Automatic Variational Inference in Stan

Variational inference is a scalable technique for approximate Bayesian inference. Deriving variational inference algorithms requires tedious model-specific calculations; this makes it difficult to automate. We propose an automatic variational inference algorithm, automatic differentiation variational inference (ADVI). The user only provides a Bayesian model and a dataset; nothing else. We make no conjugacy assumptions and support a broad class of models. The algorithm automatically determines an appropriate variational family and optimizes the variational objective. We implement ADVI in Stan (code available now), a probabilistic programming framework. We compare ADVI to MCMC sampling across hierarchical generalized linear models, nonconjugate matrix factorization, and a mixture model. We train the mixture model on a quarter million images. With ADVI we can use variational inference on any model we write in Stan

Automatic Differentiation Variational Inference

Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist only provides a probabilistic model and a dataset, nothing else. ADVI automatically derives an efficient variational inference algorithm, freeing the scientist to refine and explore many models. ADVI supports a broad class of models-no conjugacy assumptions are required. We study ADVI across ten different models and apply it to a dataset with millions of observations. ADVI is integrated into Stan, a probabilistic programming system; it is available for immediate use

Linear State-Space Model with Time-Varying Dynamics

This paper introduces a linear state-space model with time-varying dynamics. The time dependency is obtained by forming the state dynamics matrix as a time-varying linear combination of a set of matrices. The time dependency of the weights in the linear combination is modelled by another linear Gaussian dynamical model allowing the model to learn how the dynamics of the process changes. Previous approaches have used switching models which have a small set of possible state dynamics matrices and the model selects one of those matrices at each time, thus jumping between them. Our model forms the dynamics as a linear combination and the changes can be smooth and more continuous. The model is motivated by physical processes which are described by linear partial differential equations whose parameters vary in time. An example of such a process could be a temperature field whose evolution is driven by a varying wind direction. The posterior inference is performed using variational Bayesian approximation. The experiments on stochastic advection-diffusion processes and real-world weather processes show that the model with time-varying dynamics can outperform previously introduced approaches.Comment: The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-662-44851-9_2

Bayesian Deep Net GLM and GLMM

Deep feedforward neural networks (DFNNs) are a powerful tool for functional approximation. We describe flexible versions of generalized linear and generalized linear mixed models incorporating basis functions formed by a DFNN. The consideration of neural networks with random effects is not widely used in the literature, perhaps because of the computational challenges of incorporating subject specific parameters into already complex models. Efficient computational methods for high-dimensional Bayesian inference are developed using Gaussian variational approximation, with a parsimonious but flexible factor parametrization of the covariance matrix. We implement natural gradient methods for the optimization, exploiting the factor structure of the variational covariance matrix in computation of the natural gradient. Our flexible DFNN models and Bayesian inference approach lead to a regression and classification method that has a high prediction accuracy, and is able to quantify the prediction uncertainty in a principled and convenient way. We also describe how to perform variable selection in our deep learning method. The proposed methods are illustrated in a wide range of simulated and real-data examples, and the results compare favourably to a state of the art flexible regression and classification method in the statistical literature, the Bayesian additive regression trees (BART) method. User-friendly software packages in Matlab, R and Python implementing the proposed methods are available at https://github.com/VBayesLabComment: 35 pages, 7 figure, 10 table

Lightweight Probabilistic Deep Networks

Even though probabilistic treatments of neural networks have a long history, they have not found widespread use in practice. Sampling approaches are often too slow already for simple networks. The size of the inputs and the depth of typical CNN architectures in computer vision only compound this problem. Uncertainty in neural networks has thus been largely ignored in practice, despite the fact that it may provide important information about the reliability of predictions and the inner workings of the network. In this paper, we introduce two lightweight approaches to making supervised learning with probabilistic deep networks practical: First, we suggest probabilistic output layers for classification and regression that require only minimal changes to existing networks. Second, we employ assumed density filtering and show that activation uncertainties can be propagated in a practical fashion through the entire network, again with minor changes. Both probabilistic networks retain the predictive power of the deterministic counterpart, but yield uncertainties that correlate well with the empirical error induced by their predictions. Moreover, the robustness to adversarial examples is significantly increased.Comment: To appear at CVPR 201

Multi-view Learning as a Nonparametric Nonlinear Inter-Battery Factor Analysis

Factor analysis aims to determine latent factors, or traits, which summarize a given data set. Inter-battery factor analysis extends this notion to multiple views of the data. In this paper we show how a nonlinear, nonparametric version of these models can be recovered through the Gaussian process latent variable model. This gives us a flexible formalism for multi-view learning where the latent variables can be used both for exploratory purposes and for learning representations that enable efficient inference for ambiguous estimation tasks. Learning is performed in a Bayesian manner through the formulation of a variational compression scheme which gives a rigorous lower bound on the log likelihood. Our Bayesian framework provides strong regularization during training, allowing the structure of the latent space to be determined efficiently and automatically. We demonstrate this by producing the first (to our knowledge) published results of learning from dozens of views, even when data is scarce. We further show experimental results on several different types of multi-view data sets and for different kinds of tasks, including exploratory data analysis, generation, ambiguity modelling through latent priors and classification.Comment: 49 pages including appendi