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David M. Blei

Publications and source records attributed to David M. Blei.

At least 91 records · Page 5Linked to original sources
arXiv2018

Black Box FDR

Analyzing large-scale, multi-experiment studies requires scientists to test each experimental outcome for statistical significance and then assess the results as a whole. We present Black Box FDR (BB-FDR), an empirical-Bayes method for analyzing multi-experiment studies when many covariates are gathered per experiment. BB-FDR learns a series of black box predictive models to boost power and control the false discovery rate (FDR) at two stages of study analysis. In Stage 1, it uses a deep neural network prior to report which experiments yielded significant outcomes. In Stage 2, a separate black box model of each covariate is used to select features that have significant predictive power across all experiments. In benchmarks, BB-FDR outperforms competing state-of-the-art methods in both stages of analysis. We apply BB-FDR to two real studies on cancer drug efficacy. For both studies, BB-FDR increases the proportion of significant outcomes discovered and selects variables that reveal key genomic drivers of drug sensitivity and resistance in cancer.

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arXiv2018

Augment and Reduce: Stochastic Inference for Large Categorical Distributions

Categorical distributions are ubiquitous in machine learning, e.g., in classification, language models, and recommendation systems. However, when the number of possible outcomes is very large, using categorical distributions becomes computationally expensive, as the complexity scales linearly with the number of outcomes. To address this problem, we propose augment and reduce (A&R), a method to alleviate the computational complexity. A&R uses two ideas: latent variable augmentation and stochastic variational inference. It maximizes a lower bound on the marginal likelihood of the data. Unlike existing methods which are specific to softmax, A&R is more general and is amenable to other categorical models, such as multinomial probit. On several large-scale classification problems, we show that A&R provides a tighter bound on the marginal likelihood and has better predictive performance than existing approaches.

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arXiv2018

Variational Inference: A Review for Statisticians

One of the core problems of modern statistics is to approximate difficult-to-compute probability densities. This problem is especially important in Bayesian statistics, which frames all inference about unknown quantities as a calculation involving the posterior density. In this paper, we review variational inference (VI), a method from machine learning that approximates probability densities through optimization. VI has been used in many applications and tends to be faster than classical methods, such as Markov chain Monte Carlo sampling. The idea behind VI is to first posit a family of densities and then to find the member of that family which is close to the target. Closeness is measured by Kullback-Leibler divergence. We review the ideas behind mean-field variational inference, discuss the special case of VI applied to exponential family models, present a full example with a Bayesian mixture of Gaussians, and derive a variant that uses stochastic optimization to scale up to massive data. We discuss modern research in VI and highlight important open problems. VI is powerful, but it is not yet well understood. Our hope in writing this paper is to catalyze statistical research on this class of algorithms.

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arXiv2018

Equation Embeddings

We present an unsupervised approach for discovering semantic representations of mathematical equations. Equations are challenging to analyze because each is unique, or nearly unique. Our method, which we call equation embeddings, finds good representations of equations by using the representations of their surrounding words. We used equation embeddings to analyze four collections of scientific articles from the arXiv, covering four computer science domains (NLP, IR, AI, and ML) and $\sim$98.5k equations. Quantitatively, we found that equation embeddings provide better models when compared to existing word embedding approaches. Qualitatively, we found that equation embeddings provide coherent semantic representations of equations and can capture semantic similarity to other equations and to words.

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arXiv2018

Operator Variational Inference

Variational inference is an umbrella term for algorithms which cast Bayesian inference as optimization. Classically, variational inference uses the Kullback-Leibler divergence to define the optimization. Though this divergence has been widely used, the resultant posterior approximation can suffer from undesirable statistical properties. To address this, we reexamine variational inference from its roots as an optimization problem. We use operators, or functions of functions, to design variational objectives. As one example, we design a variational objective with a Langevin-Stein operator. We develop a black box algorithm, operator variational inference (OPVI), for optimizing any operator objective. Importantly, operators enable us to make explicit the statistical and computational tradeoffs for variational inference. We can characterize different properties of variational objectives, such as objectives that admit data subsampling---allowing inference to scale to massive data---as well as objectives that admit variational programs---a rich class of posterior approximations that does not require a tractable density. We illustrate the benefits of OPVI on a mixture model and a generative model of images.

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arXiv2018

Variational Sequential Monte Carlo

Many recent advances in large scale probabilistic inference rely on variational methods. The success of variational approaches depends on (i) formulating a flexible parametric family of distributions, and (ii) optimizing the parameters to find the member of this family that most closely approximates the exact posterior. In this paper we present a new approximating family of distributions, the variational sequential Monte Carlo (VSMC) family, and show how to optimize it in variational inference. VSMC melds variational inference (VI) and sequential Monte Carlo (SMC), providing practitioners with flexible, accurate, and powerful Bayesian inference. The VSMC family is a variational family that can approximate the posterior arbitrarily well, while still allowing for efficient optimization of its parameters. We demonstrate its utility on state space models, stochastic volatility models for financial data, and deep Markov models of brain neural circuits.

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arXiv2018

Stochastic Gradient Descent as Approximate Bayesian Inference

Stochastic Gradient Descent with a constant learning rate (constant SGD) simulates a Markov chain with a stationary distribution. With this perspective, we derive several new results. (1) We show that constant SGD can be used as an approximate Bayesian posterior inference algorithm. Specifically, we show how to adjust the tuning parameters of constant SGD to best match the stationary distribution to a posterior, minimizing the Kullback-Leibler divergence between these two distributions. (2) We demonstrate that constant SGD gives rise to a new variational EM algorithm that optimizes hyperparameters in complex probabilistic models. (3) We also propose SGD with momentum for sampling and show how to adjust the damping coefficient accordingly. (4) We analyze MCMC algorithms. For Langevin Dynamics and Stochastic Gradient Fisher Scoring, we quantify the approximation errors due to finite learning rates. Finally (5), we use the stochastic process perspective to give a short proof of why Polyak averaging is optimal. Based on this idea, we propose a scalable approximate MCMC algorithm, the Averaged Stochastic Gradient Sampler.

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arXiv2017

Variational Inference via $χ$-Upper Bound Minimization

Variational inference (VI) is widely used as an efficient alternative to Markov chain Monte Carlo. It posits a family of approximating distributions $q$ and finds the closest member to the exact posterior $p$. Closeness is usually measured via a divergence $D(q || p)$ from $q$ to $p$. While successful, this approach also has problems. Notably, it typically leads to underestimation of the posterior variance. In this paper we propose CHIVI, a black-box variational inference algorithm that minimizes $D_χ(p || q)$, the $χ$-divergence from $p$ to $q$. CHIVI minimizes an upper bound of the model evidence, which we term the $χ$ upper bound (CUBO). Minimizing the CUBO leads to improved posterior uncertainty, and it can also be used with the classical VI lower bound (ELBO) to provide a sandwich estimate of the model evidence. We study CHIVI on three models: probit regression, Gaussian process classification, and a Cox process model of basketball plays. When compared to expectation propagation and classical VI, CHIVI produces better error rates and more accurate estimates of posterior variance.

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arXiv2017

Hierarchical Implicit Models and Likelihood-Free Variational Inference

Implicit probabilistic models are a flexible class of models defined by a simulation process for data. They form the basis for theories which encompass our understanding of the physical world. Despite this fundamental nature, the use of implicit models remains limited due to challenges in specifying complex latent structure in them, and in performing inferences in such models with large data sets. In this paper, we first introduce hierarchical implicit models (HIMs). HIMs combine the idea of implicit densities with hierarchical Bayesian modeling, thereby defining models via simulators of data with rich hidden structure. Next, we develop likelihood-free variational inference (LFVI), a scalable variational inference algorithm for HIMs. Key to LFVI is specifying a variational family that is also implicit. This matches the model's flexibility and allows for accurate approximation of the posterior. We demonstrate diverse applications: a large-scale physical simulator for predator-prey populations in ecology; a Bayesian generative adversarial network for discrete data; and a deep implicit model for text generation.

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arXiv2017

Implicit Causal Models for Genome-wide Association Studies

Progress in probabilistic generative models has accelerated, developing richer models with neural architectures, implicit densities, and with scalable algorithms for their Bayesian inference. However, there has been limited progress in models that capture causal relationships, for example, how individual genetic factors cause major human diseases. In this work, we focus on two challenges in particular: How do we build richer causal models, which can capture highly nonlinear relationships and interactions between multiple causes? How do we adjust for latent confounders, which are variables influencing both cause and effect and which prevent learning of causal relationships? To address these challenges, we synthesize ideas from causality and modern probabilistic modeling. For the first, we describe implicit causal models, a class of causal models that leverages neural architectures with an implicit density. For the second, we describe an implicit causal model that adjusts for confounders by sharing strength across examples. In experiments, we scale Bayesian inference on up to a billion genetic measurements. We achieve state of the art accuracy for identifying causal factors: we significantly outperform existing genetics methods by an absolute difference of 15-45.3%.

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arXiv2017

Proximity Variational Inference

Variational inference is a powerful approach for approximate posterior inference. However, it is sensitive to initialization and can be subject to poor local optima. In this paper, we develop proximity variational inference (PVI). PVI is a new method for optimizing the variational objective that constrains subsequent iterates of the variational parameters to robustify the optimization path. Consequently, PVI is less sensitive to initialization and optimization quirks and finds better local optima. We demonstrate our method on three proximity statistics. We study PVI on a Bernoulli factor model and sigmoid belief network with both real and synthetic data and compare to deterministic annealing (Katahira et al., 2008). We highlight the flexibility of PVI by designing a proximity statistic for Bayesian deep learning models such as the variational autoencoder (Kingma and Welling, 2014; Rezende et al., 2014). Empirically, we show that PVI consistently finds better local optima and gives better predictive performance.

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arXiv2017

Deep Probabilistic Programming

We propose Edward, a Turing-complete probabilistic programming language. Edward defines two compositional representations---random variables and inference. By treating inference as a first class citizen, on a par with modeling, we show that probabilistic programming can be as flexible and computationally efficient as traditional deep learning. For flexibility, Edward makes it easy to fit the same model using a variety of composable inference methods, ranging from point estimation to variational inference to MCMC. In addition, Edward can reuse the modeling representation as part of inference, facilitating the design of rich variational models and generative adversarial networks. For efficiency, Edward is integrated into TensorFlow, providing significant speedups over existing probabilistic systems. For example, we show on a benchmark logistic regression task that Edward is at least 35x faster than Stan and 6x faster than PyMC3. Further, Edward incurs no runtime overhead: it is as fast as handwritten TensorFlow.

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arXiv2017

Edward: A library for probabilistic modeling, inference, and criticism

Probabilistic modeling is a powerful approach for analyzing empirical information. We describe Edward, a library for probabilistic modeling. Edward's design reflects an iterative process pioneered by George Box: build a model of a phenomenon, make inferences about the model given data, and criticize the model's fit to the data. Edward supports a broad class of probabilistic models, efficient algorithms for inference, and many techniques for model criticism. The library builds on top of TensorFlow to support distributed training and hardware such as GPUs. Edward enables the development of complex probabilistic models and their algorithms at a massive scale.

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arXiv2016

Exponential Family Embeddings

Word embeddings are a powerful approach for capturing semantic similarity among terms in a vocabulary. In this paper, we develop exponential family embeddings, a class of methods that extends the idea of word embeddings to other types of high-dimensional data. As examples, we studied neural data with real-valued observations, count data from a market basket analysis, and ratings data from a movie recommendation system. The main idea is to model each observation conditioned on a set of other observations. This set is called the context, and the way the context is defined is a modeling choice that depends on the problem. In language the context is the surrounding words; in neuroscience the context is close-by neurons; in market basket data the context is other items in the shopping cart. Each type of embedding model defines the context, the exponential family of conditional distributions, and how the latent embedding vectors are shared across data. We infer the embeddings with a scalable algorithm based on stochastic gradient descent. On all three applications - neural activity of zebrafish, users' shopping behavior, and movie ratings - we found exponential family embedding models to be more effective than other types of dimension reduction. They better reconstruct held-out data and find interesting qualitative structure.

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arXiv2016

Model Criticism for Bayesian Causal Inference

The goal of causal inference is to understand the outcome of alternative courses of action. However, all causal inference requires assumptions. Such assumptions can be more influential than in typical tasks for probabilistic modeling, and testing those assumptions is important to assess the validity of causal inference. We develop model criticism for Bayesian causal inference, building on the idea of posterior predictive checks to assess model fit. Our approach involves decomposing the problem, separately criticizing the model of treatment assignments and the model of outcomes. Conditioned on the assumption of unconfoundedness---that the treatments are assigned independently of the potential outcomes---we show how to check any additional modeling assumption. Our approach provides a foundation for diagnosing model-based causal inferences.

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arXiv2016

Recurrent switching linear dynamical systems

Many natural systems, such as neurons firing in the brain or basketball teams traversing a court, give rise to time series data with complex, nonlinear dynamics. We can gain insight into these systems by decomposing the data into segments that are each explained by simpler dynamic units. Building on switching linear dynamical systems (SLDS), we present a new model class that not only discovers these dynamical units, but also explains how their switching behavior depends on observations or continuous latent states. These "recurrent" switching linear dynamical systems provide further insight by discovering the conditions under which each unit is deployed, something that traditional SLDS models fail to do. We leverage recent algorithmic advances in approximate inference to make Bayesian inference in these models easy, fast, and scalable.

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arXiv2016

The Generalized Reparameterization Gradient

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.

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