Active learning methods automatically adapt data collection by selecting the most informative samples in order to accelerate machine learning. Because of this, real-world testing and comparing active learning algorithms requires collecting new datasets (adaptively), rather than simply applying algorithms to benchmark datasets, as is the norm in (passive) machine learning research. To facilitate the development, testing and deployment of active learning for real applications, we have built an open-source software system for large-scale active learning research and experimentation. The system, called NEXT, provides a unique platform for real-world, reproducible active learning research. This paper details the challenges of building the system and demonstrates its capabilities with several experiments. The results show how experimentation can help expose strengths and weaknesses of active learning algorithms, in sometimes unexpected and enlightening ways.

We study optimization algorithms based on variance reduction for stochastic gradientdescent (SGD). Remarkable recent progress has been made in this directionthrough development of algorithms like SAG, SVRG, SAGA. These algorithmshave been shown to outperform SGD, both theoretically and empirically. However,asynchronous versions of these algorithms—a crucial requirement for modernlarge-scale applications—have not been studied. We bridge this gap by presentinga unifying framework that captures many variance reduction techniques.Subsequently, we propose an asynchronous algorithm grounded in our framework,with fast convergence rates. An important consequence of our general approachis that it yields asynchronous versions of variance reduction algorithms such asSVRG, SAGA as a byproduct. Our method achieves near linear speedup in sparsesettings common to machine learning. We demonstrate the empirical performanceof our method through a concrete realization of asynchronous SVRG.

We introduce local expectation gradients which is a general purpose stochastic variational inference algorithm for constructing stochastic gradients by sampling from the variational distribution. This algorithm divides the problem of estimating the stochastic gradients over multiple variational parameters into smaller sub-tasks so that each sub-task explores intelligently the most relevant part of the variational distribution. This is achieved by performing an exact expectation over the single random variable that most correlates with the variational parameter of interest resulting in a Rao-Blackwellized estimate that has low variance. Our method works efficiently for both continuous and discrete random variables. Furthermore, the proposed algorithm has interesting similarities with Gibbs sampling but at the same time, unlike Gibbs sampling, can be trivially parallelized.

Sequential Monte Carlo (SMC), or particle filtering, is a popular class of methods for sampling from an intractable target distribution using a sequence of simpler intermediate distributions. Like other importance sampling-based methods, performance is critically dependent on the proposal distribution: a bad proposal can lead to arbitrarily inaccurate estimates of the target distribution. This paper presents a new method for automatically adapting the proposal using an approximation of the Kullback-Leibler divergence between the true posterior and the proposal distribution. The method is very flexible, applicable to any parameterized proposal distribution and it supports online and batch variants. We use the new framework to adapt powerful proposal distributions with rich parameterizations based upon neural networks leading to Neural Adaptive Sequential Monte Carlo (NASMC). Experiments indicate that NASMC significantly improves inference in a non-linear state space model outperforming adaptive proposal methods including the Extended Kalman and Unscented Particle Filters. Experiments also indicate that improved inference translates into improved parameter learning when NASMC is used as a subroutine of Particle Marginal Metropolis Hastings. Finally we show that NASMC is able to train a latent variable recurrent neural network (LV-RNN) achieving results that compete with the state-of-the-art for polymorphic music modelling. NASMC can be seen as bridging the gap between adaptive SMC methods and the recent work in scalable, black-box variational inference.

The Jaccard index is a standard statistics for comparing the pairwise similarity between data samples. This paper investigates the problem of estimating a Jaccard index matrix when there are missing observations in data samples. Starting from a Jaccard index matrix approximated from the incomplete data, our method calibrates the matrix to meet the requirement of positive semi-definiteness and other constraints, through a simple alternating projection algorithm. Compared with conventional approaches that estimate the similarity matrix based on the imputed data, our method has a strong advantage in that the calibrated matrix is guaranteed to be closer to the unknown ground truth in the Frobenius norm than the un-calibrated matrix (except in special cases they are identical). We carried out a series of empirical experiments and the results confirmed our theoretical justification. The evaluation also reported significantly improved results in real learning tasks on benchmarked datasets.

Gaussian Graphical Models (GGMs) are popular tools for studying network structures. However, many modern applications such as gene network discovery and social interactions analysis often involve high-dimensional noisy data with outliers or heavier tails than the Gaussian distribution. In this paper, we propose the Trimmed Graphical Lasso for robust estimation of sparse GGMs. Our method guards against outliers by an implicit trimming mechanism akin to the popular Least Trimmed Squares method used for linear regression. We provide a rigorous statistical analysis of our estimator in the high-dimensional setting. In contrast, existing approaches for robust sparse GGMs estimation lack statistical guarantees. Our theoretical results are complemented by experiments on simulated and real gene expression data which further demonstrate the value of our approach.

We explore an as yet unexploited opportunity for drastically improving the efficiency of stochastic gradient variational Bayes (SGVB) with global model parameters. Regular SGVB estimators rely on sampling of parameters once per minibatch of data, and have variance that is constant w.r.t. the minibatch size. The efficiency of such estimators can be drastically improved upon by translating uncertainty about global parameters into local noise that is independent across datapoints in the minibatch. Such reparameterizations with local noise can be trivially parallelized and have variance that is inversely proportional to the minibatch size, generally leading to much faster convergence.We find an important connection with regularization by dropout: the original Gaussian dropout objective corresponds to SGVB with local noise, a scale-invariant prior and proportionally fixed posterior variance. Our method allows inference of more flexibly parameterized posteriors; specifically, we propose \emph{variational dropout}, a generalization of Gaussian dropout, but with a more flexibly parameterized posterior, often leading to better generalization. The method is demonstrated through several experiments.

Motivated by the problem of robust factorization of a low-rank tensor, we study the question of sparse and low-rank tensor decomposition. We present an efficient computational algorithm that modifies Leurgans' algoirthm for tensor factorization. Our method relies on a reduction of the problem to sparse and low-rank matrix decomposition via the notion of tensor contraction. We use well-understood convex techniques for solving the reduced matrix sub-problem which then allows us to perform the full decomposition of the tensor. We delineate situations where the problem is recoverable and provide theoretical guarantees for our algorithm. We validate our algorithm with numerical experiments.

We provide a general theory of the expectation-maximization (EM) algorithm for inferring high dimensional latent variable models. In particular, we make two contributions: (i) For parameter estimation, we propose a novel high dimensional EM algorithm which naturally incorporates sparsity structure into parameter estimation. With an appropriate initialization, this algorithm converges at a geometric rate and attains an estimator with the (near-)optimal statistical rate of convergence. (ii) Based on the obtained estimator, we propose a new inferential procedure for testing hypotheses for low dimensional components of high dimensional parameters. For a broad family of statistical models, our framework establishes the first computationally feasible approach for optimal estimation and asymptotic inference in high dimensions.

Many neural circuits are composed of numerous distinct cell types that perform different operations on their inputs, and send their outputs to distinct targets. Therefore, a key step in understanding neural systems is to reliably distinguish cell types. An important example is the retina, for which present-day techniques for identifying cell types are accurate, but very labor-intensive. Here, we develop automated classifiers for functional identification of retinal ganglion cells, the output neurons of the retina, based solely on recorded voltage patterns on a large scale array. We use per-cell classifiers based on features extracted from electrophysiological images (spatiotemporal voltage waveforms) and interspike intervals (autocorrelations). These classifiers achieve high performance in distinguishing between the major ganglion cell classes of the primate retina, but fail in achieving the same accuracy in predicting cell polarities (ON vs. OFF). We then show how to use indicators of functional coupling within populations of ganglion cells (cross-correlation) to infer cell polarities with a matrix completion algorithm. This can result in accurate, fully automated methods for cell type classification.