Bayesian variable selection methods are powerful techniques for fitting and inferring on sparse high-dimensional linear regression models. However, many are computationally intensive or require restrictive prior distributions on model parameters. Likelihood based penalization methods are more computationally friendly, but resource intensive refitting techniques are needed for inference. In this paper, we proposed an efficient and powerful Bayesian approach for sparse high-dimensional linear regression. Minimal prior assumptions on the parameters are required through the use of plug-in empirical Bayes estimates of hyperparameters. Efficient maximum a posteriori probability (MAP) estimation is completed through the use of a partitioned and extended expectation conditional maximization (ECM) algorithm. The result is a PaRtitiOned empirical Bayes Ecm (PROBE) algorithm applied to sparse high-dimensional linear regression. We propose methods to estimate credible and prediction intervals for predictions of future values. We compare the empirical properties of predictions and our predictive inference to comparable approaches with numerous simulation studies and an analysis of cancer cell lines drug response study. The proposed approach is implemented in the R package probe.
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The method of instrumental variables provides a fundamental and practical tool for causal inference in many empirical studies where unmeasured confounding between the treatments and the outcome is present. Modern data such as the genetical genomics data from these studies are often high-dimensional. The high-dimensional linear instrumental-variables regression has been considered in the literature due to its simplicity albeit a true nonlinear relationship may exist. We propose a more data-driven approach by considering the nonparametric additive models between the instruments and the treatments while keeping a linear model between the treatments and the outcome so that the coefficients therein can directly bear causal interpretation. We provide a two-stage framework for estimation and inference under this more general setup. The group lasso regularization is first employed to select optimal instruments from the high-dimensional additive models, and the outcome variable is then regressed on the fitted values from the additive models to identify and estimate important treatment effects. We provide non-asymptotic analysis of the estimation error of the proposed estimator. A debiasing procedure is further employed to yield valid inference. Extensive numerical experiments show that our method can rival or outperform existing approaches in the literature. We finally analyze the mouse obesity data and discuss new findings from our method.
Recently emerging large-scale biomedical data pose exciting opportunities for scientific discoveries. However, the ultrahigh dimensionality and non-negligible measurement errors in the data may create difficulties in estimation. There are limited methods for high-dimensional covariates with measurement error, that usually require knowledge of the noise distribution and focus on linear or generalized linear models. In this work, we develop high-dimensional measurement error models for a class of Lipschitz loss functions that encompasses logistic regression, hinge loss and quantile regression, among others. Our estimator is designed to minimize the $L_1$ norm among all estimators belonging to suitable feasible sets, without requiring any knowledge of the noise distribution. Subsequently, we generalize these estimators to a Lasso analog version that is computationally scalable to higher dimensions. We derive theoretical guarantees in terms of finite sample statistical error bounds and sign consistency, even when the dimensionality increases exponentially with the sample size. Extensive simulation studies demonstrate superior performance compared to existing methods in classification and quantile regression problems. An application to a gender classification task based on brain functional connectivity in the Human Connectome Project data illustrates improved accuracy under our approach, and the ability to reliably identify significant brain connections that drive gender differences.
Multi-armed bandit problems provide a framework to identify the optimal intervention over a sequence of repeated experiments. Without additional assumptions, minimax optimal performance (measured by cumulative regret) is well-understood. With access to additional observed variables that d-separate the intervention from the outcome (i.e., they are a d-separator), recent "causal bandit" algorithms provably incur less regret. However, in practice it is desirable to be agnostic to whether observed variables are a d-separator. Ideally, an algorithm should be adaptive; that is, perform nearly as well as an algorithm with oracle knowledge of the presence or absence of a d-separator. In this work, we formalize and study this notion of adaptivity, and provide a novel algorithm that simultaneously achieves (a) optimal regret when a d-separator is observed, improving on classical minimax algorithms, and (b) significantly smaller regret than recent causal bandit algorithms when the observed variables are not a d-separator. Crucially, our algorithm does not require any oracle knowledge of whether a d-separator is observed. We also generalize this adaptivity to other conditions, such as the front-door criterion.
Despite the amount of research on disease mapping in recent years, the use of multivariate models for areal spatial data remains limited due to difficulties in implementation and computational burden. These problems are exacerbated when the number of small areas is very large. In this paper, we introduce an order-free multivariate scalable Bayesian modelling approach to smooth mortality (or incidence) risks of several diseases simultaneously. The proposal partitions the spatial domain into smaller subregions, fits multivariate models in each subdivision and obtains the posterior distribution of the relative risks across the entire spatial domain. The approach also provides posterior correlations among the spatial patterns of the diseases in each partition that are combined through a consensus Monte Carlo algorithm to obtain correlations for the whole study region. We implement the proposal using integrated nested Laplace approximations (INLA) in the R package bigDM and use it to jointly analyse colorectal, lung, and stomach cancer mortality data in Spanish municipalities. The new proposal permits the analysis of big data sets and provides better results than fitting a single multivariate model.
As a powerful Bayesian non-parameterized algorithm, the Gaussian process (GP) has performed a significant role in Bayesian optimization and signal processing. GPs have also advanced online decision-making systems because their posterior distribution has a closed-form solution. However, its training and inference process requires all historic data to be stored and the GP model to be trained from scratch. For those reasons, several online GP algorithms, such as O-SGPR and O-SVGP, have been specifically designed for streaming settings. In this paper, we present a new theoretical framework for online GPs based on the online probably approximately correct (PAC) Bayes theory. The framework offers both a guarantee of generalized performance and good accuracy. Instead of minimizing the marginal likelihood, our algorithm optimizes both the empirical risk function and a regularization item, which is in proportion to the divergence between the prior distribution and posterior distribution of parameters. In addition to its theoretical appeal, the algorithm performs well empirically on several regression datasets. Compared to other online GP algorithms, ours yields a generalization guarantee and very competitive accuracy.
This paper is concerned with developing an efficient numerical algorithm for fast implementation of the sparse grid method for computing the $d$-dimensional integral of a given function. The new algorithm, called the MDI-SG ({\em multilevel dimension iteration sparse grid}) method, implements the sparse grid method based on a dimension iteration/reduction procedure, it does not need to store the integration points, neither does it compute the function values independently at each integration point, instead, it re-uses the computation for function evaluations as much as possible by performing the function evaluations at all integration points in a cluster and iteratively along coordinate directions. It is shown numerically that the computational complexity (in terms of CPU time) of the proposed MDI-SG method is of polynomial order $O(Nd^3 )$ or better, compared to the exponential order $O(N(\log N)^{d-1})$ for the standard sparse grid method, where $N$ denotes the maximum number of integration points in each coordinate direction. As a result, the proposed MDI-SG method effectively circumvents the curse of dimensionality suffered by the standard sparse grid method for high-dimensional numerical integration.
It has become increasingly common to collect high-dimensional binary response data; for example, with the emergence of new sampling techniques in ecology. In smaller dimensions, multivariate probit (MVP) models are routinely used for inferences. However, algorithms for fitting such models face issues in scaling up to high dimensions due to the intractability of the likelihood, involving an integral over a multivariate normal distribution having no analytic form. Although a variety of algorithms have been proposed to approximate this intractable integral, these approaches are difficult to implement and/or inaccurate in high dimensions. Our main focus is in accommodating high-dimensional binary response data with a small to moderate number of covariates. We propose a two-stage approach for inference on model parameters while taking care of uncertainty propagation between the stages. We use the special structure of latent Gaussian models to reduce the highly expensive computation involved in joint parameter estimation to focus inference on marginal distributions of model parameters. This essentially makes the method embarrassingly parallel for both stages. We illustrate performance in simulations and applications to joint species distribution modeling in ecology.
A biomechanical model often requires parameter estimation and selection in a known but complicated nonlinear function. Motivated by observing that data from a head-neck position tracking system, one of biomechanical models, show multiplicative time dependent errors, we develop a modified penalized weighted least squares estimator. The proposed method can be also applied to a model with non-zero mean time dependent additive errors. Asymptotic properties of the proposed estimator are investigated under mild conditions on a weight matrix and the error process. A simulation study demonstrates that the proposed estimation works well in both parameter estimation and selection with time dependent error. The analysis and comparison with an existing method for head-neck position tracking data show better performance of the proposed method in terms of the variance accounted for (VAF).
In this paper, we consider recent progress in estimating the average treatment effect when extreme inverse probability weights are present and focus on methods that account for a possible violation of the positivity assumption. These methods aim at estimating the treatment effect on the subpopulation of patients for whom there is a clinical equipoise. We propose a systematic approach to determine their related causal estimands and develop new insights into the properties of the weights targeting such a subpopulation. Then, we examine the roles of overlap weights, matching weights, Shannon's entropy weights, and beta weights. This helps us characterize and compare their underlying estimators, analytically and via simulations, in terms of the accuracy, precision, and root mean squared error. Moreover, we study the asymptotic behaviors of their augmented estimators (that mimic doubly robust estimators), which lead to improved estimations when either the propensity or the regression models are correctly specified. Based on the analytical and simulation results, we conclude that overall overlap weights are preferable to matching weights, especially when there is moderate or extreme violations of the positivity assumption. Finally, we illustrate the methods using a real data example marked by extreme inverse probability weights.
This paper focuses on the expected difference in borrower's repayment when there is a change in the lender's credit decisions. Classical estimators overlook the confounding effects and hence the estimation error can be magnificent. As such, we propose another approach to construct the estimators such that the error can be greatly reduced. The proposed estimators are shown to be unbiased, consistent, and robust through a combination of theoretical analysis and numerical testing. Moreover, we compare the power of estimating the causal quantities between the classical estimators and the proposed estimators. The comparison is tested across a wide range of models, including linear regression models, tree-based models, and neural network-based models, under different simulated datasets that exhibit different levels of causality, different degrees of nonlinearity, and different distributional properties. Most importantly, we apply our approaches to a large observational dataset provided by a global technology firm that operates in both the e-commerce and the lending business. We find that the relative reduction of estimation error is strikingly substantial if the causal effects are accounted for correctly.
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