This article proposes a Bayesian nonparametric method for forecasting, imputation, and clustering in sparsely observed, multivariate time series. The method is appropriate for jointly modeling hundreds of time series with widely varying, non-stationary dynamics. Given a collection of $N$ time series, the Bayesian model first partitions them into independent clusters using a Chinese restaurant process prior. Within a cluster, all time series are modeled jointly using a novel "temporally-coupled" extension of the Chinese restaurant process mixture. Markov chain Monte Carlo techniques are used to obtain samples from the posterior distribution, which are then used to form predictive inferences. We apply the technique to challenging prediction and imputation tasks using seasonal flu data from the US Center for Disease Control and Prevention, demonstrating competitive imputation performance and improved forecasting accuracy as compared to several state-of-the art baselines. We also show that the model discovers interpretable clusters in datasets with hundreds of time series using macroeconomic data from the Gapminder Foundation.

A key limitation of sampling algorithms for approximate inference is that it is difficult to quantify their approximation error. Widely used sampling schemes, such as sequential importance sampling with resampling and Metropolis-Hastings, produce output samples drawn from a distribution that may be far from the target posterior distribution. This paper shows how to upper-bound the symmetric KL divergence between the output distribution of a broad class of sequential Monte Carlo (SMC) samplers and their target posterior distributions, subject to assumptions about the accuracy of a separate gold-standard sampler. The proposed method applies to samplers that combine multiple particles, multinomial resampling, and rejuvenation kernels. The experiments show the technique being used to estimate bounds on the divergence of SMC samplers for posterior inference in a Bayesian linear regression model and a Dirichlet process mixture model.

This paper introduces the probabilistic module interface, which allows encapsulation of complex probabilistic models with latent variables alongside custom stochastic approximate inference machinery, and provides a platform-agnostic abstraction barrier separating the model internals from the host probabilistic inference system. The interface can be seen as a stochastic generalization of a standard simulation and density interface for probabilistic primitives. We show that sound approximate inference algorithms can be constructed for networks of probabilistic modules, and we demonstrate that the interface can be implemented using learned stochastic inference networks and MCMC and SMC approximate inference programs.

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.

Gaussian Processes (GPs) are widely used tools in statistics, machine learning, robotics, computer vision, and scientific computation. However, despite their popularity, they can be difficult to apply; all but the simplest classification or regression applications require specification and inference over complex covariance functions that do not admit simple analytical posteriors. This paper shows how to embed Gaussian processes in any higher-order probabilistic programming language, using an idiom based on memoization, and demonstrates its utility by implementing and extending classic and state-of-the-art GP applications. The interface to Gaussian processes, called gpmem, takes an arbitrary real-valued computational process as input and returns a statistical emulator that automatically improve as the original process is invoked and its input-output behavior is recorded. The flexibility of gpmem is illustrated via three applications: (i) robust GP regression with hierarchical hyper-parameter learning, (ii) discovering symbolic expressions from time-series data by fully Bayesian structure learning over kernels generated by a stochastic grammar, and (iii) a bandit formulation of Bayesian optimization with automatic inference and action selection. All applications share a single 50-line Python library and require fewer than 20 lines of probabilistic code each.

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.

Recently, multiple formulations of vision problems as probabilistic inversions of generative models based on computer graphics have been proposed. However, applications to 3D perception from natural images have focused on low-dimensional latent scenes, due to challenges in both modeling and inference. Accounting for the enormous variability in 3D object shape and 2D appearance via realistic generative models seems intractable, as does inverting even simple versions of the many-to-many computations that link 3D scenes to 2D images. This paper proposes and evaluates an approach that addresses key aspects of both these challenges. We show that it is possible to solve challenging, real-world 3D vision problems by approximate inference in generative models for images based on rendering the outputs of probabilistic CAD (PCAD) programs. Our PCAD object geometry priors generate deformable 3D meshes corresponding to plausible objects and apply affine transformations to place them in a scene. Image likelihoods are based on similarity in a feature space based on standard mid-level image representations from the vision literature. Our inference algorithm integrates single-site and locally blocked Metropolis-Hastings proposals, Hamiltonian Monte Carlo and discriminative data-driven proposals learned from training data generated from our models. We apply this approach to 3D human pose estimation and object shape reconstruction from single images, achieving quantitative and qualitative performance improvements over state-of-the-art baselines.

The idea of computer vision as the Bayesian inverse problem to computer graphics has a long history and an appealing elegance, but it has proved difficult to directly implement. Instead, most vision tasks are approached via complex bottom-up processing pipelines. Here we show that it is possible to write short, simple probabilistic graphics programs that define flexible generative models and to automatically invert them to interpret real-world images. Generative probabilistic graphics programs consist of a stochastic scene generator, a renderer based on graphics software, a stochastic likelihood model linking the renderer's output and the data, and latent variables that adjust the fidelity of the renderer and the tolerance of the likelihood model. Representations and algorithms from computer graphics, originally designed to produce high-quality images, are instead used as the deterministic backbone for highly approximate and stochastic generative models. This formulation combines probabilistic programming, computer graphics, and approximate Bayesian computation, and depends only on general-purpose, automatic inference techniques. We describe two applications: reading sequences of degraded and adversarially obscured alphanumeric characters, and inferring 3D road models from vehicle-mounted camera images. Each of the probabilistic graphics programs we present relies on under 20 lines of probabilistic code, and supports accurate, approximately Bayesian inferences about ambiguous real-world images.

The idea of computer vision as the Bayesian inverse problem to computer graphics has a long history and an appealing elegance, but it has proved difficult to directly implement. Instead, most vision tasks are approached via complex bottom-up processing pipelines. Here we show that it is possible to write short, simple probabilistic graphics programs that define flexible generative models and to automatically invert them to interpret real-world images. Generative probabilistic graphics programs consist of a stochastic scene generator, a renderer based on graphics software, a stochastic likelihood model linking the renderer's output and the data, and latent variables that adjust the fidelity of the renderer and the tolerance of the likelihood model. Representations and algorithms from computer graphics, originally designed to produce high-quality images, are instead used as the deterministic backbone for highly approximate and stochastic generative models. This formulation combines probabilistic programming, computer graphics, and approximate Bayesian computation, and depends only on general-purpose, automatic inference techniques. We describe two applications: reading sequences of degraded and adversarially obscured alphanumeric characters, and inferring 3D road models from vehicle-mounted camera images. Each of the probabilistic graphics programs we present relies on under 20 lines of probabilistic code, and supports accurate, approximately Bayesian inferences about ambiguous real-world images.

The Dirichlet process (DP) is a fundamental mathematical tool for Bayesian nonparametric modeling, and is widely used in tasks such as density estimation, natural language processing, and time series modeling. Although MCMC inference methods for the DP often provide a gold standard in terms asymptotic accuracy, they can be computationally expensive and are not obviously parallelizable. We propose a reparameterization of the Dirichlet process that induces conditional independencies between the atoms that form the random measure. This conditional independence enables many of the Markov chain transition operators for DP inference to be simulated in parallel across multiple cores. Applied to mixture modeling, our approach enables the Dirichlet process to simultaneously learn clusters that describe the data and superclusters that define the granularity of parallelization. Unlike previous approaches, our technique does not require alteration of the model and leaves the true posterior distribution invariant. It also naturally lends itself to a distributed software implementation in terms of Map-Reduce, which we test in cluster configurations of over 50 machines and 100 cores. We present experiments exploring the parallel efficiency and convergence properties of our approach on both synthetic and real-world data, including runs on 1MM data vectors in 256 dimensions.