17,409 research outputs found
Block-diagonal covariance selection for high-dimensional Gaussian graphical models
Gaussian graphical models are widely utilized to infer and visualize networks
of dependencies between continuous variables. However, inferring the graph is
difficult when the sample size is small compared to the number of variables. To
reduce the number of parameters to estimate in the model, we propose a
non-asymptotic model selection procedure supported by strong theoretical
guarantees based on an oracle inequality and a minimax lower bound. The
covariance matrix of the model is approximated by a block-diagonal matrix. The
structure of this matrix is detected by thresholding the sample covariance
matrix, where the threshold is selected using the slope heuristic. Based on the
block-diagonal structure of the covariance matrix, the estimation problem is
divided into several independent problems: subsequently, the network of
dependencies between variables is inferred using the graphical lasso algorithm
in each block. The performance of the procedure is illustrated on simulated
data. An application to a real gene expression dataset with a limited sample
size is also presented: the dimension reduction allows attention to be
objectively focused on interactions among smaller subsets of genes, leading to
a more parsimonious and interpretable modular network.Comment: Accepted in JAS
Incomplete graphical model inference via latent tree aggregation
Graphical network inference is used in many fields such as genomics or
ecology to infer the conditional independence structure between variables, from
measurements of gene expression or species abundances for instance. In many
practical cases, not all variables involved in the network have been observed,
and the samples are actually drawn from a distribution where some variables
have been marginalized out. This challenges the sparsity assumption commonly
made in graphical model inference, since marginalization yields locally dense
structures, even when the original network is sparse. We present a procedure
for inferring Gaussian graphical models when some variables are unobserved,
that accounts both for the influence of missing variables and the low density
of the original network. Our model is based on the aggregation of spanning
trees, and the estimation procedure on the Expectation-Maximization algorithm.
We treat the graph structure and the unobserved nodes as missing variables and
compute posterior probabilities of edge appearance. To provide a complete
methodology, we also propose several model selection criteria to estimate the
number of missing nodes. A simulation study and an illustration flow cytometry
data reveal that our method has favorable edge detection properties compared to
existing graph inference techniques. The methods are implemented in an R
package
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