Michael I. Jordan

Bio: Michael I. Jordan is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Computer science & Inference. The author has an hindex of 176, co-authored 1016 publications receiving 216204 citations. Previous affiliations of Michael I. Jordan include Stanford University & Princeton University.

Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models

Abstract: As single-cell transcriptomics becomes a mainstream technology, the natural next step is to integrate the accumulating data in order to achieve a common ontology of cell types and states. However, owing to various nuisance factors of variation, it is not straightforward how to compare gene expression levels across data sets and how to automatically assign cell type labels in a new data set based on existing annotations. In this manuscript, we demonstrate that our previously developed method, scVI, provides an effective and fully probabilistic approach for joint representation and analysis of cohorts of single-cell RNA-seq data sets, while accounting for uncertainty caused by biological and measurement noise. We also introduce single-cell ANnotation using Variational Inference (scANVI), a semi-supervised variant of scVI designed to leverage any available cell state annotations — for instance when only one data set in a cohort is annotated, or when only a few cells in a single data set can be labeled using marker genes. We demonstrate that scVI and scANVI compare favorably to the existing methods for data integration and cell state annotation in terms of accuracy, scalability, and adaptability to challenging settings such as a hierarchical structure of cell state labels. We further show that different from existing methods, scVI and scANVI represent the integrated datasets with a single generative model that can be directly used for any probabilistic decision making task, using differential expression as our case study. scVI and scANVI are available as open source software and can be readily used to facilitate cell state annotation and help ensure consistency and reproducibility across studies.

A Dynamical Systems Perspective on Nesterov Acceleration

Abstract: We present a dynamical system framework for understanding Nesterov's accelerated gradient method. In contrast to earlier work, our derivation does not rely on a vanishing step size argument. We show that Nesterov acceleration arises from discretizing an ordinary differential equation with a semi-implicit Euler integration scheme. We analyze both the underlying differential equation as well as the discretization to obtain insights into the phenomenon of acceleration. The analysis suggests that a curvature-dependent damping term lies at the heart of the phenomenon. We further establish connections between the discretized and the continuous-time dynamics.

Less than a Single Pass: Stochastically Controlled Stochastic Gradient.

Abstract: We develop and analyze a procedure for gradient-based optimization that we refer to as stochastically controlled stochastic gradient (SCSG). As a member of the SVRG family of algorithms, SCSG makes use of gradient estimates at two scales, with the number of updates at the faster scale being governed by a geometric random variable. Unlike most existing algorithms in this family, both the computation cost and the communication cost of SCSG do not necessarily scale linearly with the sample size $n$; indeed, these costs are independent of $n$ when the target accuracy is low. An experimental evaluation on real datasets confirms the effectiveness of SCSG.

Lower bounds on the performance of polynomial-time algorithms for sparse linear regression

Abstract: Under a standard assumption in complexity theory (NP not in P/poly), we demonstrate a gap between the minimax prediction risk for sparse linear regression that can be achieved by polynomial-time algorithms, and that achieved by optimal algorithms. In particular, when the design matrix is ill-conditioned, the minimax prediction loss achievable by polynomial-time algorithms can be substantially greater than that of an optimal algorithm. This result is the first known gap between polynomial and optimal algorithms for sparse linear regression, and does not depend on conjectures in average-case complexity.

Stochastic Gradient Descent Escapes Saddle Points Efficiently.

Abstract: This paper considers the perturbed stochastic gradient descent algorithm and shows that it finds $\epsilon$-second order stationary points ($\left\| abla f(x)\right\|\leq \epsilon$ and $ abla^2 f(x) \succeq -\sqrt{\epsilon} \mathbf{I}$) in $\tilde{O}(d/\epsilon^4)$ iterations, giving the first result that has linear dependence on dimension for this setting. For the special case, where stochastic gradients are Lipschitz, the dependence on dimension reduces to polylogarithmic. In addition to giving new results, this paper also presents a simplified proof strategy that gives a shorter and more elegant proof of previously known results (Jin et al. 2017) on perturbed gradient descent algorithm.

Going deeper with convolutions

Abstract: We propose a deep convolutional neural network architecture codenamed Inception that achieves the new state of the art for classification and detection in the ImageNet Large-Scale Visual Recognition Challenge 2014 (ILSVRC14). The main hallmark of this architecture is the improved utilization of the computing resources inside the network. By a carefully crafted design, we increased the depth and width of the network while keeping the computational budget constant. To optimize quality, the architectural decisions were based on the Hebbian principle and the intuition of multi-scale processing. One particular incarnation used in our submission for ILSVRC14 is called GoogLeNet, a 22 layers deep network, the quality of which is assessed in the context of classification and detection.

Deep Learning

Abstract: Deep learning is a form of machine learning that enables computers to learn from experience and understand the world in terms of a hierarchy of concepts. Because the computer gathers knowledge from experience, there is no need for a human computer operator to formally specify all the knowledge that the computer needs. The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones; a graph of these hierarchies would be many layers deep. This book introduces a broad range of topics in deep learning. The text offers mathematical and conceptual background, covering relevant concepts in linear algebra, probability theory and information theory, numerical computation, and machine learning. It describes deep learning techniques used by practitioners in industry, including deep feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling, and practical methodology; and it surveys such applications as natural language processing, speech recognition, computer vision, online recommendation systems, bioinformatics, and videogames. Finally, the book offers research perspectives, covering such theoretical topics as linear factor models, autoencoders, representation learning, structured probabilistic models, Monte Carlo methods, the partition function, approximate inference, and deep generative models. Deep Learning can be used by undergraduate or graduate students planning careers in either industry or research, and by software engineers who want to begin using deep learning in their products or platforms. A website offers supplementary material for both readers and instructors.

Reinforcement Learning: An Introduction

Abstract: Reinforcement learning, one of the most active research areas in artificial intelligence, is a computational approach to learning whereby an agent tries to maximize the total amount of reward it receives when interacting with a complex, uncertain environment. In Reinforcement Learning, Richard Sutton and Andrew Barto provide a clear and simple account of the key ideas and algorithms of reinforcement learning. Their discussion ranges from the history of the field's intellectual foundations to the most recent developments and applications. The only necessary mathematical background is familiarity with elementary concepts of probability. The book is divided into three parts. Part I defines the reinforcement learning problem in terms of Markov decision processes. Part II provides basic solution methods: dynamic programming, Monte Carlo methods, and temporal-difference learning. Part III presents a unified view of the solution methods and incorporates artificial neural networks, eligibility traces, and planning; the two final chapters present case studies and consider the future of reinforcement learning.

Latent dirichlet allocation

Abstract: We describe latent Dirichlet allocation (LDA), a generative probabilistic model for collections of discrete data such as text corpora. LDA is a three-level hierarchical Bayesian model, in which each item of a collection is modeled as a finite mixture over an underlying set of topics. Each topic is, in turn, modeled as an infinite mixture over an underlying set of topic probabilities. In the context of text modeling, the topic probabilities provide an explicit representation of a document. We present efficient approximate inference techniques based on variational methods and an EM algorithm for empirical Bayes parameter estimation. We report results in document modeling, text classification, and collaborative filtering, comparing to a mixture of unigrams model and the probabilistic LSI model.

Latent Dirichlet Allocation

Abstract: We propose a generative model for text and other collections of discrete data that generalizes or improves on several previous models including naive Bayes/unigram, mixture of unigrams [6], and Hof-mann's aspect model, also known as probabilistic latent semantic indexing (pLSI) [3]. In the context of text modeling, our model posits that each document is generated as a mixture of topics, where the continuous-valued mixture proportions are distributed as a latent Dirichlet random variable. Inference and learning are carried out efficiently via variational algorithms. We present empirical results on applications of this model to problems in text modeling, collaborative filtering, and text classification.