Of course as an introductory book, we can only leave it at that: an introductory book. For the mathematically trained, they may cure the curiosity this text generates with other texts designed with mathematical analysis in mind. For the enthusiast with less mathematical background, or one who is not interested in the mathematics but simply the practice of Bayesian methods, this text should be sufficient and entertaining. The choice of PyMC as the probabilistic programming language is two-fold. As of this writing, there is currently no central resource for examples and explanations in the PyMC universe.

We consider maximum likelihood estimation for Gaussian Mixture Models (Gmms). This task is almost invariably solved (in theory and practice) via the Expectation Maximization (EM) algorithm. EM owes its success to various factors, of which is its ability to fulfill positive definiteness constraints in closed form is of key importance. We propose an alternative to EM by appealing to the rich Riemannian geometry of positive definite matrices, using which we cast Gmm parameter estimation as a Riemannian optimization problem. Surprisingly, such an out-of-the-box Riemannian formulation completely fails and proves much inferior to EM. This motivates us to take a closer look at the problem geometry, and derive a better formulation that is much more amenable to Riemannian optimization. We then develop (Riemannian) batch and stochastic gradient algorithms that outperform EM, often substantially. We provide a non-asymptotic convergence analysis for our stochastic method, which is also the first (to our knowledge) such global analysis for Riemannian stochastic gradient. Numerous empirical results are included to demonstrate the effectiveness of our methods.

Recently, impressive denoising results have been achieved by Bayesian approaches which assume Gaussian models for the image patches. This improvement in performance can be attributed to the use of per-patch models. Unfortunately such an approach is particularly unstable for most inverse problems beyond denoising. In this work, we propose the use of a hyperprior to model image patches, in order to stabilize the estimation procedure. There are two main advantages to the proposed restoration scheme: Firstly it is adapted to diagonal degradation matrices, and in particular to missing data problems (e.g. inpainting of missing pixels or zooming). Secondly it can deal with signal dependent noise models, particularly suited to digital cameras. As such, the scheme is especially adapted to computational photography. In order to illustrate this point, we provide an application to high dynamic range imaging from a single image taken with a modified sensor, which shows the effectiveness of the proposed scheme.

We could not so far claim that deep networks trained with stochastic gradient descent are Bayesian. And it may be because SGD biases learning towards flat minima, rather than sharp minima. It turns out, (Hochreiter and Schmidhuber, 1997) motivated their work on seeking flat minima from a Bayesian, minimum description length perspective. Seeking flat minima makes sense from a minimum description length perspective.

We tackle the problem of collaborative filtering (CF) with side information, through the lens of Gaussian Process (GP) regression. Driven by the idea of using the kernel to explicitly model user-item similarities, we formulate the GP in a way that allows the incorporation of low-rank matrix factorisation, arriving at our model, the Tucker Gaussian Process (TGP). Consequently, TGP generalises classical Bayesian matrix factorisation models, and goes beyond them to give a natural and elegant method for incorporating side information, giving enhanced predictive performance for CF problems. Moreover we show that it is a novel model for regression, especially well-suited to grid-structured data and problems where the dependence on covariates is close to being separable.

Learning the structure of dependencies among multiple random variables is a problem of considerable theoretical and practical interest. In practice, score optimisation with multiple restarts provides a practical and surprisingly successful solution, yet the conditions under which this may be a well founded strategy are poorly understood. In this paper, we prove that the problem of identifying the structure of a Bayesian Network via regularised score optimisation can be recast, in expectation, as a submodular optimisation problem, thus guaranteeing optimality with high probability. This result both explains the practical success of optimisation heuristics, and suggests a way to improve on such algorithms by artificially simulating multiple data sets via a bootstrap procedure. We show on several synthetic data sets that the resulting algorithm yields better recovery performance than the state of the art, and illustrate in a real cancer genomic study how such an approach can lead to valuable practical insights.

A Monte Carlo algorithm typically simulates some prescribed number of samples, taking some random real time to complete the computations necessary. This work considers the converse: to impose a real-time budget on the computation, so that the number of samples simulated is random. To complicate matters, the real time taken for each simulation may depend on the sample produced, so that the samples themselves are not independent of their number, and a length bias with respect to compute time is apparent. This is especially problematic when a Markov chain Monte Carlo (MCMC) algorithm is used and the final state of the Markov chain---rather than an average over all states---is required. The length bias does not diminish with the compute budget in this case. It occurs, for example, in sequential Monte Carlo (SMC) algorithms. We propose an anytime framework to address the concern, using a continuous-time Markov jump process to study the progress of the computation in real time. We show that the length bias can be eliminated for any MCMC algorithm by using a multiple chain construction. The utility of this construction is demonstrated on a large-scale SMC-squared implementation, using four billion particles distributed across a cluster of 128 graphics processing units on the Amazon EC2 service. The anytime framework imposes a real-time budget on the MCMC move steps within SMC-squared, ensuring that all processors are simultaneously ready for the resampling step, demonstrably reducing wait times and providing substantial control over the total compute budget.

Written by Chris Fonnesbeck, Assistant Professor of Biostatistics, Vanderbilt University Medical Center. You can view, fork, and play with this project on the Domino data science platform. A common applied statistics task involves building regression models to characterize non-linear relationships between variables. It is possible to fit such models by assuming a particular non-linear functional form, such as a sinusoidal, exponential, or polynomial function, to describe one variable's response to the variation in another. Unless this relationship is obvious from the outset, however, it involves possibly extensive model selection procedures to ensure the most appropriate model is retained. Alternatively, a non-parametric approach can be adopted by defining a set of knots across the variable space and use a spline or kernel regression to describe arbitrary non-linear relationships.

In order to interact intelligently with objects in the world, animals must first transform neural population responses into estimates of the dynamic, unknown stimuli which caused them. The Bayesian solution to this problem is known as a Bayes filter, which applies Bayes' rule to combine population responses with the predictions of an internal model. In this paper we present a method for learning to approximate a Bayes filter when the stimulus dynamics are unknown. To do this we use the inferential properties of probabilistic population codes to compute Bayes' rule, and train a neural network to compute approximate predictions by the method of maximum likelihood. In particular, we perform stochastic gradient descent on the negative log-likelihood with a novel approximation of the gradient. We demonstrate our methods on a finite-state, a linear, and a nonlinear filtering problem, and show how the hidden layer of the neural network develops tuning curves which are consistent with findings in experimental neuroscience.

The Expectation-Maximization (EM) algorithm is a widely used method for maximum likelihood estimation in models with latent variables. For estimating mixtures of Gaussians, its iteration can be viewed as a soft version of the k-means clustering algorithm. Despite its wide use and applications, there are essentially no known convergence guarantees for this method. We provide global convergence guarantees for mixtures of two Gaussians with known covariance matrices. We show that the population version of EM, where the algorithm is given access to infinitely many samples from the mixture, converges geometrically to the correct mean vectors, and provide simple, closed-form expressions for the convergence rate. As a simple illustration, we show that, in one dimension, ten steps of the EM algorithm initialized at infinity result in less than 1\% error estimation of the means. In the finite sample regime, we show that, under a random initialization, $\tilde{O}(d/\epsilon^2)$ samples suffice to compute the unknown vectors to within $\epsilon$ in Mahalanobis distance, where $d$ is the dimension. In particular, the error rate of the EM based estimator is $\tilde{O}\left(\sqrt{d \over n}\right)$ where $n$ is the number of samples, which is optimal up to logarithmic factors.