Evaluating Sensitivity to the Stick-Breaking Prior in Bayesian Nonparametrics

Bayesian models based on the Dirichlet process and other stick-breaking priors have been proposed as core ingredients for clustering, topic modeling, and other unsupervised learning tasks. Prior specification is, however, relatively difficult for such models, given that their flexibility implies that the consequences of prior choices are often relatively opaque. Moreover, these choices can have a substantial effect on posterior inferences. Thus, considerations of robustness need to go hand in hand with nonparametric modeling. In the current paper, we tackle this challenge by exploiting the fact that variational Bayesian methods, in addition to having computational advantages in fitting complex nonparametric models, also yield sensitivities with respect to parametric and nonparametric aspects of Bayesian models. In particular, we demonstrate how to assess the sensitivity of conclusions to the choice of concentration parameter and stick-breaking distribution for inferences under Dirichlet process mixtures and related mixture models. We provide both theoretical and empirical support for our variational approach to Bayesian sensitivity analysis.

The SKIM-FA Kernel: High-Dimensional Variable Selection and Nonlinear Interaction Discovery in Linear Time

Many scientific problems require identifying a small set of covariates that are associated with a target response and estimating their effects. Often, these effects are nonlinear and include interactions, so linear and additive methods can lead to poor estimation and variable selection. The Bayesian framework makes it straightforward to simultaneously express sparsity, nonlinearity, and interactions in a hierarchical model. But, as for the few other methods that handle this trifecta, inference is computationally intractable - with runtime at least quadratic in the number of covariates, and often worse. In the present work, we solve this computational bottleneck. We first show that suitable Bayesian models can be represented as Gaussian processes (GPs). We then demonstrate how a kernel trick can reduce computation with these GPs to O(# covariates) time for both variable selection and estimation. Our resulting fit corresponds to a sparse orthogonal decomposition of the regression function in a Hilbert space (i.e., a functional ANOVA decomposition), where interaction effects represent all variation that cannot be explained by lower-order effects. On a variety of synthetic and real datasets, our approach outperforms existing methods used for large, high-dimensional datasets while remaining competitive (or being orders of magnitude faster) in runtime.

Measuring the sensitivity of Gaussian processes to kernel choice

Gaussian processes (GPs) are used to make medical and scientific decisions, including in cardiac care and monitoring of carbon dioxide emissions. But the choice of GP kernel is often somewhat arbitrary. In particular, uncountably many kernels typically align with qualitative prior knowledge (e.g. function smoothness or stationarity). But in practice, data analysts choose among a handful of convenient standard kernels (e.g. squared exponential). In the present work, we ask: Would decisions made with a GP differ under other, qualitatively interchangeable kernels? We show how to formulate this sensitivity analysis as a constrained optimization problem over a finite-dimensional space. We can then use standard optimizers to identify substantive changes in relevant decisions made with a GP. We demonstrate in both synthetic and real-world examples that decisions made with a GP can exhibit substantial sensitivity to kernel choice, even when prior draws are qualitatively interchangeable to a user.

Independent finite approximations for Bayesian nonparametric inference: construction, error bounds, and practical implications

Bayesian nonparametrics based on completely random measures (CRMs) offers a flexible modeling approach when the number of clusters or latent components in a dataset is unknown. However, managing the infinite dimensionality of CRMs often leads to slow computation. Practical inference typically relies on either integrating out the infinite-dimensional parameter or using a finite approximation: a truncated finite approximation (TFA) or an independent finite approximation (IFA). The atom weights of TFAs are constructed sequentially, while the atoms of IFAs are independent, which (1) make them well-suited for parallel and distributed computation and (2) facilitates more convenient inference schemes. While IFAs have been developed in certain special cases in the past, there has not yet been a general template for construction or a systematic comparison to TFAs. We show how to construct IFAs for approximating distributions in a large family of CRMs, encompassing all those typically used in practice. We quantify the approximation error between IFAs and the target nonparametric prior, and prove that, in the worst-case, TFAs provide more component-efficient approximations than IFAs. However, in experiments on image denoising and topic modeling tasks with real data, we find that the error of Bayesian approximation methods overwhelms any finite approximation error, and IFAs perform very similarly to TFAs.

Approximate Cross-Validation with Low-Rank Data in High Dimensions

Many recent advances in machine learning are driven by a challenging trifecta: large data size $N$; high dimensions; and expensive algorithms. In this setting, cross-validation (CV) serves as an important tool for model assessment. Recent advances in approximate cross validation (ACV) provide accurate approximations to CV with only a single model fit, avoiding traditional CV's requirement for repeated runs of expensive algorithms. Unfortunately, these ACV methods can lose both speed and accuracy in high dimensions -- unless sparsity structure is present in the data. Fortunately, there is an alternative type of simplifying structure that is present in most data: approximate low rank (ALR). Guided by this observation, we develop a new algorithm for ACV that is fast and accurate in the presence of ALR data. Our first key insight is that the Hessian matrix -- whose inverse forms the computational bottleneck of existing ACV methods -- is ALR. We show that, despite our use of the \emph{inverse} Hessian, a low-rank approximation using the largest (rather than the smallest) matrix eigenvalues enables fast, reliable ACV. Our second key insight is that, in the presence of ALR data, error in existing ACV methods roughly grows with the (approximate, low) rank rather than with the (full, high) dimension. These insights allow us to prove theoretical guarantees on the quality of our proposed algorithm -- along with fast-to-compute upper bounds on its error. We demonstrate the speed and accuracy of our method, as well as the usefulness of our bounds, on a range of real and simulated data sets.

Finite mixture models are typically inconsistent for the number of components

Scientists and engineers are often interested in learning the number of subpopulations (or components) present in a data set. Practitioners commonly use a Dirichlet process mixture model (DPMM) for this purpose; in particular, they count the number of clusters---i.e. components containing at least one data point---in the DPMM posterior. But Miller and Harrison (2013) warn that the DPMM cluster-count posterior is severely inconsistent for the number of latent components when the data are truly generated from a finite mixture; that is, the cluster-count posterior probability on the true generating number of components goes to zero in the limit of infinite data. A potential alternative is to use a finite mixture model (FMM) with a prior on the number of components. Past work has shown the resulting FMM component-count posterior is consistent. But existing results crucially depend on the assumption that the component likelihoods are perfectly specified. In practice, this assumption is unrealistic, and empirical evidence (Miller and Dunson, 2019) suggests that the FMM posterior on the number of components is sensitive to the likelihood choice. In this paper, we add rigor to data-analysis folk wisdom by proving that under even the slightest model misspecification, the FMM posterior on the number of components is ultraseverely inconsistent: for any finite $k \in \mathbb{N}$, the posterior probability that the number of components is $k$ converges to 0 in the limit of infinite data. We illustrate practical consequences of our theory on simulated and real data sets.

Approximate Cross-Validation for Structured Models

Many modern data analyses benefit from explicitly modeling dependence structure in data -- such as measurements across time or space, ordered words in a sentence, or genes in a genome. Cross-validation is the gold standard to evaluate these analyses but can be prohibitively slow due to the need to re-run already-expensive learning algorithms many times. Previous work has shown approximate cross-validation (ACV) methods provide a fast and provably accurate alternative in the setting of empirical risk minimization. But this existing ACV work is restricted to simpler models by the assumptions that (i) data are independent and (ii) an exact initial model fit is available. In structured data analyses, (i) is always untrue, and (ii) is often untrue. In the present work, we address (i) by extending ACV to models with dependence structure. To address (ii), we verify -- both theoretically and empirically -- that ACV quality deteriorates smoothly with noise in the initial fit. We demonstrate the accuracy and computational benefits of our proposed methods on a diverse set of real-world applications.

Practical Posterior Error Bounds from Variational Objectives

Variational inference has become an increasingly attractive fast alternative to Markov chain Monte Carlo methods for approximate Bayesian inference. However, a major obstacle to the widespread use of variational methods is the lack of post-hoc accuracy measures that are both theoretically justified and computationally efficient. In this paper, we provide rigorous bounds on the error of posterior mean and uncertainty estimates that arise from full-distribution approximations, as in variational inference. Our bounds are widely applicable as they require only that the approximating and exact posteriors have polynomial moments. Our bounds are computationally efficient for variational inference in that they require only standard values from variational objectives, straightforward analytic calculations, and simple Monte Carlo estimates. We show that our analysis naturally leads to a new and improved workflow for variational inference. Finally, we demonstrate the utility of our proposed workflow and error bounds on a real-data example with a widely used multilevel hierarchical model.