Invertible Gaussian Reparameterization: Revisiting the Gumbel-Softmax

The Gumbel-Softmax is a continuous distribution over the simplex that is often used as a relaxation of discrete distributions. Because it can be readily interpreted and easily reparameterized, it enjoys widespread use. Unfortunately, we show that the cost of this aesthetic interpretability is material: the temperature hyperparameter must be set too high, KL estimates are noisy, and as a result, performance suffers. We circumvent the previous issues by proposing a much simpler and more flexible reparameterizable family of distributions that transforms Gaussian noise into a one-hot approximation through an invertible function. This invertible function is composed of a modified softmax and can incorporate diverse transformations that serve different specific purposes. For example, the stick-breaking procedure allows us to extend the reparameterization trick to distributions with countably infinite support, or normalizing flows let us increase the flexibility of the distribution. Our construction improves numerical stability and outperforms the Gumbel-Softmax in a variety of experiments while generating samples that are closer to their discrete counterparts and achieving lower-variance gradients.

Paraphrase Generation with Latent Bag of Words

Paraphrase generation is a longstanding important problem in natural language processing. In addition, recent progress in deep generative models has shown promising results on discrete latent variables for text generation. Inspired by variational autoencoders with discrete latent structures, in this work, we propose a latent bag of words (BOW) model for paraphrase generation. We ground the semantics of a discrete latent variable by the BOW from the target sentences. We use this latent variable to build a fully differentiable content planning and surface realization model. Specifically, we use source words to predict their neighbors and model the target BOW with a mixture of softmax. We use Gumbel top-k reparameterization to perform differentiable subset sampling from the predicted BOW distribution. We retrieve the sampled word embeddings and use them to augment the decoder and guide its generation search space. Our latent BOW model not only enhances the decoder, but also exhibits clear interpretability. We show the model interpretability with regard to \emph{(i)} unsupervised learning of word neighbors \emph{(ii)} the step-by-step generation procedure. Extensive experiments demonstrate the transparent and effective generation process of this model.\footnote{Our code can be found at \url{https://github.com/FranxYao/dgm_latent_bow}}

The continuous Bernoulli: fixing a pervasive error in variational autoencoders

Variational autoencoders (VAE) have quickly become a central tool in machine learning, applicable to a broad range of data types and latent variable models. By far the most common first step, taken by seminal papers and by core software libraries alike, is to model MNIST data using a deep network parameterizing a Bernoulli likelihood. This practice contains what appears to be and what is often set aside as a minor inconvenience: the pixel data is [0,1] valued, not {0,1} as supported by the Bernoulli likelihood. Here we show that, far from being a triviality or nuisance that is convenient to ignore, this error has profound importance to VAE, both qualitative and quantitative. We introduce and fully characterize a new [0,1]-supported, single parameter distribution: the continuous Bernoulli, which patches this pervasive bug in VAE. This distribution is not nitpicking; it produces meaningful performance improvements across a range of metrics and datasets, including sharper image samples, and suggests a broader class of performant VAE.

Approximating exponential family models (not single distributions) with a two-network architecture

Recently much attention has been paid to deep generative models, since they have been used to great success for variational inference, generation of complex data types, and more. In most all of these settings, the goal has been to find a particular member of that model family: optimized parameters index a distribution that is close (via a divergence or classification metric) to a target distribution. Much less attention, however, has been paid to the problem of learning a model itself. Here we introduce a two-network architecture and optimization procedure for learning intractable exponential family models (not a single distribution from those models). These exponential families are learned accurately, allowing operations like posterior inference to be executed directly and generically with an input choice of natural parameters, rather than performing inference via optimization for each particular distribution within that model.

Deep Random Splines for Point Process Intensity Estimation

Gaussian processes are the leading class of distributions on random functions, but they suffer from well known issues including difficulty scaling and inflexibility with respect to certain shape constraints (such as nonnegativity). Here we propose Deep Random Splines, a flexible class of random functions obtained by transforming Gaussian noise through a deep neural network whose output are the parameters of a spline. Unlike Gaussian processes, Deep Random Splines allow us to readily enforce shape constraints while inheriting the richness and tractability of deep generative models. We also present an observational model for point process data which uses Deep Random Splines to model the intensity function of each point process and apply it to neuroscience data to obtain a low-dimensional representation of spiking activity. Inference is performed via a variational autoencoder that uses a novel recurrent encoder architecture that can handle multiple point processes as input.

A Probabilistic Model of Cardiac Physiology and Electrocardiograms

An electrocardiogram (EKG) is a common, non-invasive test that measures the electrical activity of a patient's heart. EKGs contain useful diagnostic information about patient health that may be absent from other electronic health record (EHR) data. As multi-dimensional waveforms, they could be modeled using generic machine learning tools, such as a linear factor model or a variational autoencoder. We take a different approach:~we specify a model that directly represents the underlying electrophysiology of the heart and the EKG measurement process. We apply our model to two datasets, including a sample of emergency department EKG reports with missing data. We show that our model can more accurately reconstruct missing data (measured by test reconstruction error) than a standard baseline when there is significant missing data. More broadly, this physiological representation of heart function may be useful in a variety of settings, including prediction, causal analysis, and discovery.

Calibrating Deep Convolutional Gaussian Processes

The wide adoption of Convolutional Neural Networks (CNNs) in applications where decision-making under uncertainty is fundamental, has brought a great deal of attention to the ability of these models to accurately quantify the uncertainty in their predictions. Previous work on combining CNNs with Gaussian processes (GPs) has been developed under the assumption that the predictive probabilities of these models are well-calibrated. In this paper we show that, in fact, current combinations of CNNs and GPs are miscalibrated. We proposes a novel combination that considerably outperforms previous approaches on this aspect, while achieving state-of-the-art performance on image classification tasks.

Bayesian estimation for large scale multivariate Ornstein-Uhlenbeck model of brain connectivity

Estimation of reliable whole-brain connectivity is a crucial step towards the use of connectivity information in quantitative approaches to the study of neuropsychiatric disorders. When estimating brain connectivity a challenge is imposed by the paucity of time samples and the large dimensionality of the measurements. Bayesian estimation methods for network models offer a number of advantages in this context but are not commonly employed. Here we compare three different estimation methods for the multivariate Ornstein-Uhlenbeck model, that has recently gained some popularity for characterizing whole-brain connectivity. We first show that a Bayesian estimation of model parameters assuming uniform priors is equivalent to an application of the method of moments. Then, using synthetic data, we show that the Bayesian estimate scales poorly with number of nodes in the network as compared to an iterative Lyapunov optimization. In particular when the network size is in the order of that used for whole-brain studies (about 100 nodes) the Bayesian method needs about eight times more time samples than Lyapunov method in order to achieve similar estimation accuracy. We also show that the higher estimation accuracy of Lyapunov method is reflected in a much better classification of individuals based on the estimated connectivity from a real dataset of BOLD fMRI. Finally we show that the poor accuracy of Bayesian method is due to numerical errors, when the imaginary part of the connectivity estimate gets large compared to its real part.