The variational autoencoder (VAE) is a popular model for density estimation and representation learning. Canonically, the variational principle suggests to prefer an expressive inference model so that the variational approximation is accurate. However, it is often overlooked that an overly-expressive inference model can be detrimental to the test set performance of both the amortized posterior approximator and, more importantly, the generative density estimator. In this paper, we leverage the fact that VAEs rely on amortized inference and propose techniques for amortized inference regularization (AIR) that control the smoothness of the inference model. We demonstrate that, by applying AIR, it is possible to improve VAE generalization on both inference and generative performance. Our paper challenges the belief that amortized inference is simply a mechanism for approximating maximum likelihood training and illustrates that regularization of the amortization family provides a new direction for understanding and improving generalization in VAEs.

Effective implementations of sampling-based probabilistic inference often require manually constructed, model-specific proposals. Inspired by recent progresses in meta-learning for training learning agents that can generalize to unseen environments, we propose a meta-learning approach to building effective and generalizable MCMC proposals. We parametrize the proposal as a neural network to provide fast approximations to block Gibbs conditionals. The learned neural proposals generalize to occurrences of common structural motifs across different models, allowing for the construction of a library of learned inference primitives that can accelerate inference on unseen models with no model-specific training required. We explore several applications including open-universe Gaussian mixture models, in which our learned proposals outperform a hand-tuned sampler, and a real-world named entity recognition task, in which our sampler yields higher final F1 scores than classical single-site Gibbs sampling.

We propose a new approach, called cooperative neural networks (CoNN), which use a set of cooperatively trained neural networks to capture latent representations that exploit prior given independence structure. The model is more flexible than traditional graphical models based on exponential family distributions, but incorporates more domain specific prior structure than traditional deep networks or variational autoencoders. The framework is very general and can be used to exploit the independence structure of any graphical model. We illustrate the technique by showing that we can transfer the independence structure of the popular Latent Dirichlet Allocation (LDA) model to a cooperative neural network, CoNN-sLDA. Empirical evaluation of CoNN-sLDA on supervised text classification tasks demonstrate that the theoretical advantages of prior independence structure can be realized in practice - we demonstrate a 23 percent reduction in error on the challenging MultiSent data set compared to state-of-the-art.

Deep latent variable models (DLVMs) combine the approximation abilities of deep neural networks and the statistical foundations of generative models. Variational methods are commonly used for inference; however, the exact likelihood of these models has been largely overlooked. The purpose of this work is to study the general properties of this quantity and to show how they can be leveraged in practice. We focus on important inferential problems that rely on the likelihood: estimation and missing data imputation. First, we investigate maximum likelihood estimation for DLVMs: in particular, we show that most unconstrained models used for continuous data have an unbounded likelihood function. This problematic behaviour is demonstrated to be a source of mode collapse. We also show how to ensure the existence of maximum likelihood estimates, and draw useful connections with nonparametric mixture models. Finally, we describe an algorithm for missing data imputation using the exact conditional likelihood of a DLVM. On several data sets, our algorithm consistently and significantly outperforms the usual imputation scheme used for DLVMs.

We consider the problem of estimating the differences between two causal directed acyclic graph (DAG) models with a shared topological order given i.i.d. samples from each model. This is of interest for example in genomics, where changes in the structure or edge weights of the underlying causal graphs reflect alterations in the gene regulatory networks. We here provide the first provably consistent method for directly estimating the differences in a pair of causal DAGs without separately learning two possibly large and dense DAG models and computing their difference. Our two-step algorithm first uses invariance tests between regression coefficients of the two data sets to estimate the skeleton of the difference graph and then orients some of the edges using invariance tests between regression residual variances. We demonstrate the properties of our method through a simulation study and apply it to the analysis of gene expression data from ovarian cancer and during T-cell activation.

We introduce the Kronecker factored online Laplace approximation for overcoming catastrophic forgetting in neural networks. The method is grounded in a Bayesian online learning framework, where we recursively approximate the posterior after every task with a Gaussian, leading to a quadratic penalty on changes to the weights. The Laplace approximation requires calculating the Hessian around a mode, which is typically intractable for modern architectures. In order to make our method scalable, we leverage recent block-diagonal Kronecker factored approximations to the curvature. Our algorithm achieves over 90% test accuracy across a sequence of 50 instantiations of the permuted MNIST dataset, substantially outperforming related methods for overcoming catastrophic forgetting.

Recent advances in recording technologies have allowed neuroscientists to record simultaneous spiking activity from hundreds to thousands of neurons in multiple brain regions. Such large-scale recordings pose a major challenge to existing statistical methods for neural data analysis. Here we develop highly scalable approximate inference methods for Poisson generalized linear models (GLMs) that require only a single pass over the data. Our approach relies on a recently proposed method for obtaining approximate sufficient statistics for GLMs using polynomial approximations [Huggins et al., 2017], which we adapt to the Poisson GLM setting. We focus on inference using quadratic approximations to nonlinear terms in the Poisson GLM log-likelihood with Gaussian priors, for which we derive closed-form solutions to the approximate maximum likelihood and MAP estimates, posterior distribution, and marginal likelihood. We introduce an adaptive procedure to select the polynomial approximation interval and show that the resulting method allows for efficient and accurate inference and regularization of high-dimensional parameters. We use the quadratic estimator to fit a fully-coupled Poisson GLM to spike train data recorded from 831 neurons across five regions of the mouse brain for a duration of 41 minutes, binned at 1 ms resolution. Across all neurons, this model is fit to over 2 billion spike count bins and identifies fine-timescale statistical dependencies between neurons within and across cortical and subcortical areas.

Gaussian processes provide a flexible framework for forecasting, removing noise, and interpreting long temporal datasets. State space modelling (Kalman filtering) enables these non-parametric models to be deployed on long datasets by reducing the complexity to linear in the number of data points. The complexity is still cubic in the state dimension m which is an impediment to practical application. In certain special cases (Gaussian likelihood, regular spacing) the GP posterior will reach a steady posterior state when the data are very long. We leverage this and formulate an inference scheme for GPs with general likelihoods, where inference is based on single-sweep EP (assumed density filtering). The infinite-horizon model tackles the cubic cost in the state dimensionality and reduces the cost in the state dimension m to O(m^2) per data point. The model is extended to online-learning of hyperparameters. We show examples for large finite-length modelling problems, and present how the method runs in real-time on a smartphone on a continuous data stream updated at 100 Hz.

In this paper we present a hybrid active sampling strategy for pairwise preference aggregation, which aims at recovering the underlying rating of the test candidates from sparse and noisy pairwise labelling. Our method employs Bayesian optimization frameworkand Bradley-Terry model to construct the utility function, then to obtain the Expected Information Gain (EIG) of each pair. For computational efficiency, Gaussian-Hermite quadrature is used for estimation of EIG. In this work, a hybrid active sampling strategy is proposed, either using Global Maximum (GM) EIG sampling or Minimum Spanning Tree (MST) sampling in each trial, which is determined by the test budget. The proposed method has been validated on both simulated and real-world datasets, where it shows higher preference aggregation ability than the state-of-the-art methods.

We present an approach for simultaneously separating and localizing multiple sound sources using recorded microphone data. Inspired by topic models, our approach is based on a probabilistic model of inter-microphone phase differences, and poses separation and localization as a Bayesian inference problem. We assume sound activity is locally smooth across time, frequency, and location, and use the known position of the microphones to obtain a consistent separation. We compare the performance of our method against existing algorithms on simulated anechoic voice data and find that it obtains high performance across a variety of input conditions.