No Arabic abstract
We propose a novel approach to estimating the precision matrix of multivariate Gaussian data that relies on decomposing them into a low-rank and a diagonal component. Such decompositions are very popular for modeling large covariance matrices as they admit a latent factor based representation that allows easy inference. The same is not true for precision matrices, due to the lack of computationally convenient representation, which restricts the use to low to moderate dimensional problems. We address this remarkable gap in the literature by introducing a novel latent variable representation for such decomposition for precision matrices as well. The construction leads to an efficient Gibbs sampler that scales very well to high-dimensional problems far beyond the limits of the current state-of-the-art. The ability to efficiently explore the full posterior space allows the model uncertainty to be easily assessed. The decomposition also crucially allows us to adapt sparsity inducing priors to shrink the insignificant entries of the precision matrix toward zero, making the approach adaptable to high-dimensional small-sample-size sparse settings. Exact zeros in the matrix encoding the underlying conditional independence graph are then determined via a novel posterior false discovery rate control procedure. We evaluate the methods empirical performance through synthetic experiments and illustrate its practical utility in data sets from two different application domains.
Most of previous works and applications of Bayesian factor model have assumed the normal likelihood regardless of its validity. We propose a Bayesian factor model for heavy-tailed high-dimensional data based on multivariate Student-$t$ likelihood to obtain better covariance estimation. We use multiplicative gamma process shrinkage prior and factor number adaptation scheme proposed in Bhattacharya & Dunson [Biometrika (2011) 291-306]. Since a naive Gibbs sampler for the proposed model suffers from slow mixing, we propose a Markov Chain Monte Carlo algorithm where fast mixing of Hamiltonian Monte Carlo is exploited for some parameters in proposed model. Simulation results illustrate the gain in performance of covariance estimation for heavy-tailed high-dimensional data. We also provide a theoretical result that the posterior of the proposed model is weakly consistent under reasonable conditions. We conclude the paper with the application of proposed factor model on breast cancer metastasis prediction given DNA signature data of cancer cell.
This paper investigates the high-dimensional linear regression with highly correlated covariates. In this setup, the traditional sparsity assumption on the regression coefficients often fails to hold, and consequently many model selection procedures do not work. To address this challenge, we model the variations of covariates by a factor structure. Specifically, strong correlations among covariates are explained by common factors and the remaining variations are interpreted as idiosyncratic components of each covariate. This leads to a factor-adjusted regression model with both common factors and idiosyncratic components as covariates. We generalize the traditional sparsity assumption accordingly and assume that all common factors but only a small number of idiosyncratic components contribute to the response. A Bayesian procedure with a spike-and-slab prior is then proposed for parameter estimation and model selection. Simulation studies show that our Bayesian method outperforms its lasso analogue, manifests insensitivity to the overestimates of the number of common factors, pays a negligible price in the no correlation case, and scales up well with increasing sample size, dimensionality and sparsity. Numerical results on a real dataset of U.S. bond risk premia and macroeconomic indicators lend strong support to our methodology.
Graphical models express conditional independence relationships among variables. Although methods for vector-valued data are well established, functional data graphical models remain underdeveloped. We introduce a notion of conditional independence between random functions, and construct a framework for Bayesian inference of undirected, decomposable graphs in the multivariate functional data context. This framework is based on extending Markov distributions and hyper Markov laws from random variables to random processes, providing a principled alternative to naive application of multivariate methods to discretized functional data. Markov properties facilitate the composition of likelihoods and priors according to the decomposition of a graph. Our focus is on Gaussian process graphical models using orthogonal basis expansions. We propose a hyper-inverse-Wishart-process prior for the covariance kernels of the infinite coefficient sequences of the basis expansion, establish existence, uniqueness, strong hyper Markov property, and conjugacy. Stochastic search Markov chain Monte Carlo algorithms are developed for posterior inference, assessed through simulations, and applied to a study of brain activity and alcoholism.
Graphical models are ubiquitous tools to describe the interdependence between variables measured simultaneously such as large-scale gene or protein expression data. Gaussian graphical models (GGMs) are well-established tools for probabilistic exploration of dependence structures using precision matrices and they are generated under a multivariate normal joint distribution. However, they suffer from several shortcomings since they are based on Gaussian distribution assumptions. In this article, we propose a Bayesian quantile based approach for sparse estimation of graphs. We demonstrate that the resulting graph estimation is robust to outliers and applicable under general distributional assumptions. Furthermore, we develop efficient variational Bayes approximations to scale the methods for large data sets. Our methods are applied to a novel cancer proteomics data dataset wherein multiple proteomic antibodies are simultaneously assessed on tumor samples using reverse-phase protein arrays (RPPA) technology.
Its conceptual appeal and effectiveness has made latent factor modeling an indispensable tool for multivariate analysis. Despite its popularity across many fields, there are outstanding methodological challenges that have hampered practical deployments. One major challenge is the selection of the number of factors, which is exacerbated for dynamic factor models, where factors can disappear, emerge, and/or reoccur over time. Existing tools that assume a fixed number of factors may provide a misguided representation of the data mechanism, especially when the number of factors is crudely misspecified. Another challenge is the interpretability of the factor structure, which is often regarded as an unattainable objective due to the lack of identifiability. Motivated by a topical macroeconomic application, we develop a flexible Bayesian method for dynamic factor analysis (DFA) that can simultaneously accommodate a time-varying number of factors and enhance interpretability without strict identifiability constraints. To this end, we turn to dynamic sparsity by employing Dynamic Spike-and-Slab (DSS) priors within DFA. Scalable Bayesian EM estimation is proposed for fast posterior mode identification via rotations to sparsity, enabling Bayesian data analysis at scales that would have been previously time-consuming. We study a large-scale balanced panel of macroeconomic variables covering multiple facets of the US economy, with a focus on the Great Recession, to highlight the efficacy and usefulness of our proposed method.