This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100036). Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian inference for models associated with intractable likelihood functions. Most ABC implementations require the preliminary selection of a vector of informative statistics summarizing raw data. Furthermore, in almost all existing implementations, the tolerance level that separates acceptance from rejection of simulated parameter values needs to be calibrated. We propose to conduct likelihood-free Bayesian inferences about parameters with no prior selection of the relevant components of the summary statistics and bypassing the derivation of the associated tolerance level. The approach relies on the random forest methodology of Breiman (2001) applied in a (non parametric) regression setting. We advocate the derivation of a new random forest for each component of the parameter vector of interest. When compared with earlier ABC solutions, this method offers significant gains in terms of robustness to the choice of the summary statistics, does not depend on any type of tolerance level, and is a good trade-off in term of quality of point estimator precision and credible interval estimations for a given computing time. We illustrate the performance of our methodological proposal and compare it with earlier ABC methods on a Normal toy example and a population genetics example dealing with human population evolution. All methods designed here have been incorporated in the R package abcrf (version 1.7) available on CRAN.

This repository contains the Tensorflow implementation of the Bayesian GAN by Yunus Saatchi and Andrew Gordon Wilson. This paper will be appearing at NIPS 2017. In the Bayesian GAN we propose conditional posteriors for the generator and discriminator weights, and marginalize these posteriors through stochastic gradient Hamiltonian Monte Carlo. Key properties of the Bayesian approach to GANs include (1) accurate predictions on semi-supervised learning problems; (2) minimal intervention for good performance; (3) a probabilistic formulation for inference in response to adversarial feedback; (4) avoidance of mode collapse; and (5) a representation of multiple complementary generative and discriminative models for data, forming a probabilistic ensemble. We illustrate a multimodal posterior over the parameters of the generator.

The extended model(s) can again be subjected to criticism, and the process continues until a satisfactory model is found (O'Hagan, 2003). Model criticism is contrasted with model comparison in that model criticism assesses a single model, while model comparison deals with at least two models to decide which model is a better fit. Model comparison can be applied to compare the original and the extended model after model criticism and extension (O'Hagan, 2003, p. 2). Most work on model criticism makes use of the idea that "if the model fits, then replicated data generated under the model should look similar to observed data" (Gelman et al., 2004, p. 165). In contrast, in this paper we focus on the idea that for latent variable models, we can probabilistically pull back the data into the space of the latent variables, and carry out model criticism in that space.

Generalized linear models (GLMs) -- such as logistic regression, Poisson regression, and robust regression -- provide interpretable models for diverse data types. Probabilistic approaches, particularly Bayesian ones, allow coherent estimates of uncertainty, incorporation of prior information, and sharing of power across experiments via hierarchical models. In practice, however, the approximate Bayesian methods necessary for inference have either failed to scale to large data sets or failed to provide theoretical guarantees on the quality of inference. We propose a new approach based on constructing polynomial approximate sufficient statistics for GLMs (PASS-GLM). We demonstrate that our method admits a simple algorithm as well as trivial streaming and distributed extensions that do not compound error across computations. We provide theoretical guarantees on the quality of point (MAP) estimates, the approximate posterior, and posterior mean and uncertainty estimates. We validate our approach empirically in the case of logistic regression using a quadratic approximation and show competitive performance with stochastic gradient descent, MCMC, and the Laplace approximation in terms of speed and multiple measures of accuracy -- including on an advertising data set with 40 million data points and 20,000 covariates.

Efficiently aggregating data from different sources is a challenging problem, particularly when samples from each source are distributed differently. These differences can be inherent to the inference task or present for other reasons: sensors in a sensor network may be placed far apart, affecting their individual measurements. Conversely, it is computationally advantageous to split Bayesian inference tasks across subsets of data, but data need not be identically distributed across subsets. One principled way to fuse probability distributions is via the lens of optimal transport: the Wasserstein barycenter is a single distribution that summarizes a collection of input measures while respecting their geometry. However, computing the barycenter scales poorly and requires discretization of all input distributions and the barycenter itself. Improving on this situation, we present a scalable, communication-efficient, parallel algorithm for computing the Wasserstein barycenter of arbitrary distributions. Our algorithm can operate directly on continuous input distributions and is optimized for streaming data. Our method is even robust to nonstationary input distributions and produces a barycenter estimate that tracks the input measures over time. The algorithm is semi-discrete, needing to discretize only the barycenter estimate. To the best of our knowledge, we also provide the first bounds on the quality of the approximate barycenter as the discretization becomes finer. Finally, we demonstrate the practical effectiveness of our method, both in tracking moving distributions on a sphere, as well as in a large-scale Bayesian inference task.

When used as a surrogate objective for maximum likelihood estimation in latent variable models, the evidence lower bound (ELBO) produces state-of-the-art results. Inspired by this, we consider the extension of the ELBO to a family of lower bounds defined by a particle filter's estimator of the marginal likelihood, the filtering variational objectives (FIVOs). FIVOs take the same arguments as the ELBO, but can exploit a model's sequential structure to form tighter bounds. We present results that relate the tightness of FIVO's bound to the variance of the particle filter's estimator by considering the generic case of bounds defined as log-transformed likelihood estimators. Experimentally, we show that training with FIVO results in substantial improvements over training the same model architecture with the ELBO on sequential data.

Epileptic seizure activity shows complicated dynamics in both space and time. To understand the evolution and propagation of seizures spatially extended sets of data need to be analysed. We have previously described an efficient filtering scheme using variational Laplace that can be used in the Dynamic Causal Modelling (DCM) framework [Friston, 2003] to estimate the temporal dynamics of seizures recorded using either invasive or non-invasive electrical recordings (EEG/ECoG). Spatiotemporal dynamics are modelled using a partial differential equation -- in contrast to the ordinary differential equation used in our previous work on temporal estimation of seizure dynamics [Cooray, 2016]. We provide the requisite theoretical background for the method and test the ensuing scheme on simulated seizure activity data and empirical invasive ECoG data. The method provides a framework to assimilate the spatial and temporal dynamics of seizure activity, an aspect of great physiological and clinical importance.

Many countries are suffering from severe air pollution. Understanding how different air pollutants accumulate and propagate is critical to making relevant public policies. In this paper, we use urban big data (air quality data and meteorological data) to identify the \emph{spatiotemporal (ST) causal pathways} for air pollutants. This problem is challenging because: (1) there are numerous noisy and low-pollution periods in the raw air quality data, which may lead to unreliable causality analysis, (2) for large-scale data in the ST space, the computational complexity of constructing a causal structure is very high, and (3) the \emph{ST causal pathways} are complex due to the interactions of multiple pollutants and the influence of environmental factors. Therefore, we present \emph{p-Causality}, a novel pattern-aided causality analysis approach that combines the strengths of \emph{pattern mining} and \emph{Bayesian learning} to efficiently and faithfully identify the \emph{ST causal pathways}. First, \emph{Pattern mining} helps suppress the noise by capturing frequent evolving patterns (FEPs) of each monitoring sensor, and greatly reduce the complexity by selecting the pattern-matched sensors as "causers". Then, \emph{Bayesian learning} carefully encodes the local and ST causal relations with a Gaussian Bayesian network (GBN)-based graphical model, which also integrates environmental influences to minimize biases in the final results. We evaluate our approach with three real-world data sets containing 982 air quality sensors, in three regions of China from 01-Jun-2013 to 19-Dec-2015. Results show that our approach outperforms the traditional causal structure learning methods in time efficiency, inference accuracy and interpretability.

Gaussian multiplicative noise is commonly used as a stochastic regularisation technique in training of deterministic neural networks. A recent paper reinterpreted the technique as a specific algorithm for approximate inference in Bayesian neural networks; several extensions ensued. We show that the log-uniform prior used in all the above publications does not generally induce a proper posterior, and thus Bayesian inference in such models is ill-posed. Independent of the log-uniform prior, the correlated weight noise approximation has further issues leading to either infinite objective or high risk of overfitting. The above implies that the reported sparsity of obtained solutions cannot be explained by Bayesian or the related minimum description length arguments. We thus study the objective from a non-Bayesian perspective, provide its previously unknown analytical form which allows exact gradient evaluation, and show that the later proposed additive reparametrisation introduces minima not present in the original multiplicative parametrisation. Implications and future research directions are discussed.

This work brings together two powerful concepts in Gaussian processes: the variational approach to sparse approximation and the spectral representation of Gaussian processes. This gives rise to an approximation that inherits the benefits of the variational approach but with the representational power and computational scalability of spectral representations. The work hinges on a key result that there exist spectral features related to a finite domain of the Gaussian process which exhibit almost-independent covariances. We derive these expressions for Matern kernels in one dimension, and generalize to more dimensions using kernels with specific structures. Under the assumption of additive Gaussian noise, our method requires only a single pass through the dataset, making for very fast and accurate computation. We fit a model to 4 million training points in just a few minutes on a standard laptop. With non-conjugate likelihoods, our MCMC scheme reduces the cost of computation from O(NM2) (for a sparse Gaussian process) to O(NM) per iteration, where N is the number of data and M is the number of features.