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Gaussian Graphical models (GGM) are widely used to estimate the network structures in many applications ranging from biology to finance. In practice, data is often corrupted by latent confounders which biases inference of the underlying true graphical structure. In this paper, we compare and contrast two strategies for inference in graphical models with latent confounders: Gaussian graphical models with latent variables (LVGGM) and PCA-based removal of confounding (PCA+GGM). While these two approaches have similar goals, they are motivated by different assumptions about confounding. In this paper, we explore the connection between these two approaches and propose a new method, which combines the strengths of these two approaches. We prove the consistency and convergence rate for the PCA-based method and use these results to provide guidance about when to use each method. We demonstrate the effectiveness of our methodology using both simulations and in two real-world applications.
Transfer learning for high-dimensional Gaussian graphical models (GGMs) is studied with the goal of estimating the target GGM by utilizing the data from similar and related auxiliary studies. The similarity between the target graph and each auxiliary
We study parameter identifiability of directed Gaussian graphical models with one latent variable. In the scenario we consider, the latent variable is a confounder that forms a source node of the graph and is a parent to all other nodes, which corres
Though Gaussian graphical models have been widely used in many scientific fields, limited progress has been made to link graph structures to external covariates because of substantial challenges in theory and computation. We propose a Gaussian graphi
Cognitive Diagnosis Models (CDMs) are a special family of discrete latent variable models that are widely used in modern educational, psychological, social and biological sciences. A key component of CDMs is a binary $Q$-matrix characterizing the dep
We propose a Bayesian approximate inference method for learning the dependence structure of a Gaussian graphical model. Using pseudo-likelihood, we derive an analytical expression to approximate the marginal likelihood for an arbitrary graph structur