We propose an efficient way to sample from a class of structured multivariate Gaussian distributions which routinely arise as conditional posteriors of model parameters that are assigned a conditionally Gaussian prior. The proposed algorithm only requires matrix operations in the form of matrix multiplications and linear system solutions. We exhibit that the computational complexity of the proposed algorithm grows linearly with the dimension unlike existing algorithms relying on Cholesky factorizations with cubic orders of complexity. The algorithm should be broadly applicable in settings where Gaussian scale mixture priors are used on high dimensional model parameters. We provide an illustration through posterior sampling in a high dimensional regression setting with a horseshoe prior on the vector of regression coefficients.
In this paper, we propose an adaptive algorithm that iteratively updates both the weights and component parameters of a mixture importance sampling density so as to optimise the importance sampling performances, as measured by an entropy criterion. The method is shown to be applicable to a wide class of importance sampling densities, which includes in particular mixtures of multivariate Student t distributions. The performances of the proposed scheme are studied on both artificial and real examples, highlighting in particular the benefit of a novel Rao-Blackwellisation device which can be easily incorporated in the updating scheme.
We study a mean-field spike and slab variational Bayes (VB) approximation to Bayesian model selection priors in sparse high-dimensional linear regression. Under compatibility conditions on the design matrix, oracle inequalities are derived for the mean-field VB approximation, implying that it converges to the sparse truth at the optimal rate and gives optimal prediction of the response vector. The empirical performance of our algorithm is studied, showing that it works comparably well as other state-of-the-art Bayesian variable selection methods. We also numerically demonstrate that the widely used coordinate-ascent variational inference (CAVI) algorithm can be highly sensitive to the parameter updating order, leading to potentially poor performance. To mitigate this, we propose a novel prioritized updating scheme that uses a data-driven updating order and performs better in simulations. The variational algorithm is implemented in the R package sparsevb.
Efficient sampling from a high-dimensional Gaussian distribution is an old but high-stake issue. Vanilla Cholesky samplers imply a computational cost and memory requirements which can rapidly become prohibitive in high dimension. To tackle these issues, multiple methods have been proposed from different communities ranging from iterative numerical linear algebra to Markov chain Monte Carlo (MCMC) approaches. Surprisingly, no complete review and comparison of these methods have been conducted. This paper aims at reviewing all these approaches by pointing out their differences, close relations, benefits and limitations. In addition to this state of the art, this paper proposes a unifying Gaussian simulation framework by deriving a stochastic counterpart of the celebrated proximal point algorithm in optimization. This framework offers a novel and unifying revisit of most of the existing MCMC approaches while extending them. Guidelines to choose the appropriate Gaussian simulation method for a given sampling problem in high dimension are proposed and illustrated with numerical examples.
Riemann manifold Hamiltonian Monte Carlo (RMHMC) has the potential to produce high-quality Markov chain Monte Carlo-output even for very challenging target distributions. To this end, a symmetric positive definite scaling matrix for RMHMC, which derives, via a modified Cholesky factorization, from the potentially indefinite negative Hessian of the target log-density is proposed. The methodology is able to exploit the sparsity of the Hessian, stemming from conditional independence modeling assumptions, and thus admit fast implementation of RMHMC even for high-dimensional target distributions. Moreover, the methodology can exploit log-concave conditional target densities, often encountered in Bayesian hierarchical models, for faster sampling and more straight forward tuning. The proposed methodology is compared to alternatives for some challenging targets, and is illustrated by applying a state space model to real data.
Many processes in chemistry and physics take place on timescales that cannot be explored using standard molecular dynamics simulations. This renders the use of enhanced sampling mandatory. Here we introduce an enhanced sampling method that is based on constructing a model probability density from which a bias potential is derived. The model relies on the fact that in a physical system most of the configurations visited can be grouped into isolated metastable islands. To each island we associate a distribution that is fitted to a Gaussian mixture. The different distributions are linearly combined together with coefficients that are computed self consistently. Remarkably, from this biased dynamics, rates of transition between different metastable states can be straightforwardly computed.