1,298 research outputs found

    Gibbs Sampling using Anti-correlation Gaussian Data Augmentation, with Applications to L1-ball-type Models

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    L1-ball-type priors are a recent generalization of the spike-and-slab priors. By transforming a continuous precursor distribution to the L1-ball boundary, it induces exact zeros with positive prior and posterior probabilities. With great flexibility in choosing the precursor and threshold distributions, we can easily specify models under structured sparsity, such as those with dependent probability for zeros and smoothness among the non-zeros. Motivated to significantly accelerate the posterior computation, we propose a new data augmentation that leads to a fast block Gibbs sampling algorithm. The latent variable, named ``anti-correlation Gaussian'', cancels out the quadratic exponent term in the latent Gaussian distribution, making the parameters of interest conditionally independent so that they can be updated in a block. Compared to existing algorithms such as the No-U-Turn sampler, the new blocked Gibbs sampler has a very low computing cost per iteration and shows rapid mixing of Markov chains. We establish the geometric ergodicity guarantee of the algorithm in linear models. Further, we show useful extensions of our algorithm for posterior estimation of general latent Gaussian models, such as those involving multivariate truncated Gaussian or latent Gaussian process. Keywords: Blocked Gibbs sampler; Fast Mixing of Markov Chains; Latent Gaussian Models; Soft-thresholding

    Sparse Linear Identifiable Multivariate Modeling

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    In this paper we consider sparse and identifiable linear latent variable (factor) and linear Bayesian network models for parsimonious analysis of multivariate data. We propose a computationally efficient method for joint parameter and model inference, and model comparison. It consists of a fully Bayesian hierarchy for sparse models using slab and spike priors (two-component delta-function and continuous mixtures), non-Gaussian latent factors and a stochastic search over the ordering of the variables. The framework, which we call SLIM (Sparse Linear Identifiable Multivariate modeling), is validated and bench-marked on artificial and real biological data sets. SLIM is closest in spirit to LiNGAM (Shimizu et al., 2006), but differs substantially in inference, Bayesian network structure learning and model comparison. Experimentally, SLIM performs equally well or better than LiNGAM with comparable computational complexity. We attribute this mainly to the stochastic search strategy used, and to parsimony (sparsity and identifiability), which is an explicit part of the model. We propose two extensions to the basic i.i.d. linear framework: non-linear dependence on observed variables, called SNIM (Sparse Non-linear Identifiable Multivariate modeling) and allowing for correlations between latent variables, called CSLIM (Correlated SLIM), for the temporal and/or spatial data. The source code and scripts are available from http://cogsys.imm.dtu.dk/slim/.Comment: 45 pages, 17 figure
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