arXiv subjects

Jeffrey Regier

Publications and source records attributed to Jeffrey Regier.

34 records · Page 2Linked to original sources

arXiv2022

Normalizing Flows for Knockoff-free Controlled Feature Selection

Controlled feature selection aims to discover the features a response depends on while limiting the false discovery rate (FDR) to a predefined level. Recently, multiple deep-learning-based methods have been proposed to perform controlled feature selection through the Model-X knockoff framework. We demonstrate, however, that these methods often fail to control the FDR for two reasons. First, these methods often learn inaccurate models of features. Second, the "swap" property, which is required for knockoffs to be valid, is often not well enforced. We propose a new procedure called FlowSelect to perform controlled feature selection that does not suffer from either of these two problems. To more accurately model the features, FlowSelect uses normalizing flows, the state-of-the-art method for density estimation. Instead of enforcing the "swap" property, FlowSelect uses a novel MCMC-based procedure to calculate p-values for each feature directly. Asymptotically, FlowSelect computes valid p-values. Empirically, FlowSelect consistently controls the FDR on both synthetic and semi-synthetic benchmarks, whereas competing knockoff-based approaches do not. FlowSelect also demonstrates greater power on these benchmarks. Additionally, FlowSelect correctly infers the genetic variants associated with specific soybean traits from GWAS data.

stat.ML↗

arXiv2022

Scalable Bayesian Inference for Detection and Deblending in Astronomical Images

We present a new probabilistic method for detecting, deblending, and cataloging astronomical sources called the Bayesian Light Source Separator (BLISS). BLISS is based on deep generative models, which embed neural networks within a Bayesian model. For posterior inference, BLISS uses a new form of variational inference known as Forward Amortized Variational Inference. The BLISS inference routine is fast, requiring a single forward pass of the encoder networks on a GPU once the encoder networks are trained. BLISS can perform fully Bayesian inference on megapixel images in seconds, and produces highly accurate catalogs. BLISS is highly extensible, and has the potential to directly answer downstream scientific questions in addition to producing probabilistic catalogs.

astro-ph.IM↗

arXiv2021

An Empirical Comparison of GANs and Normalizing Flows for Density Estimation

Generative adversarial networks (GANs) and normalizing flows are both approaches to density estimation that use deep neural networks to transform samples from an uninformative prior distribution to an approximation of the data distribution. There is great interest in both for general-purpose statistical modeling, but the two approaches have seldom been compared to each other for modeling non-image data. The difficulty of computing likelihoods with GANs, which are implicit models, makes conducting such a comparison challenging. We work around this difficulty by considering several low-dimensional synthetic datasets. An extensive grid search over GAN architectures, hyperparameters, and training procedures suggests that no GAN is capable of modeling our simple low-dimensional data well, a task we view as a prerequisite for an approach to be considered suitable for general-purpose statistical modeling. Several normalizing flows, on the other hand, excelled at these tasks, even substantially outperforming WGAN in terms of Wasserstein distance -- the metric that WGAN alone targets. Scientists and other practitioners should be wary of relying on WGAN for applications that require accurate density estimation.

cs.LG↗

arXiv2020

Decision-Making with Auto-Encoding Variational Bayes

To make decisions based on a model fit with auto-encoding variational Bayes (AEVB), practitioners often let the variational distribution serve as a surrogate for the posterior distribution. This approach yields biased estimates of the expected risk, and therefore leads to poor decisions for two reasons. First, the model fit with AEVB may not equal the underlying data distribution. Second, the variational distribution may not equal the posterior distribution under the fitted model. We explore how fitting the variational distribution based on several objective functions other than the ELBO, while continuing to fit the generative model based on the ELBO, affects the quality of downstream decisions. For the probabilistic principal component analysis model, we investigate how importance sampling error, as well as the bias of the model parameter estimates, varies across several approximate posteriors when used as proposal distributions. Our theoretical results suggest that a posterior approximation distinct from the variational distribution should be used for making decisions. Motivated by these theoretical results, we propose learning several approximate proposals for the best model and combining them using multiple importance sampling for decision-making. In addition to toy examples, we present a full-fledged case study of single-cell RNA sequencing. In this challenging instance of multiple hypothesis testing, our proposed approach surpasses the current state of the art.

stat.ML↗

arXiv2019

Rao-Blackwellized Stochastic Gradients for Discrete Distributions

We wish to compute the gradient of an expectation over a finite or countably infinite sample space having $K \leq \infty$ categories. When $K$ is indeed infinite, or finite but very large, the relevant summation is intractable. Accordingly, various stochastic gradient estimators have been proposed. In this paper, we describe a technique that can be applied to reduce the variance of any such estimator, without changing its bias---in particular, unbiasedness is retained. We show that our technique is an instance of Rao-Blackwellization, and we demonstrate the improvement it yields on a semi-supervised classification problem and a pixel attention task.

stat.ML↗

arXiv2019

A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements

Spatial studies of transcriptome provide biologists with gene expression maps of heterogeneous and complex tissues. However, most experimental protocols for spatial transcriptomics suffer from the need to select beforehand a small fraction of genes to be quantified over the entire transcriptome. Standard single-cell RNA sequencing (scRNA-seq) is more prevalent, easier to implement and can in principle capture any gene but cannot recover the spatial location of the cells. In this manuscript, we focus on the problem of imputation of missing genes in spatial transcriptomic data based on (unpaired) standard scRNA-seq data from the same biological tissue. Building upon domain adaptation work, we propose gimVI, a deep generative model for the integration of spatial transcriptomic data and scRNA-seq data that can be used to impute missing genes. After describing our generative model and an inference procedure for it, we compare gimVI to alternative methods from computational biology or domain adaptation on real datasets and outperform Seurat Anchors, Liger and CORAL to impute held-out genes.

cs.LG↗

arXiv2019

Approximate Inference for Constructing Astronomical Catalogs from Images

We present a new, fully generative model for constructing astronomical catalogs from optical telescope image sets. Each pixel intensity is treated as a random variable with parameters that depend on the latent properties of stars and galaxies. These latent properties are themselves modeled as random. We compare two procedures for posterior inference. One procedure is based on Markov chain Monte Carlo (MCMC) while the other is based on variational inference (VI). The MCMC procedure excels at quantifying uncertainty, while the VI procedure is 1000 times faster. On a supercomputer, the VI procedure efficiently uses 665,000 CPU cores to construct an astronomical catalog from 50 terabytes of images in 14.6 minutes, demonstrating the scaling characteristics necessary to construct catalogs for upcoming astronomical surveys.

stat.AP↗

arXiv2018

Information Constraints on Auto-Encoding Variational Bayes

Parameterizing the approximate posterior of a generative model with neural networks has become a common theme in recent machine learning research. While providing appealing flexibility, this approach makes it difficult to impose or assess structural constraints such as conditional independence. We propose a framework for learning representations that relies on Auto-Encoding Variational Bayes and whose search space is constrained via kernel-based measures of independence. In particular, our method employs the $d$-variable Hilbert-Schmidt Independence Criterion (dHSIC) to enforce independence between the latent representations and arbitrary nuisance factors. We show how to apply this method to a range of problems, including the problems of learning invariant representations and the learning of interpretable representations. We also present a full-fledged application to single-cell RNA sequencing (scRNA-seq). In this setting the biological signal is mixed in complex ways with sequencing errors and sampling effects. We show that our method out-performs the state-of-the-art in this domain.

cs.LG↗

arXiv2018

A Deep Generative Model for Semi-Supervised Classification with Noisy Labels

Class labels are often imperfectly observed, due to mistakes and to genuine ambiguity among classes. We propose a new semi-supervised deep generative model that explicitly models noisy labels, called the Mislabeled VAE (M-VAE). The M-VAE can perform better than existing deep generative models which do not account for label noise. Additionally, the derivation of M-VAE gives new theoretical insights into the popular M1+M2 semi-supervised model.

cs.LG↗

arXiv2018

Cataloging the Visible Universe through Bayesian Inference at Petascale

Astronomical catalogs derived from wide-field imaging surveys are an important tool for understanding the Universe. We construct an astronomical catalog from 55 TB of imaging data using Celeste, a Bayesian variational inference code written entirely in the high-productivity programming language Julia. Using over 1.3 million threads on 650,000 Intel Xeon Phi cores of the Cori Phase II supercomputer, Celeste achieves a peak rate of 1.54 DP PFLOP/s. Celeste is able to jointly optimize parameters for 188M stars and galaxies, loading and processing 178 TB across 8192 nodes in 14.6 minutes. To achieve this, Celeste exploits parallelism at multiple levels (cluster, node, and thread) and accelerates I/O through Cori's Burst Buffer. Julia's native performance enables Celeste to employ high-level constructs without resorting to hand-written or generated low-level code (C/C++/Fortran), and yet achieve petascale performance.

cs.DC↗

arXiv2018

A deep generative model for gene expression profiles from single-cell RNA sequencing

We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for technical effects that may erroneously set some observations of gene expression levels to zero. Conditional distributions are specified by neural networks, giving the proposed model enough flexibility to fit the data well. We use variational inference and stochastic optimization to approximate the posterior distribution. The inference procedure scales to over one million cells, whereas competing algorithms do not. Even for smaller datasets, for several tasks, the proposed procedure outperforms state-of-the-art methods like ZIFA and ZINB-WaVE. We also extend our framework to account for batch effects and other confounding factors, and propose a Bayesian hypothesis test for differential expression that outperforms DESeq2.

cs.LG↗

arXiv2017

Stochastic Cubic Regularization for Fast Nonconvex Optimization

This paper proposes a stochastic variant of a classic algorithm---the cubic-regularized Newton method [Nesterov and Polyak 2006]. The proposed algorithm efficiently escapes saddle points and finds approximate local minima for general smooth, nonconvex functions in only $\mathcal{\tilde{O}}(ε^{-3.5})$ stochastic gradient and stochastic Hessian-vector product evaluations. The latter can be computed as efficiently as stochastic gradients. This improves upon the $\mathcal{\tilde{O}}(ε^{-4})$ rate of stochastic gradient descent. Our rate matches the best-known result for finding local minima without requiring any delicate acceleration or variance-reduction techniques.

cs.LG↗

arXiv2017

Fast Black-box Variational Inference through Stochastic Trust-Region Optimization

We introduce TrustVI, a fast second-order algorithm for black-box variational inference based on trust-region optimization and the reparameterization trick. At each iteration, TrustVI proposes and assesses a step based on minibatches of draws from the variational distribution. The algorithm provably converges to a stationary point. We implemented TrustVI in the Stan framework and compared it to two alternatives: Automatic Differentiation Variational Inference (ADVI) and Hessian-free Stochastic Gradient Variational Inference (HFSGVI). The former is based on stochastic first-order optimization. The latter uses second-order information, but lacks convergence guarantees. TrustVI typically converged at least one order of magnitude faster than ADVI, demonstrating the value of stochastic second-order information. TrustVI often found substantially better variational distributions than HFSGVI, demonstrating that our convergence theory can matter in practice.

cs.LG↗

arXiv2017

A deep generative model for single-cell RNA sequencing with application to detecting differentially expressed genes

We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for technical effects that may erroneously set some observations of gene expression levels to zero. Conditional distributions are specified by neural networks, giving the proposed model enough flexibility to fit the data well. We use variational inference and stochastic optimization to approximate the posterior distribution. The inference procedure scales to over one million cells, whereas competing algorithms do not. Even for smaller datasets, for several tasks, the proposed procedure outperforms state-of-the-art methods like ZIFA and ZINB-WaVE. We also extend our framework to take into account batch effects and other confounding factors and propose a natural Bayesian hypothesis framework for differential expression that outperforms tradition DESeq2.

cs.LG↗

arXiv2016

Learning an Astronomical Catalog of the Visible Universe through Scalable Bayesian Inference

Celeste is a procedure for inferring astronomical catalogs that attains state-of-the-art scientific results. To date, Celeste has been scaled to at most hundreds of megabytes of astronomical images: Bayesian posterior inference is notoriously demanding computationally. In this paper, we report on a scalable, parallel version of Celeste, suitable for learning catalogs from modern large-scale astronomical datasets. Our algorithmic innovations include a fast numerical optimization routine for Bayesian posterior inference and a statistically efficient scheme for decomposing astronomical optimization problems into subproblems. Our scalable implementation is written entirely in Julia, a new high-level dynamic programming language designed for scientific and numerical computing. We use Julia's high-level constructs for shared and distributed memory parallelism, and demonstrate effective load balancing and efficient scaling on up to 8192 Xeon cores on the NERSC Cori supercomputer.

cs.DC↗

arXiv2015

Celeste: Variational inference for a generative model of astronomical images

We present a new, fully generative model of optical telescope image sets, along with a variational procedure for inference. Each pixel intensity is treated as a Poisson random variable, with a rate parameter dependent on latent properties of stars and galaxies. Key latent properties are themselves random, with scientific prior distributions constructed from large ancillary data sets. We check our approach on synthetic images. We also run it on images from a major sky survey, where it exceeds the performance of the current state-of-the-art method for locating celestial bodies and measuring their colors.

astro-ph.IM↗