when the number of observations is small relative to the dimension of the covariance matrix. The article also shows empirically that there is minimal change in statistical efficiency in using the mixture over decomposable graphs prior for estimating a general covariance compared to the Bayesian estimator by Wong et al. (2003), even when the graph of the covariance matrix is nondecomposable. However, our approach has some important advantages over that of Wong et al. (2003). Our method requires the number of decomposable graphs for each graph size. We show how to estimate these numbers using simulation and that the simulation results agree with analytic results when such results are known. We also show how to estimate the posterior distribution of the covariance matrix using Markov chain Monte Carlo with the elements of the covariance matrix integrated out and give empirical results that show the sampler is computationally efficient and converges rapidly. Finally, we note that both the prior and the simulation method to evaluate the prior apply generally to any decomposable graphical model.

If you experience problems downloading a file, check if you have the proper application to view it first. In case of further problems read the IDEAS help page. Note that these files are not on the IDEAS site. Please be patient as the files may be large.

File URL:
Download Restriction: no

Paper provided by School of Economics, The University of New South Wales in its series Discussion Papers with number 2007-13.

in new window

Length: 27 pages
Date of creation: Apr 2007
Handle: RePEc:swe:wpaper:2007-13
Contact details of provider: Postal:
Australian School of Business Building, Sydney 2052

Phone: (+61)-2-9385-3380
Fax: +61)-2- 9313- 6337
Web page:

More information through EDIRC

References listed on IDEAS
Please report citation or reference errors to , or , if you are the registered author of the cited work, log in to your RePEc Author Service profile, click on "citations" and make appropriate adjustments.:

in new window

  1. S. P. Brooks & P. Giudici & G. O. Roberts, 2003. "Efficient construction of reversible jump Markov chain Monte Carlo proposal distributions," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 65(1), pages 3-39.
  2. Smith M. & Kohn R., 2002. "Parsimonious Covariance Matrix Estimation for Longitudinal Data," Journal of the American Statistical Association, American Statistical Association, vol. 97, pages 1141-1153, December.
  3. Alberto Roverato, 2002. "Hyper Inverse Wishart Distribution for Non-decomposable Graphs and its Application to Bayesian Inference for Gaussian Graphical Models," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 29(3), pages 391-411.
  4. Frederick Wong, 2003. "Efficient estimation of covariance selection models," Biometrika, Biometrika Trust, vol. 90(4), pages 809-830, December.
  5. Mathias Drton, 2004. "Model selection for Gaussian concentration graphs," Biometrika, Biometrika Trust, vol. 91(3), pages 591-602, September.
Full references (including those not matched with items on IDEAS)

This item is not listed on Wikipedia, on a reading list or among the top items on IDEAS.

When requesting a correction, please mention this item's handle: RePEc:swe:wpaper:2007-13. See general information about how to correct material in RePEc.

For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: (Hongyi Li)

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 references are entirely missing, you can add them using this form.

If the full references list an item that is present in RePEc, but the system did not link 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 profile, as there may be some citations waiting for confirmation.

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

This information is provided to you by IDEAS at the Research Division of the Federal Reserve Bank of St. Louis using RePEc data.