We develop a method to carry out MAP estimation for a class of Bayesian regression models in which coefficients are assigned with Gaussian-based spike and slab priors. The objective function in the corresponding optimization problem has a Lagrangian form in that regression coefficients are regularized by a mixture of squared $l_2$ and $l_0$ norms. A tight approximation to the $l_0$ norm using majorization-minimization techniques is derived, and a coordinate descent algorithm in conjunction with a soft-thresholding scheme is used in searching for the optimizer of the approximate objective. Simulation studies show that the proposed method can lead to more accurate variable selection than other benchmark methods. Theoretical results show that under regular conditions, sign consistency can be established, even when the Irrepresentable Condition is violated. Results on posterior model consistency and estimation consistency, and an extension to parameter estimation in the generalized linear models are provided.
High-dimensional data sets have become ubiquitous in the past few decades, often with many more covariates than observations. In the frequentist setting, penalized likelihood methods are the most popular approach for variable selection and estimation in high-dimensional data. In the Bayesian framework, spike-and-slab methods are commonly used as probabilistic constructs for high-dimensional modeling. Within the context of linear regression, Rockova and George (2018) introduced the spike-and-slab LASSO (SSL), an approach based on a prior which provides a continuum between the penalized likeliho…
The impracticality of posterior sampling has prevented the widespread adoption of spike-and-slab priors in high-dimensional applications. To alleviate the computational burden, optimization strategies have been proposed that quickly find local posterior modes. Trading off uncertainty quantification for computational speed, these strategies have enabled spike-and-slab deployments at scales that would be previously unfeasible. We build on one recent development in this strand of work: the Spike-and-Slab LASSO procedure of Ročková and George (2018). Instead of optimization, however, we explore mu…
We address the problem of dynamic variable selection in time series regression with unknown residual variances, where the set of active predictors is allowed to evolve over time. To capture time-varying variable selection uncertainty, we introduce new dynamic shrinkage priors for the time series of regression coefficients. These priors are characterized by two main ingredients: smooth parameter evolutions and intermittent zeroes for modeling predictive breaks. More formally, our proposed Dynamic Spike-and-Slab (DSS) priors are constructed as mixtures of two processes: a spike process for the i…
In this paper we study grouped variable selection problems by proposing a specified prior, called the nested spike and slab prior, to model collective behavior of regression coefficients. At the group level, the nested spike and slab prior puts positive mass on the event that the l2-norm of the grouped coefficients is equal to zero. At the individual level, each coefficient is assumed to follow a spike and slab prior. We carry out maximum a posteriori estimation for the model by applying blockwise coordinate descent algorithms to solve an optimization problem involving an approximate objective…
We propose a Bayesian procedure for simultaneous variable and covariance selection using continuous spike-and-slab priors in multivariate linear regression models where q possibly correlated responses are regressed onto p predictors. Rather than relying on a stochastic search through the high-dimensional model space, we develop an ECM algorithm similar to the EMVS procedure of Rockova & George (2014) targeting modal estimates of the matrix of regression coefficients and residual precision matrix. Varying the scale of the continuous spike densities facilitates dynamic posterior exploration and …
Rescaled spike and slab models are a new Bayesian variable selection method for linear regression models. In high dimensional orthogonal settings such models have been shown to possess optimal model selection properties. We review background theory and discuss applications of rescaled spike and slab models to prediction problems involving orthogonal polynomials. We first consider global smoothing and discuss potential weaknesses. Some of these deficiencies are remedied by using local regression. The local regression approach relies on an intimate connection between local weighted regression an…
We introduce the spike-and-slab group lasso (SSGL) for Bayesian estimation and variable selection in linear regression with grouped variables. We further extend the SSGL to sparse generalized additive models (GAMs), thereby introducing the first nonparametric variant of the spike-and-slab lasso methodology. Our model simultaneously performs group selection and estimation, while our fully Bayes treatment of the mixture proportion allows for model complexity control and automatic self-adaptivity to different levels of sparsity. We develop theory to uniquely characterize the global posterior mode…
Sparseness of the regression coefficient vector is often a desirable property, since, among other benefits, sparseness improves interpretability. In practice, many true regression coefficients might be negligibly small, but non-zero, which we refer to as quasi-sparseness. Spike-and-slab priors as introduced in (Chipman et al., 2001) can be tuned to ignore very small regression coefficients, and, as a consequence provide a trade-off between prediction accuracy and interpretability. However, spike-and-slab priors with full support lead to inconsistent Bayes factors, in the sense that the Bayes f…
We study inference and learning based on a sparse coding model with `spike-and-slab' prior. As in standard sparse coding, the model used assumes independent latent sources that linearly combine to generate data points. However, instead of using a standard sparse prior such as a Laplace distribution, we study the application of a more flexible `spike-and-slab' distribution which models the absence or presence of a source's contribution independently of its strength if it contributes. We investigate two approaches to optimize the parameters of spike-and-slab sparse coding: a novel truncated EM a…
We consider the problem of using a factor model we call {\em spike-and-slab sparse coding} (S3C) to learn features for a classification task. The S3C model resembles both the spike-and-slab RBM and sparse coding. Since exact inference in this model is intractable, we derive a structured variational inference procedure and employ a variational EM training algorithm. Prior work on approximate inference for this model has not prioritized the ability to exploit parallel architectures and scale to enormous problem sizes. We present an inference procedure appropriate for use with GPUs which allows u…
We consider the problem of object recognition with a large number of classes. In order to overcome the low amount of labeled examples available in this setting, we introduce a new feature learning and extraction procedure based on a factor model we call spike-and-slab sparse coding (S3C). Prior work on S3C has not prioritized the ability to exploit parallel architectures and scale S3C to the enormous problem sizes needed for object recognition. We present a novel inference procedure for appropriate for use with GPUs which allows us to dramatically increase both the training set size and the am…
The paper revisits the Bayesian group lasso and uses spike and slab priors for group variable selection. In the process, the connection of our model with penalized regression is demonstrated, and the role of posterior median for thresholding is pointed out. We show that the posterior median estimator has the oracle property for group variable selection and estimation under orthogonal designs, while the group lasso has suboptimal asymptotic estimation rate when variable selection consistency is achieved. Next we consider bi-level selection problem and propose the Bayesian sparse group selection…
There are proposals that extend the classical generalized additive models (GAMs) to accommodate high-dimensional data ($p>>n$) using group sparse regularization. However, the sparse regularization may induce excess shrinkage when estimating smooth functions, damaging predictive performance. Moreover, most of these GAMs consider an "all-in-all-out" approach for functional selection, rendering them difficult to answer if nonlinear effects are necessary. While some Bayesian models can address these shortcomings, using Markov chain Monte Carlo algorithms for model fitting creates a new challenge, …
Covariate-Elaborated Robust Partial Information Transfer with Conditional Spike-and-Slab Prior
Department of Statistics and Data Science, Fudan University（复旦大学统计与数据科学系）；Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania（宾夕法尼亚大学生物统计学、流行病学与信息学系）；Department of Statistics and Applied Probability, University of California, Santa Barbara（加州大学圣芭芭拉分校统计学与应用概率系）
The R package spikeSlabGAM implements Bayesian variable selection, model choice, and regularized estimation in (geo-)additive mixed models for Gaussian, binomial, and Poisson responses. Its purpose is to (1) choose an appropriate subset of potential covariates and their interactions, (2) to determine whether linear or more flexible functional forms are required to model the effects of the respective covariates, and (3) to estimate their shapes. Selection and regularization of the model terms is based on a novel spike-and-slab-type prior on coefficient groups associated with parametric and semi…
Spike-and-slab priors are popular Bayesian solutions for high-dimensional linear regression problems. Previous theoretical studies on spike-and-slab methods focus on specific prior formulations and use prior-dependent conditions and analyses, and thus can not be generalized directly. In this paper, we propose a class of generic spike-and-slab priors and develop a unified framework to rigorously assess their theoretical properties. Technically, we provide general conditions under which generic spike-and-slab priors can achieve the nearly-optimal posterior contraction rate and the model selectio…
An important task in building regression models is to decide which regressors should be included in the final model. In a Bayesian approach, variable selection can be performed using mixture priors with a spike and a slab component for the effects subject to selection. As the spike is concentrated at zero, variable selection is based on the probability of assigning the corresponding regression effect to the slab component. These posterior inclusion probabilities can be determined by MCMC sampling. In this paper we compare the MCMC implementations for several spike and slab priors with regard t…
Imperial College London（帝国理工学院）；Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）
Variational Bayes (VB) is a popular scalable alternative to Markov chain Monte Carlo for Bayesian inference. We study a mean-field spike and slab VB approximation of widely used Bayesian model selection priors in sparse high-dimensional logistic regression. We provide non-asymptotic theoretical guarantees for the VB posterior in both $\ell_2$ and prediction loss for a sparse truth, giving optimal (minimax) convergence rates. Since the VB algorithm does not depend on the unknown truth to achieve optimality, our results shed light on effective prior choices. We confirm the improved performance o…
We study the use of spike and slab priors for consistent estimation of the number of change points and their locations. Leveraging recent results in the variable selection literature, we show that an estimator based on spike and slab priors achieves optimal localization rate in the multiple offline change point detection problem. Based on this estimator, we propose a Bayesian change point detection method, which is one of the fastest Bayesian methodologies, and it is more robust to misspecification of the error terms than the competing methods. We demonstrate through empirical work the good pe…
Estimation of the covariance matrix of asset returns from high frequency data is complicated by asynchronous returns, market mi- crostructure noise and jumps. One technique for addressing both asynchronous returns and market microstructure is the Kalman-EM (KEM) algorithm. However the KEM approach assumes log-normal prices and does not address jumps in the return process which can corrupt estimation of the covariance matrix. In this paper we extend the KEM algorithm to price models that include jumps. We propose two sparse Kalman filtering approaches to this problem. In the first approach we d…
In linear regression models, fusion of coefficients is used to identify predictors having similar relationships with a response. This is called variable fusion. This paper presents a novel variable fusion method in terms of Bayesian linear regression models. We focus on hierarchical Bayesian models based on a spike-and-slab prior approach. A spike-and-slab prior is tailored to perform variable fusion. To obtain estimates of the parameters, we develop a Gibbs sampler for the parameters. Simulation studies and a real data analysis show that our proposed method achieves better performance than pr…
Thompson sampling is a heuristic algorithm for the multi-armed bandit problem which has a long tradition in machine learning. The algorithm has a Bayesian spirit in the sense that it selects arms based on posterior samples of reward probabilities of each arm. By forging a connection between combinatorial binary bandits and spike-and-slab variable selection, we propose a stochastic optimization approach to subset selection called Thompson Variable Selection (TVS). TVS is a framework for interpretable machine learning which does not rely on the underlying model to be linear. TVS brings together …
Harvard University（哈佛大学）；Microsoft Research New England（微软新英格兰研究院）
Spike-and-slab priors are commonly used for Bayesian variable selection, due to their interpretability and favorable statistical properties. However, existing samplers for spike-and-slab posteriors incur prohibitive computational costs when the number of variables is large. In this article, we propose Scalable Spike-and-Slab ($S^3$), a scalable Gibbs sampling implementation for high-dimensional Bayesian regression with the continuous spike-and-slab prior of George and McCulloch (1993). For a dataset with $n$ observations and $p$ covariates, $S^3$ has order $\max\{ n^2 p_t, np \}$ computational…
In this work, we address the problem of solving a series of underdetermined linear inverse problems subject to a sparsity constraint. We generalize the spike-and-slab prior distribution to encode a priori correlation of the support of the solution in both space and time by imposing a transformed Gaussian process on the spike-and-slab probabilities. An expectation propagation (EP) algorithm for posterior inference under the proposed model is derived. For large scale problems, the standard EP algorithm can be prohibitively slow. We therefore introduce three different approximation schemes to red…
We consider exact algorithms for Bayesian inference with model selection priors (including spike-and-slab priors) in the sparse normal sequence model. Because the best existing exact algorithm becomes numerically unstable for sample sizes over n=500, there has been much attention for alternative approaches like approximate algorithms (Gibbs sampling, variational Bayes, etc.), shrinkage priors (e.g. the Horseshoe prior and the Spike-and-Slab LASSO) or empirical Bayesian methods. However, by introducing algorithmic ideas from online sequential prediction, we show that exact calculations are feas…
Variable Fusion and Selection via a Spike-and-Slab Approach with Nonlocal Priors
The Institute of Statistical Mathematics（统计数学研究所）；Graduate School of Mathematics, Kyushu University（九州大学大学院数学院）；Faculty of Mathematics, Kyushu University（九州大学数学系）
We propose a Bayesian methodology for estimating spiked covariance matrices with jointly sparse structure in high dimensions. The spiked covariance matrix is reparametrized in terms of the latent factor model, where the loading matrix is equipped with a novel matrix spike-and-slab LASSO prior, which is a continuous shrinkage prior for modeling jointly sparse matrices. We establish the rate-optimal posterior contraction for the covariance matrix with respect to the operator norm as well as that for the principal subspace with respect to the projection operator norm loss. We also study the poste…
PliableBVS: A flexible Bayesian variable selection method for modeling interactions with mandatory modifying variables
University of Oslo（奥斯陆大学）；Oslo University Hospital Rikshospitalet（奥斯陆大学医院里克斯霍斯皮塔勒分院）；Institute of Clinical Medicine, Faculty of Medicine, University of Oslo（奥斯陆大学医学院临床医学科）
The paper discusses shrinkage priors which impose increasing shrinkage in a sequence of parameters. We review the cumulative shrinkage process (CUSP) prior of Legramanti et al. (2020), which is a spike-and-slab shrinkage prior where the spike probability is stochastically increasing and constructed from the stick-breaking representation of a Dirichlet process prior. As a first contribution, this CUSP prior is extended by involving arbitrary stick-breaking representations arising from beta distributions. As a second contribution, we prove that exchangeable spike-and-slab priors, which are popul…
Spike-and-slab shrinkage priors for structurally sparse Bayesian neural networks
Computational Science Initiative, Brookhaven National Laboratory（布鲁克海文国家实验室计算科学倡议）；Department of Statistics and Probability, Michigan State University（密歇根州立大学统计与概率系）
Structured additive regression provides a general framework for complex Gaussian and non-Gaussian regression models, with predictors comprising arbitrary combinations of nonlinear functions and surfaces, spatial effects, varying coefficients, random effects and further regression terms. The large flexibility of structured additive regression makes function selection a challenging and important task, aiming at (1) selecting the relevant covariates, (2) choosing an appropriate and parsimonious representation of the impact of covariates on the predictor and (3) determining the required interactio…
In this article, we propose a novel spatial global-local spike-and-slab selection prior for image-on-scalar regression. We consider a Bayesian hierarchical Gaussian process model for image smoothing, that uses a flexible Inverse-Wishart process prior to handle within-image dependency, and propose a general global-local spatial selection prior that extends a rich class of well-studied selection priors. Unlike existing constructions, we achieve simultaneous global (i.e, at covariate-level) and local (i.e., at pixel/voxel-level) selection by introducing `participation rate' parameters that measur…
In observational studies, estimation of a causal effect of a treatment on an outcome relies on proper adjustment for confounding. If the number of the potential confounders ($p$) is larger than the number of observations ($n$), then direct control for all potential confounders is infeasible. Existing approaches for dimension reduction and penalization are generally aimed at predicting the outcome, and are less suited for estimation of causal effects. Under standard penalization approaches (e.g. Lasso), if a variable $X_j$ is strongly associated with the treatment $T$ but weakly with the outcom…
We introduce a Bayesian prior distribution, the Logit-Normal continuous analogue of the spike-and-slab (LN-CASS), which enables flexible parameter estimation and variable/model selection in a variety of settings. We demonstrate its use and efficacy in three case studies -- a simulation study and two studies on real biological data from the fields of metabolomics and genomics. The prior allows the use of classical statistical models, which are easily interpretable and well-known to applied scientists, but performs comparably to common machine learning methods in terms of generalisability to pre…
A Cumulative Ordered Spike-and-Slab Prior for Adaptive Dimension Selection in Joint Latent Space Models
Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University（华东师范大学统计学院，统计学与数据科学教育部重点实验室）
