Testing the equality of two proportions is a common procedure in science, especially in medicine and public health. In these domains it is crucial to be able to quantify evidence for the absence of a treatment effect. Bayesian hypothesis testing by means of the Bayes factor provides one avenue to do so, requiring the specification of prior distributions for parameters. The most popular analysis approach views the comparison of proportions from a contingency table perspective, assigning prior distributions directly to the two proportions. Another, less popular approach views the problem from a logistic regression perspective, assigning prior distributions to logit-transformed parameters. Reanalyzing 39 null results from the New England Journal of Medicine with both approaches, we find that they can lead to markedly different conclusions, especially when the observed proportions are at the extremes (i.e., very low or very high). We explain these stark differences and provide recommendations for researchers interested in testing the equality of two proportions and users of Bayes factors more generally. The test that assigns prior distributions to logit-transformed parameters creates prior dependence between the two proportions and yields weaker evidence when the observations are at the extremes. When comparing two proportions, we argue that this test should become the new default.
Approximate Bayesian Computation (ABC) enables statistical inference in complex models whose likelihoods are difficult to calculate but easy to simulate from. ABC constructs a kernel-type approximation to the posterior distribution through an accept/reject mechanism which compares summary statistics of real and simulated data. To obviate the need for summary statistics, we directly compare empirical distributions with a Kullback-Leibler (KL) divergence estimator obtained via classification. In particular, we blend flexible machine learning classifiers within ABC to automate fake/real data comparisons. We consider the traditional accept/reject kernel as well as an exponential weighting scheme which does not require the ABC acceptance threshold. Our theoretical results show that the rate at which our ABC posterior distributions concentrate around the true parameter depends on the estimation error of the classifier. We derive limiting posterior shape results and find that, with a properly scaled exponential kernel, asymptotic normality holds. We demonstrate the usefulness of our approach on simulated examples as well as real data in the context of stock volatility estimation.
We are interested in privatizing an approximate posterior inference algorithm called Expectation Propagation (EP). EP approximates the posterior by iteratively refining approximations to the local likelihoods, and is known to provide better posterior uncertainties than those by variational inference (VI). However, EP needs a large memory to maintain all local approximates associated with each datapoint in the training data. To overcome this challenge, stochastic expectation propagation (SEP) considers a single unique local factor that captures the average effect of each likelihood term to the posterior and refines it in a way analogous to EP. In terms of privacy, SEP is more tractable than EP because at each refining step of a factor, the remaining factors are fixed and do not depend on other datapoints as in EP, which makes the sensitivity analysis straightforward. We provide a theoretical analysis of the privacy-accuracy trade-off in the posterior estimates under our method, called differentially private stochastic expectation propagation (DP-SEP). Furthermore, we demonstrate the performance of our DP-SEP algorithm evaluated on both synthetic and real-world datasets in terms of the quality of posterior estimates at different levels of guaranteed privacy.
Comparing probability distributions is an indispensable and ubiquitous task in machine learning and statistics. The most common way to compare a pair of Borel probability measures is to compute a metric between them, and by far the most widely used notions of metric are the Wasserstein metric and the total variation metric. The next most common way is to compute a divergence between them, and in this case almost every known divergences such as those of Kullback--Leibler, Jensen--Shannon, R\'enyi, and many more, are special cases of the $f$-divergence. Nevertheless these metrics and divergences may only be computed, in fact, are only defined, when the pair of probability measures are on spaces of the same dimension. How would one quantify, say, a KL-divergence between the uniform distribution on the interval $[-1,1]$ and a Gaussian distribution on $\mathbb{R}^3$? We show that these common notions of metrics and divergences give rise to natural distances between Borel probability measures defined on spaces of different dimensions, e.g., one on $\mathbb{R}^m$ and another on $\mathbb{R}^n$ where $m, n$ are distinct, so as to give a meaningful answer to the previous question.
The network influence model is a model for binary outcome variables that accounts for dependencies between outcomes for units that are relationally tied. The basic influence model was previously extended to afford a suite of new dependence assumptions and because of its relation to traditional Markov random field models it is often referred to as the auto logistic actor-attribute model (ALAAM). We extend on current approaches for fitting ALAAMs by presenting a comprehensive Bayesian inference scheme that supports testing of dependencies across subsets of data and the presence of missing data. We illustrate different aspects of the procedures through three empirical examples: masculinity attitudes in an all-male Australian school class, educational progression in Swedish schools, and un-employment among adults in a community sample in Australia.
Posterior contractions rates (PCRs) strengthen the notion of Bayesian consistency, quantifying the speed at which the posterior distribution concentrates on arbitrarily small neighborhoods of the true model, with probability tending to 1 or almost surely, as the sample size goes to infinity. Under the Bayesian nonparametric framework, a common assumption in the study of PCRs is that the model is dominated for the observations; that is, it is assumed that the posterior can be written through the Bayes formula. In this paper, we consider the problem of establishing PCRs in Bayesian nonparametric models where the posterior distribution is not available through the Bayes formula, and hence models that are non-dominated for the observations. By means of the Wasserstein distance and a suitable sieve construction, our main result establishes PCRs in Bayesian nonparametric models where the posterior is available through a more general disintegration than the Bayes formula. To the best of our knowledge, this is the first general approach to provide PCRs in non-dominated Bayesian nonparametric models, and it relies on minimal modeling assumptions and on a suitable continuity assumption for the posterior distribution. Some refinements of our result are presented under additional assumptions on the prior distribution, and applications are given with respect to the Dirichlet process prior and the normalized extended Gamma process prior.
We study Martin-L\"{o}f random (ML-random) points on computable probability measures on sample and parameter spaces (Bayes models). We consider four variants of conditional random sequences with respect to the conditional distributions: two of them are defined by ML-randomness on Bayes models and the others are defined by blind tests for conditional distributions. We consider a weak criterion for conditional ML-randomness and show that only variants of ML-randomness on Bayes models satisfy the criterion. We show that these four variants of conditional randomness are identical when the conditional probability measure is computable and the posterior distribution converges weakly to almost all parameters. We compare ML-randomness on Bayes models with randomness for uniformly computable parametric models. It is known that two computable probability measures are orthogonal if and only if their ML-random sets are disjoint. We extend these results for uniformly computable parametric models. Finally, we present an algorithmic solution to a classical problem in Bayes statistics, i.e.~the posterior distributions converge weakly to almost all parameters if and only if the posterior distributions converge weakly to all ML-random parameters.
The posterior over Bayesian neural network (BNN) parameters is extremely high-dimensional and non-convex. For computational reasons, researchers approximate this posterior using inexpensive mini-batch methods such as mean-field variational inference or stochastic-gradient Markov chain Monte Carlo (SGMCMC). To investigate foundational questions in Bayesian deep learning, we instead use full-batch Hamiltonian Monte Carlo (HMC) on modern architectures. We show that (1) BNNs can achieve significant performance gains over standard training and deep ensembles; (2) a single long HMC chain can provide a comparable representation of the posterior to multiple shorter chains; (3) in contrast to recent studies, we find posterior tempering is not needed for near-optimal performance, with little evidence for a "cold posterior" effect, which we show is largely an artifact of data augmentation; (4) BMA performance is robust to the choice of prior scale, and relatively similar for diagonal Gaussian, mixture of Gaussian, and logistic priors; (5) Bayesian neural networks show surprisingly poor generalization under domain shift; (6) while cheaper alternatives such as deep ensembles and SGMCMC methods can provide good generalization, they provide distinct predictive distributions from HMC. Notably, deep ensemble predictive distributions are similarly close to HMC as standard SGLD, and closer than standard variational inference.
Stochastic gradient Markov chain Monte Carlo (SGMCMC) has become a popular method for scalable Bayesian inference. These methods are based on sampling a discrete-time approximation to a continuous time process, such as the Langevin diffusion. When applied to distributions defined on a constrained space, such as the simplex, the time-discretisation error can dominate when we are near the boundary of the space. We demonstrate that while current SGMCMC methods for the simplex perform well in certain cases, they struggle with sparse simplex spaces; when many of the components are close to zero. However, most popular large-scale applications of Bayesian inference on simplex spaces, such as network or topic models, are sparse. We argue that this poor performance is due to the biases of SGMCMC caused by the discretization error. To get around this, we propose the stochastic CIR process, which removes all discretization error and we prove that samples from the stochastic CIR process are asymptotically unbiased. Use of the stochastic CIR process within a SGMCMC algorithm is shown to give substantially better performance for a topic model and a Dirichlet process mixture model than existing SGMCMC approaches.
We consider the task of learning the parameters of a {\em single} component of a mixture model, for the case when we are given {\em side information} about that component, we call this the "search problem" in mixture models. We would like to solve this with computational and sample complexity lower than solving the overall original problem, where one learns parameters of all components. Our main contributions are the development of a simple but general model for the notion of side information, and a corresponding simple matrix-based algorithm for solving the search problem in this general setting. We then specialize this model and algorithm to four common scenarios: Gaussian mixture models, LDA topic models, subspace clustering, and mixed linear regression. For each one of these we show that if (and only if) the side information is informative, we obtain parameter estimates with greater accuracy, and also improved computation complexity than existing moment based mixture model algorithms (e.g. tensor methods). We also illustrate several natural ways one can obtain such side information, for specific problem instances. Our experiments on real data sets (NY Times, Yelp, BSDS500) further demonstrate the practicality of our algorithms showing significant improvement in runtime and accuracy.
Discrete random structures are important tools in Bayesian nonparametrics and the resulting models have proven effective in density estimation, clustering, topic modeling and prediction, among others. In this paper, we consider nested processes and study the dependence structures they induce. Dependence ranges between homogeneity, corresponding to full exchangeability, and maximum heterogeneity, corresponding to (unconditional) independence across samples. The popular nested Dirichlet process is shown to degenerate to the fully exchangeable case when there are ties across samples at the observed or latent level. To overcome this drawback, inherent to nesting general discrete random measures, we introduce a novel class of latent nested processes. These are obtained by adding common and group-specific completely random measures and, then, normalising to yield dependent random probability measures. We provide results on the partition distributions induced by latent nested processes, and develop an Markov Chain Monte Carlo sampler for Bayesian inferences. A test for distributional homogeneity across groups is obtained as a by product. The results and their inferential implications are showcased on synthetic and real data.