Expectation Maximization (EM) is among the most popular algorithms for estimating parameters of statistical models. However, EM, which is an iterative algorithm based on the maximum likelihood principle, is generally only guaranteed to find stationary points of the likelihood objective, and these points may be far from any maximizer. This article addresses this disconnect between the statistical principles behind EM and its algorithmic properties. Specifically, it provides a global analysis of EM for specific models in which the observations comprise an i.i.d. sample from a mixture of two Gaussians. This is achieved by (i) studying the sequence of parameters from idealized execution of EM in the infinite sample limit, and fully characterizing the limit points of the sequence in terms of the initial parameters; and then (ii) based on this convergence analysis, establishing statistical consistency (or lack thereof) for the actual sequence of parameters produced by EM.

We propose two stochastic gradient MCMC methods for sampling from Bayesian posterior distributions defined on Riemann manifolds with a known geodesic flow, e.g. hyperspheres. Our methods are the first scalable sampling methods on these manifolds, with the aid of stochastic gradients. Novel dynamics are conceived and 2nd-order integrators are developed. By adopting embedding techniques and the geodesic integrator, the methods do not require a global coordinate system of the manifold and do not involve inner iterations. Synthetic experiments show the validity of the method, and its application to the challenging inference for spherical topic models indicate practical usability and efficiency.

Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Longitudinal data extracted from individual electronic health records (EHR) offer an exciting new way to study subtle differences in the way these diseases progress over time. In this paper, we focus on answering two questions that can be asked using these databases of longitudinal EHR data. First, we want to understand whether there are individuals with similar disease trajectories and whether there are a small number of degrees of freedom that account for differences in trajectories across the population. Second, we want to understand how important clinical outcomes are associated with disease trajectories. To answer these questions, we propose the Disease Trajectory Map (DTM), a novel probabilistic model that learns low-dimensional representations of sparse and irregularly sampled longitudinal data. We propose a stochastic variational inference algorithm for learning the DTM that allows the model to scale to large modern medical datasets. To demonstrate the DTM, we analyze data collected on patients with the complex autoimmune disease, scleroderma. We find that DTM learns meaningful representations of disease trajectories and that the representations are significantly associated with important clinical outcomes.

Markov chain Monte Carlo (MCMC) is one of the main workhorses of probabilistic inference, but it is notoriously hard to measure the quality of approximate posterior samples. This challenge is particularly salient in black box inference methods, which can hide details and obscure inference failures. In this work, we extend the recently introduced bidirectional Monte Carlo [GGA15] technique to evaluate MCMC-based posterior inference algorithms. By running annealed importance sampling (AIS) chains both from prior to posterior and vice versa on simulated data, we upper bound in expectation the symmetrized KL divergence between the true posterior distribution and the distribution of approximate samples. We integrate our method into two probabilistic programming languages, WebPPL [GS] and Stan [CGHL p], and validate it on several models and datasets. As an example of how our method be used to guide the design of inference algorithms, we apply it to study the effectiveness of different model representations in WebPPL and Stan.

Latent Dirichlet Allocation (LDA) is a very popular model for topic modeling as well as many other problems with latent groups. It is both simple and effective. When the number of topics (or latent groups) is unknown, the Hierarchical Dirichlet Process (HDP) provides an elegant non-parametric extension; however, it is a complex model and it is difficult to incorporate prior knowledge since the distribution over topics is implicit. We propose two new models that extend LDA in a simple and intuitive fashion by directly expressing a distribution over the number of topics. We also propose a new online Bayesian moment matching technique to learn the parameters and the number of topics of those models based on streaming data. The approach achieves higher log-likelihood than batch and online HDP with fixed hyperparameters on several corpora.

In this work, we propose an infinite restricted Boltzmann machine (RBM), whose maximum likelihood estimation (MLE) corresponds to a constrained convex optimization. We consider the Frank-Wolfe algorithm to solve the program, which provides a sparse solution that can be interpreted as inserting a hidden unit at each iteration, so that the optimization process takes the form of a sequence of finite models of increasing complexity. As a side benefit, this can be used to easily and efficiently identify an appropriate number of hidden units during the optimization. The resulting model can also be used as an initialization for typical state-of-the-art RBM training algorithms such as contrastive divergence, leading to models with consistently higher test likelihood than random initialization.

Missing records are a perennial problem in analysis of complex data of all types, when the target of inference is some function of the full data law. In simple cases, where data is missing at random or completely at random (Rubin, 1976), well-known adjustments exist that result in consistent estimators of target quantities. Assumptions underlying these estimators are generally not realistic in practical missing data problems. Unfortunately, consistent estimators in more complex cases where data is missing not at random, and where no ordering on variables induces monotonicity of missingness status are not known in general, with some notable exceptions (Robins, 1997), (Tchetgen Tchetgen et al, 2016), (Sadinle and Reiter, 2016). In this paper, we propose a general class of consistent estimators for cases where data is missing not at random, and missingness status is non-monotonic. Our estimators, which are generalized inverse probability weighting estimators, make no assumptions on the underlying full data law, but instead place independence restrictions, and certain other fairly mild assumptions, on the distribution of missingness status conditional on the data. The assumptions we place on the distribution of missingness status conditional on the data can be viewed as a version of a conditional Markov random field (MRF) corresponding to a chain graph. Assumptions embedded in our model permit identification from the observed data law, and admit a natural fitting procedure based on the pseudo likelihood approach of (Besag, 1975). We illustrate our approach with a simple simulation study, and an analysis of risk of premature birth in women in Botswana exposed to highly active anti-retroviral therapy.

Probabilistic techniques are central to data analysis, but different approaches can be challenging to apply, combine, and compare. This paper introduces composable generative population models (CGPMs), a computational abstraction that extends directed graphical models and can be used to describe and compose a broad class of probabilistic data analysis techniques. Examples include discriminative machine learning, hierarchical Bayesian models, multivariate kernel methods, clustering algorithms, and arbitrary probabilistic programs. We demonstrate the integration of CGPMs into BayesDB, a probabilistic programming platform that can express data analysis tasks using a modeling definition language and structured query language. The practical value is illustrated in two ways. First, the paper describes an analysis on a database of Earth satellites, which identifies records that probably violate Kepler’s Third Law by composing causal probabilistic programs with non-parametric Bayes in 50 lines of probabilistic code. Second, it reports the lines of code and accuracy of CGPMs compared with baseline solutions from standard machine learning libraries.

The reparameterization gradient has become a widely used method to obtain Monte Carlo gradients to optimize the variational objective. However, this technique does not easily apply to commonly used distributions such as beta or gamma without further approximations, and most practical applications of the reparameterization gradient fit Gaussian distributions. In this paper, we introduce the generalized reparameterization gradient, a method that extends the reparameterization gradient to a wider class of variational distributions. Generalized reparameterizations use invertible transformations of the latent variables which lead to transformed distributions that weakly depend on the variational parameters. This results in new Monte Carlo gradients that combine reparameterization gradients and score function gradients. We demonstrate our approach on variational inference for two complex probabilistic models. The generalized reparameterization is effective: even a single sample from the variational distribution is enough to obtain a low-variance gradient.

Maximum Mean Discrepancy (MMD) is a distance on the space of probability measures which has found numerous applications in machine learning and nonparametric testing. This distance is based on the notion of embedding probabilities in a reproducing kernel Hilbert space. In this paper, we present the first known lower bounds for the estimation of MMD based on finite samples. Our lower bounds hold for any radial universal kernel on $\R^d$ and match the existing upper bounds up to constants that depend only on the properties of the kernel. Using these lower bounds, we establish the minimax rate optimality of the empirical estimator and its $U$-statistic variant, which are usually employed in applications.