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A Bayesian coreset is a small, weighted subset of a data set that replaces the full data during inference to reduce computational cost. The state-of-the-art coreset construction algorithm, Coreset Markov chain Monte Carlo (Coreset MCMC), uses draws from an adaptive Markov chain targeting the coreset posterior to train the coreset weights via stochastic gradient optimization. However, the quality of the constructed coreset, and thus the quality of its posterior approximation, is sensitive to the stochastic optimization learning rate. In this work, we propose a learning-rate-free stochastic gradient optimization procedure, Hot-start Distance over Gradient (Hot DoG), for training coreset weights in Coreset MCMC without user tuning effort. Empirical results demonstrate that Hot DoG provides higher quality posterior approximations than other learning-rate-free stochastic gradient methods, and performs competitively to optimally-tuned ADAM.

Mixture models are often used to identify meaningful subpopulations (i.e., clusters) in observed data such that the subpopulations have a real-world interpretation (e.g., as cell types). However, when used for subpopulation discovery, mixture model inference is usually ill-defined a priori because the assumed observation model is only an approximation to the true data-generating process. Thus, as the number of observations increases, rather than obtaining better inferences, the opposite occurs: the data is explained by adding spurious subpopulations that compensate for the shortcomings of the observation model. However, there are two important sources of prior knowledge that we can exploit to obtain well-defined results no matter the dataset size: known causal structure (e.g., knowing that the latent subpopulations cause the observed signal but not vice-versa) and a rough sense of how wrong the observation model is (e.g., based on small amounts of expert-labeled data or some understanding of the data-generating process). We propose a new model selection criteria that, while model-based, uses this available knowledge to obtain mixture model inferences that are robust to misspecification of the observation model. We provide theoretical support for our approach by proving a first-of-its-kind consistency result under intuitive assumptions. Simulation studies and an application to flow cytometry data demonstrate our model selection criteria consistently finds the correct number of subpopulations.

Under model misspecification, it is known that Bayesian posteriors often do not properly quantify uncertainty about true or pseudo-true parameters. Even more fundamentally, misspecification leads to a lack of reproducibility in the sense that the same model will yield contradictory posteriors on independent data sets from the true distribution. To define a criterion for reproducible uncertainty quantification under misspecification, we consider the probability that two confidence sets constructed from independent data sets have nonempty overlap, and we establish a lower bound on this overlap probability that holds for any valid confidence sets. We prove that credible sets from the standard posterior can strongly violate this bound, particularly in high-dimensional settings (i.e., with dimension increasing with sample size), indicating that it is not internally coherent under misspecification. To improve reproducibility in an easy-to-use and widely applicable way, we propose to apply bagging to the Bayesian posterior ("BayesBag"'); that is, to use the average of posterior distributions conditioned on bootstrapped datasets. We motivate BayesBag from first principles based on Jeffrey conditionalization and show that the bagged posterior typically satisfies the overlap lower bound. Further, we prove a Bernstein--Von Mises theorem for the bagged posterior, establishing its asymptotic normal distribution. We demonstrate the benefits of BayesBag via simulation experiments and an application to crime rate prediction., Comment: arXiv admin note: text overlap with arXiv:1912.07104

Variational Inference (VI) is an attractive alternative to Markov Chain Monte Carlo (MCMC) due to its computational efficiency in the case of large datasets and/or complex models with high-dimensional parameters. However, evaluating the accuracy of variational approximations remains a challenge. Existing methods characterize the quality of the whole variational distribution, which is almost always poor in realistic applications, even if specific posterior functionals such as the component-wise means or variances are accurate. Hence, these diagnostics are of practical value only in limited circumstances. To address this issue, we propose the TArgeted Diagnostic for Distribution Approximation Accuracy (TADDAA), which uses many short parallel MCMC chains to obtain lower bounds on the error of each posterior functional of interest. We also develop a reliability check for TADDAA to determine when the lower bounds should not be trusted. Numerical experiments validate the practical utility and computational efficiency of our approach on a range of synthetic distributions and real-data examples, including sparse logistic regression and Bayesian neural network models., Comment: Code to reproduce all of our experiments is available at https://github.com/TARPS-group/TADDAA

The tuning of stochastic gradient algorithms (SGAs) for optimization and sampling is often based on heuristics and trial-and-error rather than generalizable theory. We address this theory--practice gap by characterizing the large-sample statistical asymptotics of SGAs via a joint step-size--sample-size scaling limit. We show that iterate averaging with a large fixed step size is robust to the choice of tuning parameters and asymptotically has covariance proportional to that of the MLE sampling distribution. We also prove a Bernstein--von Mises-like theorem to guide tuning, including for generalized posteriors that are robust to model misspecification. Numerical experiments validate our results and recommendations in realistic finite-sample regimes. Our work lays the foundation for a systematic analysis of other stochastic gradient Markov chain Monte Carlo algorithms for a wide range of models., Comment: 42 pgs

Black-box variational inference (BBVI) now sees widespread use in machine learning and statistics as a fast yet flexible alternative to Markov chain Monte Carlo methods for approximate Bayesian inference. However, stochastic optimization methods for BBVI remain unreliable and require substantial expertise and hand-tuning to apply effectively. In this paper, we propose Robust and Automated Black-box VI (RABVI), a framework for improving the reliability of BBVI optimization. RABVI is based on rigorously justified automation techniques, includes just a small number of intuitive tuning parameters, and detects inaccurate estimates of the optimal variational approximation. RABVI adaptively decreases the learning rate by detecting convergence of the fixed--learning-rate iterates, then estimates the symmetrized Kullback--Leibler (KL) divergence between the current variational approximation and the optimal one. It also employs a novel optimization termination criterion that enables the user to balance desired accuracy against computational cost by comparing (i) the predicted relative decrease in the symmetrized KL divergence if a smaller learning were used and (ii) the predicted computation required to converge with the smaller learning rate. We validate the robustness and accuracy of RABVI through carefully designed simulation studies and on a diverse set of real-world model and data examples.

Checking how well a fitted model explains the data is one of the most fundamental parts of a Bayesian data analysis. However, existing model checking methods suffer from trade-offs between being well-calibrated, automated, and computationally efficient. To overcome these limitations, we propose split predictive checks (SPCs), which combine the ease-of-use and speed of posterior predictive checks with the good calibration properties of predictive checks that rely on model-specific derivations or inference schemes. We develop an asymptotic theory for two types of SPCs: single SPCs and the divided SPCs. Our results demonstrate that they offer complementary strengths. Single SPCs work well with smaller datasets and provide excellent power when there is substantial misspecification, such as when the estimate uncertainty in the test statistic is significantly underestimated. When the sample size is large, divided SPCs can provide better power and are able to detect more subtle form of misspecification. We validate the finite-sample utility of SPCs through extensive simulation experiments in exponential family and hierarchical models, and provide three real-data examples where SPCs offer novel insights and additional flexibility beyond what is available when using posterior predictive checks., Comment: v3: updated some discussion of model criticism and predictive checks; improved some figures

Current black-box variational inference (BBVI) methods require the user to make numerous design choices -- such as the selection of variational objective and approximating family -- yet there is little principled guidance on how to do so. We develop a conceptual framework and set of experimental tools to understand the effects of these choices, which we leverage to propose best practices for maximizing posterior approximation accuracy. Our approach is based on studying the pre-asymptotic tail behavior of the density ratios between the joint distribution and the variational approximation, then exploiting insights and tools from the importance sampling literature. Our framework and supporting experiments help to distinguish between the behavior of BBVI methods for approximating low-dimensional versus moderate-to-high-dimensional posteriors. In the latter case, we show that mass-covering variational objectives are difficult to optimize and do not improve accuracy, but flexible variational families can improve accuracy and the effectiveness of importance sampling -- at the cost of additional optimization challenges. Therefore, for moderate-to-high-dimensional posteriors we recommend using the (mode-seeking) exclusive KL divergence since it is the easiest to optimize, and improving the variational family or using model parameter transformations to make the posterior and optimal variational approximation more similar. On the other hand, in low-dimensional settings, we show that heavy-tailed variational families and mass-covering divergences are effective and can increase the chances that the approximation can be improved by importance sampling.

Completely random measures (CRMs) and their normalizations (NCRMs) offer flexible models in Bayesian nonparametrics. But their infinite dimensionality presents challenges for inference. Two popular finite approximations are truncated finite approximations (TFAs) and independent finite approximations (IFAs). While the former have been well-studied, IFAs lack similarly general bounds on approximation error, and there has been no systematic comparison between the two options. In the present work, we propose a general recipe to construct practical finite-dimensional approximations for homogeneous CRMs and NCRMs, in the presence or absence of power laws. We call our construction the automated independent finite approximation (AIFA). Relative to TFAs, we show that AIFAs facilitate more straightforward derivations and use of parallel computing in approximate inference. We upper bound the approximation error of AIFAs for a wide class of common CRMs and NCRMs -- and thereby develop guidelines for choosing the approximation level. Our lower bounds in key cases suggest that our upper bounds are tight. We prove that, for worst-case choices of observation likelihoods, TFAs are more efficient than AIFAs. Conversely, we find that in real-data experiments with standard likelihoods, AIFAs and TFAs perform similarly. Moreover, we demonstrate that AIFAs can be used for hyperparameter estimation even when other potential IFA options struggle or do not apply., Comment: The paper has been accepted for publication in Bayesian Analysis. Currently, it is posted on Bayesian Analysis Advance Publication

We consider the problem of fitting variational posterior approximations using stochastic optimization methods. The performance of these approximations depends on (1) how well the variational family matches the true posterior distribution,(2) the choice of divergence, and (3) the optimization of the variational objective. We show that even in the best-case scenario when the exact posterior belongs to the assumed variational family, common stochastic optimization methods lead to poor variational approximations if the problem dimension is moderately large. We also demonstrate that these methods are not robust across diverse model types. Motivated by these findings, we develop a more robust and accurate stochastic optimization framework by viewing the underlying optimization algorithm as producing a Markov chain. Our approach is theoretically motivated and includes a diagnostic for convergence and a novel stopping rule, both of which are robust to noisy evaluations of the objective function. We show empirically that the proposed framework works well on a diverse set of models: it can automatically detect stochastic optimization failure or inaccurate variational approximation

Bayesian model selection is premised on the assumption that the data are generated from one of the postulated models. However, in many applications, all of these models are incorrect (that is, there is misspecification). When the models are misspecified, two or more models can provide a nearly equally good fit to the data, in which case Bayesian model selection can be highly unstable, potentially leading to self-contradictory findings. To remedy this instability, we propose to use bagging on the posterior distribution ("BayesBag") -- that is, to average the posterior model probabilities over many bootstrapped datasets. We provide theoretical results characterizing the asymptotic behavior of the posterior and the bagged posterior in the (misspecified) model selection setting. We empirically assess the BayesBag approach on synthetic and real-world data in (i) feature selection for linear regression and (ii) phylogenetic tree reconstruction. Our theory and experiments show that, when all models are misspecified, BayesBag (a) provides greater reproducibility and (b) places posterior mass on optimal models more reliably, compared to the usual Bayesian posterior; on the other hand, under correct specification, BayesBag is slightly more conservative than the usual posterior, in the sense that BayesBag posterior probabilities tend to be slightly farther from the extremes of zero and one. Overall, our results demonstrate that BayesBag provides an easy-to-use and widely applicable approach that improves upon Bayesian model selection by making it more stable and reproducible., Comment: Corrections and clarified recommendations. arXiv admin note: text overlap with arXiv:1912.07104

Standard Bayesian inference is known to be sensitive to model misspecification, leading to unreliable uncertainty quantification and poor predictive performance. However, finding generally applicable and computationally feasible methods for robust Bayesian inference under misspecification has proven to be a difficult challenge. An intriguing, easy-to-use, and widely applicable approach is to use bagging on the Bayesian posterior ("BayesBag"); that is, to use the average of posterior distributions conditioned on bootstrapped datasets. In this paper, we develop the asymptotic theory of BayesBag, propose a model-data mismatch index for model criticism using BayesBag, and empirically validate our theory and methodology on synthetic and real-world data in linear regression, sparse logistic regression, and a hierarchical mixed effects model. We find that in the presence of significant misspecification, BayesBag yields more reproducible inferences and has better predictive accuracy than the standard Bayesian posterior; on the other hand, when the model is correctly specified, BayesBag produces superior or equally good results. Overall, our results demonstrate that BayesBag combines the attractive modeling features of standard Bayesian inference with the distributional robustness properties of frequentist methods, providing benefits over both Bayes alone and the bootstrap alone.

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 also computationally efficient for variational inference because 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 validated variational inference. Finally, we demonstrate the utility of our proposed workflow and error bounds on a robust regression problem and on a real-data example with a widely used multilevel hierarchical model., Comment: A python package for carrying out our validated variational inference workflow -- including doing black-box variational inference and computing the bounds we develop in this paper -- is available at https://github.com/jhuggins/viabel. The same repository also contains code for reproducing all of our experiments

Due to the ease of modern data collection, applied statisticians often have access to a large set of covariates that they wish to relate to some observed outcome. Generalized linear models (GLMs) offer a particularly interpretable framework for such an analysis. In these high-dimensional problems, the number of covariates is often large relative to the number of observations, so we face non-trivial inferential uncertainty; a Bayesian approach allows coherent quantification of this uncertainty. Unfortunately, existing methods for Bayesian inference in GLMs require running times roughly cubic in parameter dimension, and so are limited to settings with at most tens of thousand parameters. We propose to reduce time and memory costs with a low-rank approximation of the data in an approach we call LR-GLM. When used with the Laplace approximation or Markov chain Monte Carlo, LR-GLM provides a full Bayesian posterior approximation and admits running times reduced by a full factor of the parameter dimension. We rigorously establish the quality of our approximation and show how the choice of rank allows a tunable computational-statistical trade-off. Experiments support our theory and demonstrate the efficacy of LR-GLM on real large-scale datasets., Comment: Accepted at ICML 2019

Discovering interaction effects on a response of interest is a fundamental problem faced in biology, medicine, economics, and many other scientific disciplines. In theory, Bayesian methods for discovering pairwise interactions enjoy many benefits such as coherent uncertainty quantification, the ability to incorporate background knowledge, and desirable shrinkage properties. In practice, however, Bayesian methods are often computationally intractable for even moderate-dimensional problems. Our key insight is that many hierarchical models of practical interest admit a particular Gaussian process (GP) representation; the GP allows us to capture the posterior with a vector of O(p) kernel hyper-parameters rather than O(p^2) interactions and main effects. With the implicit representation, we can run Markov chain Monte Carlo (MCMC) over model hyper-parameters in time and memory linear in p per iteration. We focus on sparsity-inducing models and show on datasets with a variety of covariate behaviors that our method: (1) reduces runtime by orders of magnitude over naive applications of MCMC, (2) provides lower Type I and Type II error relative to state-of-the-art LASSO-based approaches, and (3) offers improved computational scaling in high dimensions relative to existing Bayesian and LASSO-based approaches., Comment: Accepted at ICML 2019. 20 pages, 4 figures, 3 tables

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has led to the intriguing discovery that individual cell profiles can reflect the imprint of time or dynamic processes. However, synthesizing this information to reconstruct dynamic biological phenomena from data that are noisy, heterogenous, and sparse---and from processes that may unfold asynchronously---poses a complex computational and statistical challenge. Here, we develop a full generative model for probabilistically reconstructing trees of cellular differentiation from single-cell RNA-seq data. Specifically, we extend the framework of the classical Dirichlet diffusion tree to simultaneously infer branch topology and latent cell states along continuous trajectories over the full tree. In tandem, we construct a novel Markov chain Monte Carlo sampler that interleaves Metropolis-Hastings and message passing to leverage model structure for efficient inference. Finally, we demonstrate that these techniques can recover latent trajectories from simulated single-cell transcriptomes. While this work is motivated by cellular differentiation, we derive a tractable model that provides flexible densities for any data (coupled with an appropriate noise model) that arise from continuous evolution along a latent nonparametric tree., Comment: 18 pages, 6 figures. Preliminary work appeared in the 2017 NeurIPS workshops in Advances in Approximate Bayesian Inference (http://approximateinference.org/2017) and Machine Learning for Computational Biology (https://mlcb.github.io)

Kernel methods offer the flexibility to learn complex relationships in modern, large data sets while enjoying strong theoretical guarantees on quality. Unfortunately, these methods typically require cubic running time in the data set size, a prohibitive cost in the large-data setting. Random feature maps (RFMs) and the Nystrom method both consider low-rank approximations to the kernel matrix as a potential solution. But, in order to achieve desirable theoretical guarantees, the former may require a prohibitively large number of features J+, and the latter may be prohibitively expensive for high-dimensional problems. We propose to combine the simplicity and generality of RFMs with a data-dependent feature selection scheme to achieve desirable theoretical approximation properties of Nystrom with just O(log J+) features. Our key insight is to begin with a large set of random features, then reduce them to a small number of weighted features in a data-dependent, computationally efficient way, while preserving the statistical guarantees of using the original large set of features. We demonstrate the efficacy of our method with theory and experiments--including on a data set with over 50 million observations. In particular, we show that our method achieves small kernel matrix approximation error and better test set accuracy with provably fewer random features than state-of-the-art methods., Comment: 24 pages, 8 figures, to appear in AISTATS 2019

Bayesian inference typically requires the computation of an approximation to the posterior distribution. An important requirement for an approximate Bayesian inference algorithm is to output high-accuracy posterior mean and uncertainty estimates. Classical Monte Carlo methods, particularly Markov Chain Monte Carlo, remain the gold standard for approximate Bayesian inference because they have a robust finite-sample theory and reliable convergence diagnostics. However, alternative methods, which are more scalable or apply to problems where Markov Chain Monte Carlo cannot be used, lack the same finite-data approximation theory and tools for evaluating their accuracy. In this work, we develop a flexible new approach to bounding the error of mean and uncertainty estimates of scalable inference algorithms. Our strategy is to control the estimation errors in terms of Wasserstein distance, then bound the Wasserstein distance via a generalized notion of Fisher distance. Unlike computing the Wasserstein distance, which requires access to the normalized posterior distribution, the Fisher distance is tractable to compute because it requires access only to the gradient of the log posterior density. We demonstrate the usefulness of our Fisher distance approach by deriving bounds on the Wasserstein error of the Laplace approximation and Hilbert coresets. We anticipate that our approach will be applicable to many other approximate inference methods such as the integrated Laplace approximation, variational inference, and approximate Bayesian computation, Comment: 22 pages, 2 figures

Gaussian processes (GPs) offer a flexible class of priors for nonparametric Bayesian regression, but popular GP posterior inference methods are typically prohibitively slow or lack desirable finite-data guarantees on quality. We develop an approach to scalable approximate GP regression with finite-data guarantees on the accuracy of pointwise posterior mean and variance estimates. Our main contribution is a novel objective for approximate inference in the nonparametric setting: the preconditioned Fisher (pF) divergence. We show that unlike the Kullback--Leibler divergence (used in variational inference), the pF divergence bounds the 2-Wasserstein distance, which in turn provides tight bounds the pointwise difference of the mean and variance functions. We demonstrate that, for sparse GP likelihood approximations, we can minimize the pF divergence efficiently. Our experiments show that optimizing the pF divergence has the same computational requirements as variational sparse GPs while providing comparable empirical performance--in addition to our novel finite-data quality guarantees., Comment: 20 pages, 7 figures, 1 table, including Appendix. Code available at https://github.com/trevorcampbell/fishergp

Computable Stein discrepancies have been deployed for a variety of applications, ranging from sampler selection in posterior inference to approximate Bayesian inference to goodness-of-fit testing. Existing convergence-determining Stein discrepancies admit strong theoretical guarantees but suffer from a computational cost that grows quadratically in the sample size. While linear-time Stein discrepancies have been proposed for goodness-of-fit testing, they exhibit avoidable degradations in testing power -- even when power is explicitly optimized. To address these shortcomings, we introduce feature Stein discrepancies ($\Phi$SDs), a new family of quality measures that can be cheaply approximated using importance sampling. We show how to construct $\Phi$SDs that provably determine the convergence of a sample to its target and develop high-accuracy approximations -- random $\Phi$SDs (R$\Phi$SDs) -- which are computable in near-linear time. In our experiments with sampler selection for approximate posterior inference and goodness-of-fit testing, R$\Phi$SDs perform as well or better than quadratic-time KSDs while being orders of magnitude faster to compute., Comment: In Proceedings of the 32nd Annual Conference on Neural Information Processing Systems (NeurIPS 2018). Code available at: https://bitbucket.org/jhhuggins/random-feature-stein-discrepancies

Generalized linear models (GLMs) -- such as logistic regression, Poisson regression, and robust regression -- provide interpretable models for diverse data types. Probabilistic approaches, particularly Bayesian ones, allow coherent estimates of uncertainty, incorporation of prior information, and sharing of power across experiments via hierarchical models. In practice, however, the approximate Bayesian methods necessary for inference have either failed to scale to large data sets or failed to provide theoretical guarantees on the quality of inference. We propose a new approach based on constructing polynomial approximate sufficient statistics for GLMs (PASS-GLM). We demonstrate that our method admits a simple algorithm as well as trivial streaming and distributed extensions that do not compound error across computations. We provide theoretical guarantees on the quality of point (MAP) estimates, the approximate posterior, and posterior mean and uncertainty estimates. We validate our approach empirically in the case of logistic regression using a quadratic approximation and show competitive performance with stochastic gradient descent, MCMC, and the Laplace approximation in terms of speed and multiple measures of accuracy -- including on an advertising data set with 40 million data points and 20,000 covariates., Comment: In Proceedings of the 31st Annual Conference on Neural Information Processing Systems (NIPS 2017). v3: corrected typos in Appendix A

Bayesian hierarchical models are increasing popular in economics. When using hierarchical models, it is useful not only to calculate posterior expectations, but also to measure the robustness of these expectations to reasonable alternative prior choices. We use variational Bayes and linear response methods to provide fast, accurate posterior means and robustness measures with an application to measuring the effectiveness of microcredit in the developing world., Comment: presented at 2016 ICML Workshop on #Data4Good: Machine Learning in Social Good Applications, New York, NY

The use of Bayesian methods in large-scale data settings is attractive because of the rich hierarchical models, uncertainty quantification, and prior specification they provide. Standard Bayesian inference algorithms are computationally expensive, however, making their direct application to large datasets difficult or infeasible. Recent work on scaling Bayesian inference has focused on modifying the underlying algorithms to, for example, use only a random data subsample at each iteration. We leverage the insight that data is often redundant to instead obtain a weighted subset of the data (called a coreset) that is much smaller than the original dataset. We can then use this small coreset in any number of existing posterior inference algorithms without modification. In this paper, we develop an efficient coreset construction algorithm for Bayesian logistic regression models. We provide theoretical guarantees on the size and approximation quality of the coreset -- both for fixed, known datasets, and in expectation for a wide class of data generative models. Crucially, the proposed approach also permits efficient construction of the coreset in both streaming and parallel settings, with minimal additional effort. We demonstrate the efficacy of our approach on a number of synthetic and real-world datasets, and find that, in practice, the size of the coreset is independent of the original dataset size. Furthermore, constructing the coreset takes a negligible amount of time compared to that required to run MCMC on it., Comment: In Proceedings of Advances in Neural Information Processing Systems (NIPS 2016)

Markov chains and diffusion processes are indispensable tools in machine learning and statistics that are used for inference, sampling, and modeling. With the growth of large-scale datasets, the computational cost associated with simulating these stochastic processes can be considerable, and many algorithms have been proposed to approximate the underlying Markov chain or diffusion. A fundamental question is how the computational savings trade off against the statistical error incurred due to approximations. This paper develops general results that address this question. We bound the Wasserstein distance between the equilibrium distributions of two diffusions as a function of their mixing rates and the deviation in their drifts. We show that this error bound is tight in simple Gaussian settings. Our general result on continuous diffusions can be discretized to provide insights into the computational-statistical trade-off of Markov chains. As an illustration, we apply our framework to derive finite-sample error bounds of approximate unadjusted Langevin dynamics. We characterize computation-constrained settings where, by using fast-to-compute approximate gradients in the Langevin dynamics, we obtain more accurate samples compared to using the exact gradients. Finally, as an additional application of our approach, we quantify the accuracy of approximate zig-zag sampling. Our theoretical analyses are supported by simulation experiments., Comment: In Proceedings of the 19th International Conference on Artificial Intelligence and Statistics (AISTATS 2017)

Completely random measures (CRMs) and their normalizations are a rich source of Bayesian nonparametric priors. Examples include the beta, gamma, and Dirichlet processes. In this paper we detail two major classes of sequential CRM representations---series representations and superposition representations---within which we organize both novel and existing sequential representations that can be used for simulation and posterior inference. These two classes and their constituent representations subsume existing ones that have previously been developed in an ad hoc manner for specific processes. Since a complete infinite-dimensional CRM cannot be used explicitly for computation, sequential representations are often truncated for tractability. We provide truncation error analyses for each type of sequential representation, as well as their normalized versions, thereby generalizing and improving upon existing truncation error bounds in the literature. We analyze the computational complexity of the sequential representations, which in conjunction with our error bounds allows us to directly compare representations and discuss their relative efficiency. We include numerous applications of our theoretical results to commonly-used (normalized) CRMs, demonstrating that our results enable a straightforward representation and analysis of CRMs that has not previously been available in a Bayesian nonparametric context., Comment: To appear in Bernoulli; 58 pages, 3 figures

Common statistical practice has shown that the full power of Bayesian methods is not realized until hierarchical priors are used, as these allow for greater "robustness" and the ability to "share statistical strength." Yet it is an ongoing challenge to provide a learning-theoretically sound formalism of such notions that: offers practical guidance concerning when and how best to utilize hierarchical models; provides insights into what makes for a good hierarchical prior; and, when the form of the prior has been chosen, can guide the choice of hyperparameter settings. We present a set of analytical tools for understanding hierarchical priors in both the online and batch learning settings. We provide regret bounds under log-loss, which show how certain hierarchical models compare, in retrospect, to the best single model in the model class. We also show how to convert a Bayesian log-loss regret bound into a Bayesian risk bound for any bounded loss, a result which may be of independent interest. Risk and regret bounds for Student's $t$ and hierarchical Gaussian priors allow us to formalize the concepts of "robustness" and "sharing statistical strength." Priors for feature selection are investigated as well. Our results suggest that the learning-theoretic benefits of using hierarchical priors can often come at little cost on practical problems., Comment: In Proceedings of the 32nd International Conference on Machine Learning (ICML 2015)

Sequential Monte Carlo (SMC) algorithms were originally designed for estimating intractable conditional expectations within state-space models, but are now routinely used to generate approximate samples in the context of general-purpose Bayesian inference. In particular, SMC algorithms are often used as subroutines within larger Monte Carlo schemes, and in this context, the demands placed on SMC are different: control of mean-squared error is insufficient---one needs to control the divergence from the target distribution directly. Towards this goal, we introduce the conditional adaptive resampling particle filter, building on the work of Gordon, Salmond, and Smith (1993), Andrieu, Doucet, and Holenstein (2010), and Whiteley, Lee, and Heine (2016). By controlling a novel notion of effective sample size, the $\infty$-ESS, we establish the efficiency of the resulting SMC sampling algorithm, providing an adaptive resampling extension of the work of Andrieu, Lee, and Vihola (2013). We apply our results to arrive at new divergence bounds for SMC samplers with adaptive resampling as well as an adaptive resampling version of the Particle Gibbs algorithm with the same geometric-ergodicity guarantees as its nonadaptive counterpart., Comment: 34 pages

Markov jump processes (MJPs) are used to model a wide range of phenomena from disease progression to RNA path folding. However, maximum likelihood estimation of parametric models leads to degenerate trajectories and inferential performance is poor in nonparametric models. We take a small-variance asymptotics (SVA) approach to overcome these limitations. We derive the small-variance asymptotics for parametric and nonparametric MJPs for both directly observed and hidden state models. In the parametric case we obtain a novel objective function which leads to non-degenerate trajectories. To derive the nonparametric version we introduce the gamma-gamma process, a novel extension to the gamma-exponential process. We propose algorithms for each of these formulations, which we call \emph{JUMP-means}. Our experiments demonstrate that JUMP-means is competitive with or outperforms widely used MJP inference approaches in terms of both speed and reconstruction accuracy., Comment: In Proceedings of the 32nd International Conference on Machine Learning (ICML 2015)

In this note we provide detailed derivations of two versions of small-variance asymptotics for hierarchical Dirichlet process (HDP) mixture models and the HDP hidden Markov model (HDP-HMM, a.k.a. the infinite HMM). We include derivations for the probabilities of certain CRP and CRF partitions, which are of more general interest., Comment: 7 pages

This paper reviews recent advances in Bayesian nonparametric techniques for constructing and performing inference in infinite hidden Markov models. We focus on variants of Bayesian nonparametric hidden Markov models that enhance a posteriori state-persistence in particular. This paper also introduces a new Bayesian nonparametric framework for generating left-to-right and other structured, explicit-duration infinite hidden Markov models that we call the infinite structured hidden semi-Markov model., Comment: 23 pages, 10 figures

This paper formalizes a latent variable inference problem we call {\em supervised pattern discovery}, the goal of which is to find sets of observations that belong to a single ``pattern.'' We discuss two versions of the problem and prove uniform risk bounds for both. In the first version, collections of patterns can be generated in an arbitrary manner and the data consist of multiple labeled collections. In the second version, the patterns are assumed to be generated independently by identically distributed processes. These processes are allowed to take an arbitrary form, so observations within a pattern are not in general independent of each other. The bounds for the second version of the problem are stated in terms of a new complexity measure, the quasi-Rademacher complexity., Comment: 12 pages, 1 figure. Title change. Full version. Appearing at the SIAM International Conference on Data Mining (SDM) 2014