Sparse Inverse Covariance Estimation for Chordal Structures

In this paper, we consider the Graphical Lasso (GL), a popular optimization problem for learning the sparse representations of high-dimensional datasets, which is well-known to be computationally expensive for large-scale problems. Recently, we have shown that the sparsity pattern of the optimal solution of GL is equivalent to the one obtained from simply thresholding the sample covariance matrix, for sparse graphs under different conditions. We have also derived a closed-form solution that is optimal when the thresholded sample covariance matrix has an acyclic structure. As a major generalization of the previous result, in this paper we derive a closed-form solution for the GL for graphs with chordal structures. We show that the GL and thresholding equivalence conditions can significantly be simplified and are expected to hold for high-dimensional problems if the thresholded sample covariance matrix has a chordal structure. We then show that the GL and thresholding equivalence is enough to reduce the GL to a maximum determinant matrix completion problem and drive a recursive closed-form solution for the GL when the thresholded sample covariance matrix has a chordal structure. For large-scale problems with up to 450 million variables, the proposed method can solve the GL problem in less than 2 minutes, while the state-of-the-art methods converge in more than 2 hours

Graphical continuous Lyapunov models

The linear Lyapunov equation of a covariance matrix parametrizes the equilibrium covariance matrix of a stochastic process. This parametrization can be interpreted as a new graphical model class, and we show how the model class behaves under marginalization and introduce a method for structure learning via $\ell_1$-penalized loss minimization. Our proposed method is demonstrated to outperform alternative structure learning algorithms in a simulation study, and we illustrate its application for protein phosphorylation network reconstruction.Comment: 10 pages, 5 figure

iPACOSE: an iterative algorithm for the estimation of gene regulation networks

In the context of Gaussian Graphical Models (GGMs) with high- dimensional small sample data, we present a simple procedure to esti- mate partial correlations under the constraint that some of them are strictly zero. This method can also be extended to covariance selection. If the goal is to estimate a GGM, our new procedure can be applied to re-estimate the partial correlations after a first graph has been esti- mated in the hope to improve the estimation of non-zero coefficients. In a simulation study, we compare our new covariance selection procedure to existing methods and show that the re-estimated partial correlation coefficients may be closer to the real values in important cases