Stochastic gradient Markov chain Monte Carlo (SGMCMC) has become a popular method for scalable Bayesian inference. These methods are based on sampling a discrete-time approximation to a continuous time process, such as the Langevin diffusion. When applied to distributions defined on a constrained space the time-discretization error can dominate when we are near the boundary of the space. We demonstrate that because of this, current SGMCMC methods for the simplex struggle with sparse simplex spaces; when many of the components are close to zero. Unfortunately, many popular large-scale Bayesian models, such as network or topic models, require inference on sparse simplex spaces. To avoid the biases caused by this discretization error, we propose the stochastic Cox-Ingersoll-Ross process (SCIR), which removes all discretization error and we prove that samples from the SCIR process are asymptotically unbiased. We discuss how this idea can be extended to target other constrained spaces. Use of the SCIR process within a SGMCMC algorithm is shown to give substantially better performance for a topic model and a Dirichlet process mixture model than existing SGMCMC approaches.

Expectation Maximization (EM) is among the most popular algorithms for maximum likelihood estimation, but it is generally only guaranteed to find its stationary points of the log-likelihood objective. The goal of this article is to present theoretical and empirical evidence that over-parameterization can help EM avoid spurious local optima in the log-likelihood. We consider the problem of estimating the mean vectors of a Gaussian mixture model in a scenario where the mixing weights are known. Our study shows that the global behavior of EM, when one uses an over-parameterized model in which the mixing weights are treated as unknown, is better than that when one uses the (correct) model with the mixing weights fixed to the known values. For symmetric Gaussians mixtures with two components, we prove that introducing the (statistically redundant) weight parameters enables EM to find the global maximizer of the log-likelihood starting from almost any initial mean parameters, whereas EM without this over-parameterization may very often fail. For other Gaussian mixtures, we provide empirical evidence that shows similar behavior. Our results corroborate the value of over-parameterization in solving non-convex optimization problems, previously observed in other domains.

We present an approach for simultaneously separating and localizing multiple sound sources using recorded microphone data. Inspired by topic models, our approach is based on a probabilistic model of inter-microphone phase differences, and poses separation and localization as a Bayesian inference problem. We assume sound activity is locally smooth across time, frequency, and location, and use the known position of the microphones to obtain a consistent separation. We compare the performance of our method against existing algorithms on simulated anechoic voice data and find that it obtains high performance across a variety of input conditions.

Understanding how humans and animals learn about statistical regularities in stable and volatile environments, and utilize these regularities to make predictions and decisions, is an important problem in neuroscience and psychology. Using a Bayesian modeling framework, specifically the Dynamic Belief Model (DBM), it has previously been shown that humans tend to make the {\it default} assumption that environmental statistics undergo abrupt, unsignaled changes, even when environmental statistics are actually stable. Because exact Bayesian inference in this setting, an example of switching state space models, is computationally intense, a number of approximately Bayesian and heuristic algorithms have been proposed to account for learning/prediction in the brain. Here, we examine a neurally plausible algorithm, a special case of leaky integration dynamics we denote as EXP (for exponential filtering), that is significantly simpler than all previously suggested algorithms except for the delta-learning rule, and which far outperforms the delta rule in approximating Bayesian prediction performance. We derive the theoretical relationship between DBM and EXP, and show that EXP gains computational efficiency by foregoing the representation of inferential uncertainty (as does the delta rule), but that it nevertheless achieves near-Bayesian performance due to its ability to incorporate a persistent prior influence unique to DBM and absent from the other algorithms. Furthermore, we show that EXP is comparable to DBM but better than all other models in reproducing human behavior in a visual search task, suggesting that human learning and prediction also incorporates an element of persistent prior. More broadly, our work demonstrates that when observations are information-poor, detecting changes or modulating the learning rate is both {\it difficult} and (thus) {\it unnecessary} for making Bayes-optimal predictions.

Many probabilistic models of interest in scientific computing and machine learning have expensive, black-box likelihoods that prevent the application of standard techniques for Bayesian inference, such as MCMC, which would require access to the gradient or a large number of likelihood evaluations. We introduce here a novel sample-efficient inference framework, Variational Bayesian Monte Carlo (VBMC). VBMC combines variational inference with Gaussian-process based, active-sampling Bayesian quadrature, using the latter to efficiently approximate the intractable integral in the variational objective. Our method produces both a nonparametric approximation of the posterior distribution and an approximate lower bound of the model evidence, useful for model selection. We demonstrate VBMC both on several synthetic likelihoods and on a neuronal model with data from real neurons. Across all tested problems and dimensions (up to D = 10), VBMC performs consistently well in reconstructing the posterior and the model evidence with a limited budget of likelihood evaluations, unlike other methods that work only in very low dimensions. Our framework shows great promise as a novel tool for posterior and model inference with expensive, black-box likelihoods.

Conditional Density Estimation (CDE) models deal with estimating conditional distributions. The conditions imposed on the distribution are the inputs of the model. CDE is a challenging task as there is a fundamental trade-off between model complexity, representational capacity and overfitting. In this work, we propose to extend the model's input with latent variables and use Gaussian processes (GP) to map this augmented input onto samples from the conditional distribution. Our Bayesian approach allows for the modeling of small datasets, but we also provide the machinery for it to be applied to big data using stochastic variational inference. Our approach can be used to model densities even in sparse data regions, and allows for sharing learned structure between conditions. We illustrate the effectiveness and wide-reaching applicability of our model on a variety of real-world problems, such as spatio-temporal density estimation of taxi drop-offs, non-Gaussian noise modeling, and few-shot learning on omniglot images.

Effective implementations of sampling-based probabilistic inference often require manually constructed, model-specific proposals. Inspired by recent progresses in meta-learning for training learning agents that can generalize to unseen environments, we propose a meta-learning approach to building effective and generalizable MCMC proposals. We parametrize the proposal as a neural network to provide fast approximations to block Gibbs conditionals. The learned neural proposals generalize to occurrences of common structural motifs across different models, allowing for the construction of a library of learned inference primitives that can accelerate inference on unseen models with no model-specific training required. We explore several applications including open-universe Gaussian mixture models, in which our learned proposals outperform a hand-tuned sampler, and a real-world named entity recognition task, in which our sampler yields higher final F1 scores than classical single-site Gibbs sampling.

The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter learning capabilities of a dynamic Bayesian network (DBN) peptide-scoring algorithm, Didea, by deriving emission distributions for which its conditional log-likelihood scoring function remains concave. We show that this class of emission distributions, called Convex Virtual Emissions (CVEs), naturally generalizes the log-sum-exp function while rendering both maximum likelihood estimation and conditional maximum likelihood estimation concave for a wide range of Bayesian networks. Utilizing CVEs in Didea allows efficient learning of a large number of parameters while ensuring global convergence, in stark contrast to Didea's previous parameter learning framework (which could only learn a single parameter using a costly grid search) and other trainable models (which only ensure convergence to local optima). The newly trained scoring function substantially outperforms the state-of-the-art in both scoring function accuracy and downstream Fisher kernel analysis. Furthermore, we significantly improve Didea's runtime performance through successive optimizations to its message passing schedule and derive explicit connections between Didea's new concave score and related MS/MS scoring functions.

Recent advances in recording technologies have allowed neuroscientists to record simultaneous spiking activity from hundreds to thousands of neurons in multiple brain regions. Such large-scale recordings pose a major challenge to existing statistical methods for neural data analysis. Here we develop highly scalable approximate inference methods for Poisson generalized linear models (GLMs) that require only a single pass over the data. Our approach relies on a recently proposed method for obtaining approximate sufficient statistics for GLMs using polynomial approximations [Huggins et al., 2017], which we adapt to the Poisson GLM setting. We focus on inference using quadratic approximations to nonlinear terms in the Poisson GLM log-likelihood with Gaussian priors, for which we derive closed-form solutions to the approximate maximum likelihood and MAP estimates, posterior distribution, and marginal likelihood. We introduce an adaptive procedure to select the polynomial approximation interval and show that the resulting method allows for efficient and accurate inference and regularization of high-dimensional parameters. We use the quadratic estimator to fit a fully-coupled Poisson GLM to spike train data recorded from 831 neurons across five regions of the mouse brain for a duration of 41 minutes, binned at 1 ms resolution. Across all neurons, this model is fit to over 2 billion spike count bins and identifies fine-timescale statistical dependencies between neurons within and across cortical and subcortical areas.

Approximate inference in probabilistic graphical models (PGMs) can be grouped into deterministic methods and Monte-Carlo-based methods. The former can often provide accurate and rapid inferences, but are typically associated with biases that are hard to quantify. The latter enjoy asymptotic consistency, but can suffer from high computational costs. In this paper we present a way of bridging the gap between deterministic and stochastic inference. Specifically, we suggest an efficient sequential Monte Carlo (SMC) algorithm for PGMs which can leverage the output from deterministic inference methods. While generally applicable, we show explicitly how this can be done with loopy belief propagation, expectation propagation, and Laplace approximations. The resulting algorithm can be viewed as a post-correction of the biases associated with these methods and, indeed, numerical results show clear improvements over the baseline deterministic methods as well as over plain SMC.