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Register a new userNonparametric Empirical Bayes Estimation and Testing for Sparse and Heteroscedastic Signals
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Large-scale modern data often involves estimation and testing for high-dimensional unknown parameters. It is desirable to identify the sparse signals, ``the needles in the haystack, with accuracy and false discovery control. However, the unprecedented complexity and heterogeneity in modern data structure require new machine learning tools to effectively exploit commonalities and to robustly adjust for both sparsity and heterogeneity. In addition, estimates for high-dimensional parameters often lack uncertainty quantification. In this paper, we propose a novel Spike-and-Nonparametric mixture prior (SNP) -- a spike to promote the sparsity and a nonparametric structure to capture signals. In contrast to the state-of-the-art methods, the proposed methods solve the estimation and testing problem at once with several merits: 1) an accurate sparsity estimation; 2) point estimates with shrinkage/soft-thresholding property; 3) credible intervals for uncertainty quantification; 4) an optimal multiple testing procedure that controls false discovery rate. Our method exhibits promising empirical performance on both simulated data and a gene expression case study.
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The simultaneous estimation of many parameters $eta_i$, based on a corresponding set of observations $x_i$, for $i=1,ldots, n$, is a key research problem that has received renewed attention in the high-dimensional setting. %The classic example involves estimating a vector of normal means $mu_i$ subject to a fixed variance term $sigma^2$. However, Many practical situations involve heterogeneous data $(x_i, theta_i)$ where $theta_i$ is a known nuisance parameter. Effectively pooling information across samples while correctly accounting for heterogeneity presents a significant challenge in large-scale estimation problems. We address this issue by introducing the Nonparametric Empirical Bayes Smoothing Tweedie (NEST) estimator, which efficiently estimates $eta_i$ and properly adjusts for heterogeneity %by approximating the marginal density of the data $f_{theta_i}(x_i)$ and applying this density to via a generalized version of Tweedies formula. NEST is capable of handling a wider range of settings than previously proposed heterogeneous approaches as it does not make any parametric assumptions on the prior distribution of $eta_i$. The estimation framework is simple but general enough to accommodate any member of the exponential family of distributions. %; a thorough study of the normal means problem subject to heterogeneous variances is presented to illustrate the proposed framework. Our theoretical results show that NEST is asymptotically optimal, while simulation studies show that it outperforms competing methods, with substantial efficiency gains in many settings. The method is demonstrated on a data set measuring the performance gap in math scores between socioeconomically advantaged and disadvantaged students in K-12 schools.
Nonparametric empirical Bayes methods provide a flexible and attractive approach to high-dimensional data analysis. One particularly elegant empirical Bayes methodology, involving the Kiefer-Wolfowitz nonparametric maximum likelihood estimator (NPMLE) for mixture models, has been known for decades. However, implementation and theoretical analysis of the Kiefer-Wolfowitz NPMLE are notoriously difficult. A fast algorithm was recently proposed that makes NPMLE-based procedures feasible for use in large-scale problems, but the algorithm calculates only an approximation to the NPMLE. In this paper we make two contributions. First, we provide upper bounds on the convergence rate of the approximate NPMLEs statistical error, which have the same order as the best known bounds for the true NPMLE. This suggests that the approximate NPMLE is just as effective as the true NPMLE for statistical applications. Second, we illustrate the promise of NPMLE procedures in a high-dimensional binary classification problem. We propose a new procedure and show that it vastly outperforms existing methods in experiments with simulated data. In real data analyses involving cancer survival and gene expression data, we show that it is very competitive with several recently proposed methods for regularized linear discriminant analysis, another popular approach to high-dimensional classification.
We develop a Nonparametric Empirical Bayes (NEB) framework for compound estimation in the discrete linear exponential family, which includes a wide class of discrete distributions frequently arising from modern big data applications. We propose to directly estimate the Bayes shrinkage factor in the generalized Robbins formula via solving a scalable convex program, which is carefully developed based on a RKHS representation of the Steins discrepancy measure. The new NEB estimation framework is flexible for incorporating various structural constraints into the data driven rule, and provides a unified approach to compound estimation with both regular and scaled squared error losses. We develop theory to show that the class of NEB estimators enjoys strong asymptotic properties. Comprehensive simulation studies as well as analyses of real data examples are carried out to demonstrate the superiority of the NEB estimator over competing methods.
In the sparse normal means model, coverage of adaptive Bayesian posterior credible sets associated to spike and slab prior distributions is considered. The key sparsity hyperparameter is calibrated via marginal maximum likelihood empirical Bayes. First, adaptive posterior contraction rates are derived with respect to $d_q$--type--distances for $qleq 2$. Next, under a type of so-called excessive-bias conditions, credible sets are constructed that have coverage of the true parameter at prescribed $1-alpha$ confidence level and at the same time are of optimal diameter. We also prove that the previous conditions cannot be significantly weakened from the minimax perspective.
We study the posterior contraction rates of a Bayesian method with Gaussian process priors in nonparametric regression and its plug-in property for differential operators. For a general class of kernels, we establish convergence rates of the posterior measure of the regression function and its derivatives, which are both minimax optimal up to a logarithmic factor for functions in certain classes. Our calculation shows that the rate-optimal estimation of the regression function and its derivatives share the same choice of hyperparameter, indicating that the Bayes procedure remarkably adapts to the order of derivatives and enjoys a generalized plug-in property that extends real-valued functionals to function-valued functionals. This leads to a practically simple method for estimating the regression function and its derivatives, whose finite sample performance is assessed using simulations. Our proof shows that, under certain conditions, to any convergence rate of Bayes estimators there corresponds the same convergence rate of the posterior distributions (i.e., posterior contraction rate), and vice versa. This equivalence holds for a general class of Gaussian processes and covers the regression function and its derivative functionals, under both the $L_2$ and $L_{infty}$ norms. In addition to connecting these two fundamental large sample properties in Bayesian and non-Bayesian regimes, such equivalence enables a new routine to establish posterior contraction rates by calculating convergence rates of nonparametric point estimators. At the core of our argument is an operator-theoretic framework for kernel ridge regression and equivalent kernel techniques. We derive a range of sharp non-asymptotic bounds that are pivotal in establishing convergence rates of nonparametric point estimators and the equivalence theory, which may be of independent interest.
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