Fitting very large sparse Gaussian graphical models
In this paper we consider some methods for the maximum likelihood estimation of sparse Gaussian graphical (covariance selection) models when the number of variables is very large (tens of thousands or more). We present a procedure for determining the pattern of zeros in the model and we discuss the use of limited memory quasi-Newton algorithms and truncated Newton algorithms to fit the model by maximum likelihood. We present efficient ways of computing the gradients and likelihood function values for such models suitable for a desktop computer. For the truncated Newton method we also present an efficient way of computing the action of the Hessian matrix on an arbitrary vector which does not require the computation and storage of the Hessian matrix. The methods are illustrated and compared on simulated data and applied to a real microarray data set.
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.
As the access to this document is restricted, you may want to look for a different version under "Related research" (further below) or search for a different version of it.
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.:
- Fan J. & Li R., 2001. "Variable Selection via Nonconcave Penalized Likelihood and its Oracle Properties," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1348-1360, December.
- Søren Højsgaard & Steffen L. Lauritzen, 2008. "Graphical Gaussian models with edge and vertex symmetries," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(5), pages 1005-1027.
- Smyth Gordon K, 2004. "Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-28, February.
- Jiahua Chen & Zehua Chen, 2008. "Extended Bayesian information criteria for model selection with large model spaces," Biometrika, Biometrika Trust, vol. 95(3), pages 759-771.
When requesting a correction, please mention this item's handle: RePEc:eee:csdana:v:56:y:2012:i:9:p:2626-2636. 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: (Shamier, Wendy)
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.