Black box variational inference allows researchers to easily prototype and evaluate an array of models. Recent advances allow such algorithms to scale to high dimensions. However, a central question remains: How to specify an expressive variational distribution that maintains efficient computation? To address this, we develop hierarchical variational models (HVMs). HVMs augment a variational approximation with a prior on its parameters, which allows it to capture complex structure for both discrete and continuous latent variables. The algorithm we develop is black box, can be used for any HVM, and has the same computational efficiency as the original approximation. We study HVMs on a variety of deep discrete latent variable models. HVMs generalize other expressive variational distributions and maintains higher fidelity to the posterior.
Recent advances in neural variational inference have spawned a renaissance in deep latent variable models. In this paper we introduce a generic variational inference framework for generative and conditional models of text. While traditional variational methods derive an analytic approximation for the intractable distributions over latent variables, here we construct an inference network conditioned on the discrete text input to provide the variational distribution. We validate this framework on two very different text modelling applications, generative document modelling and supervised question answering. Our neural variational document model combines a continuous stochastic document representation with a bag-of-words generative model and achieves the lowest reported perplexities on two standard test corpora. The neural answer selection model employs a stochastic representation layer within an attention mechanism to extract the semantics between a question and answer pair. On two question answering benchmarks this model exceeds all previous published benchmarks.
Spreadsheet workbook contents are simple programs. Because of this, probabilistic programming techniques can be used to perform Bayesian inversion of spreadsheet computations. What is more, existing execution engines in spreadsheet applications such as Microsoft Excel can be made to do this using only built-in functionality. We demonstrate this by developing a native Excel implementation of both a particle Markov Chain Monte Carlo variant and black-box variational inference for spreadsheet probabilistic programming. The resulting engine performs probabilistically coherent inference over spreadsheet computations, notably including spreadsheets that include user-defined black-box functions. Spreadsheet engines that choose to integrate the functionality we describe in this paper will give their users the ability to both easily develop probabilistic models and maintain them over time by including actuals via a simple user-interface mechanism. For spreadsheet end-users this would mean having access to efficient and probabilistically coherent probabilistic modeling and inference for use in all kinds of decision making under uncertainty.
Approximate variational inference has shown to be a powerful tool for modeling unknown complex probability distributions. Recent advances in the field allow us to learn probabilistic models of sequences that actively exploit spatial and temporal structure. We apply a Stochastic Recurrent Network (STORN) to learn robot time series data. Our evaluation demonstrates that we can robustly detect anomalies both off- and on-line.
The choice of approximate posterior distribution is one of the core problems in variational inference. Most applications of variational inference employ simple families of posterior approximations in order to allow for efficient inference, focusing on mean-field or other simple structured approximations. This restriction has a significant impact on the quality of inferences made using variational methods. We introduce a new approach for specifying flexible, arbitrarily complex and scalable approximate posterior distributions. Our approximations are distributions constructed through a normalizing flow, whereby a simple initial density is transformed into a more complex one by applying a sequence of invertible transformations until a desired level of complexity is attained. We use this view of normalizing flows to develop categories of finite and infinitesimal flows and provide a unified view of approaches for constructing rich posterior approximations. We demonstrate that the theoretical advantages of having posteriors that better match the true posterior, combined with the scalability of amortized variational approaches, provides a clear improvement in performance and applicability of variational inference.
Approximate Bayesian Computation (ABC) is a framework for performing likelihood-free posterior inference for simulation models. Stochastic Variational inference (SVI) is an appealing alternative to the inefficient sampling approaches commonly used in ABC. However, SVI is highly sensitive to the variance of the gradient estimators, and this problem is exacerbated by approximating the likelihood. We draw upon recent advances in variance reduction for SV and likelihood-free inference using deterministic simulations to produce low variance gradient estimators of the variational lower-bound. By then exploiting automatic differentiation libraries we can avoid nearly all model-specific derivations. We demonstrate performance on three problems and compare to existing SVI algorithms. Our results demonstrate the correctness and efficiency of our algorithm.
Unsupervised learning on imbalanced data is challenging because, when given imbalanced data, current model is often dominated by the major category and ignores the categories with small amount of data. We develop a latent variable model that can cope with imbalanced data by dividing the latent space into a shared space and a private space. Based on Gaussian Process Latent Variable Models, we propose a new kernel formulation that enables the separation of latent space and derives an efficient variational inference method. The performance of our model is demonstrated with an imbalanced medical image dataset.
Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Time series data extracted from individual electronic health records (EHR) offer an exciting new way to study subtle differences in the way these diseases progress over time. In this paper, we focus on answering two questions that can be asked using these databases of time series. First, we want to understand whether there are individuals with similar disease trajectories and whether there are a small number of degrees of freedom that account for differences in trajectories across the population. Second, we want to understand how important clinical outcomes are associated with disease trajectories. To answer these questions, we propose the Disease Trajectory Map (DTM), a novel probabilistic model that learns low-dimensional representations of sparse and irregularly sampled time series. We propose a stochastic variational inference algorithm for learning the DTM that allows the model to scale to large modern medical datasets. To demonstrate the DTM, we analyze data collected on patients with the complex autoimmune disease, scleroderma. We find that DTM learns meaningful representations of disease trajectories and that the representations are significantly associated with important clinical outcomes.
The ability to backpropagate stochastic gradients through continuous latent distributions has been crucial to the emergence of variational autoencoders and stochastic gradient variational Bayes. The key ingredient is an unbiased and low-variance way of estimating gradients with respect to distribution parameters from gradients evaluated at distribution samples. The "reparameterization trick" provides a class of transforms yielding such estimators for many continuous distributions, including the Gaussian and other members of the location-scale family. However the trick does not readily extend to mixture density models, due to the difficulty of reparameterizing the discrete distribution over mixture weights. This report describes an alternative transform, applicable to any continuous multivariate distribution with a differentiable density function from which samples can be drawn, and uses it to derive an unbiased estimator for mixture density weight derivatives. Combined with the reparameterization trick applied to the individual mixture components, this estimator makes it straightforward to train variational autoencoders with mixture-distributed latent variables, or to perform stochastic variational inference with a mixture density variational posterior.
Community detection has been an active research area for decades. Among all probabilistic models, Stochastic Block Model has been the most popular one. This paper introduces a novel probabilistic model: RW-HDP, based on random walks and Hierarchical Dirichlet Process, for community extraction. In RW-HDP, random walks conducted in a social network are treated as documents; nodes are treated as words. By using Hierarchical Dirichlet Process, a nonparametric Bayesian model, we are not only able to cluster nodes into different communities, but also determine the number of communities automatically. We use Stochastic Variational Inference for our model inference, which makes our method time efficient and can be easily extended to an online learning algorithm.
Word embedding maps words into a low-dimensional continuous embedding space by exploiting the local word collocation patterns in a small context window. On the other hand, topic modeling maps documents onto a low-dimensional topic space, by utilizing the global word collocation patterns in the same document. These two types of patterns are complementary. In this paper, we propose a generative topic embedding model to combine the two types of patterns. In our model, topics are represented by embedding vectors, and are shared across documents. The probability of each word is influenced by both its local context and its topic. A variational inference method yields the topic embeddings as well as the topic mixing proportions for each document. Jointly they represent the document in a low-dimensional continuous space. In two document classification tasks, our method performs better than eight existing methods, with fewer features. In addition, we illustrate with an example that our method can generate coherent topics even based on only one document.
Several recent works have explored stochastic gradient methods for variational inference that exploit the geometry of the variational-parameter space. However, the theoretical properties of these methods are not well-understood and these methods typically only apply to conditionally-conjugate models. We present a new stochastic method for variational inference which exploits the geometry of the variational-parameter space and also yields simple closed-form updates even for non-conjugate models. We also give a convergence-rate analysis of our method and many other previous methods which exploit the geometry of the space. Our analysis generalizes existing convergence results for stochastic mirror-descent on non-convex objectives by using a more general class of divergence functions. Beyond giving a theoretical justification for a variety of recent methods, our experiments show that new algorithms derived in this framework lead to state of the art results on a variety of problems. Further, due to its generality, we expect that our theoretical analysis could also apply to other applications.
Prediction of the future trajectory of a disease is an important challenge for personalized medicine and population health management. However, many complex chronic diseases exhibit large degrees of heterogeneity, and furthermore there is not always a single readily available biomarker to quantify disease severity. Even when such a clinical variable exists, there are often additional related biomarkers routinely measured for patients that may better inform the predictions of their future disease state. To this end, we propose a novel probabilistic generative model for multivariate longitudinal data that captures dependencies between multivariate trajectories. We use a Gaussian process based regression model for each individual trajectory, and build off ideas from latent class models to induce dependence between their mean functions. We fit our method using a scalable variational inference algorithm to a large dataset of longitudinal electronic patient health records, and find that it improves dynamic predictions compared to a recent state of the art method. Our local accountable care organization then uses the model predictions during chart reviews of high risk patients with chronic kidney disease.
We propose a general purpose variational inference algorithm that forms a natural counterpart of gradient descent for optimization. Our method iteratively transports a set of particles to match the target distribution, by applying a form of functional gradient descent that minimizes the KL divergence. Empirical studies are performed on various real world models and datasets, on which our method is competitive with existing state-of-the-art methods. The derivation of our method is based on a new theoretical result that connects the derivative of KL divergence under smooth transforms with Stein's identity and a recently proposed kernelized Stein discrepancy, which is of independent interest.
Dense conditional random fields (CRF) with Gaussian pairwise potentials have emerged as a popular framework for several computer vision applications such as stereo correspondence and semantic segmentation. By modeling long-range interactions, dense CRFs provide a more detailed labelling compared to their sparse counterparts. Variational inference in these dense models is performed using a filtering-based mean-field algorithm in order to obtain a fully-factorized distribution minimising the Kullback-Leibler divergence to the true distribution. In contrast to the continuous relaxation-based energy minimisation algorithms used for sparse CRFs, the mean-field algorithm fails to provide strong theoretical guarantees on the quality of its solutions. To address this deficiency, we show that it is possible to use the same filtering approach to speed-up the optimisation of several continuous relaxations. Specifically, we solve a convex quadratic programming (QP) relaxation using the efficient Frank-Wolfe algorithm. This also allows us to solve difference-of-convex relaxations via the iterative concave-convex procedure where each iteration requires solving a convex QP. Finally, we develop a novel divide-and-conquer method to compute the subgradients of a linear programming relaxation that provides the best theoretical bounds for energy minimisation. We demonstrate the advantage of continuous relaxations over the widely used mean-field algorithm on publicly available datasets.
We develop an automated variational inference method for Bayesian structured prediction problems with Gaussian process (GP) priors and linear-chain likelihoods. Our approach does not need to know the details of the structured likelihood model and can scale up to a large number of observations. Furthermore, we show that the required expected likelihood term and its gradients in the variational objective (ELBO) can be estimated efficiently by using expectations over very low-dimensional Gaussian distributions. Optimization of the ELBO is fully parallelizable over sequences and amenable to stochastic optimization, which we use along with control variate techniques and state-of-the-art incremental optimization to make our framework useful in practice. Results on a set of natural language processing tasks show that our method can be as good as (and sometimes better than) hard-coded approaches including SVM-struct and CRFs, and overcomes the scalability limitations of previous inference algorithms based on sampling. Overall, this is a fundamental step to developing automated inference methods for Bayesian structured prediction.
Variational inference lies at the core of many state-of-the-art algorithms. To improve the approximation of the posterior beyond parametric families, it was proposed to include MCMC steps into the variational lower bound. In this work we explore this idea using steps of the Hamiltonian Monte Carlo (HMC) algorithm, an efficient MCMC method. In particular, we incorporate the acceptance step of the HMC algorithm, guaranteeing asymptotic convergence to the true posterior. Additionally, we introduce some extensions to the HMC algorithm geared towards faster convergence. The theoretical advantages of these modifications are reflected by performance improvements in our experimental results.
We present a new method for identifying the latent categorization of items based on their rankings. Complimenting a recent work that uses a Dirichlet prior on preference vectors and variational inference, we show that this problem can be effectively dealt with using existing community detection algorithms, with the communities corresponding to item categories. In particular we convert the bipartite ranking data to a unipartite graph of item affinities, and apply community detection algorithms. In this context we modify an existing algorithm - namely the label propagation algorithm to a variant that uses the distance between the nodes for weighting the label propagation - to identify the categories. We propose and analyze a synthetic ordinal ranking model and show its relation to the recently much studied stochastic block model. We test our algorithms on synthetic data and compare performance with several popular community detection algorithms. We also test the method on real data sets of movie categorization from the Movie Lens database. In all of the cases our algorithm is able to identify the categories for a suitable choice of tuning parameter.
Recurrent neural networks (RNNs) stand at the forefront of many recent developments in deep learning. Yet a major difficulty with these models is their tendency to overfit, with dropout shown to fail when applied to recurrent layers. Recent results at the intersection of Bayesian modelling and deep learning offer a Bayesian interpretation of common deep learning techniques such as dropout. This grounding of dropout in approximate Bayesian inference suggests an extension of the theoretical results, offering insights into the use of dropout with RNN models. We apply this new variational inference based dropout technique in LSTM and GRU models, assessing it on language modelling and sentiment analysis tasks. The new approach outperforms existing techniques, and to the best of our knowledge improves on the single model state-of-the-art in language modelling with the Penn Treebank (73.4 test perplexity). This extends our arsenal of variational tools in deep learning.
The reparameterization gradient has become a widely used method to obtain Monte Carlo gradients to optimize the variational objective. However, this technique does not easily apply to commonly used distributions such as beta or gamma without further approximations, and most practical applications of the reparameterization gradient fit Gaussian distributions. In this paper, we introduce the generalized reparameterization gradient, a method that extends the reparameterization gradient to a wider class of variational distributions. Generalized reparameterizations use invertible transformations of the latent variables which lead to transformed distributions that weakly depend on the variational parameters. This results in new Monte Carlo gradients that combine reparameterization gradients and score function gradients. We demonstrate our approach on variational inference for two complex probabilistic models. The generalized reparameterization is effective: even a single sample from the variational distribution is enough to obtain a low-variance gradient.