Recent advances in optical voltage sensors have brought us closer to a critical goal in cellular neuroscience: imaging the full spatiotemporal voltage on a dendritic tree. However, current sensors and imaging approaches still face significant limitations in SNR and sampling frequency; therefore statistical denoising and interpolation methods remain critical for understanding single-trial spatiotemporal dendritic voltage dynamics. Previous denoising approaches were either based on an inadequate linear voltage model or scaled poorly to large trees. Here we introduce a scalable fully Bayesian approach. We develop a generative nonlinear model that requires few parameters per compartment of the cell but is nonetheless flexible enough to sample realistic spatiotemporal data. The model captures different dynamics in each compartment and leverages biophysical knowledge to constrain intra- and inter-compartmental dynamics. We obtain a full posterior distribution over spatiotemporal voltage via an augmented Gibbs sampling algorithm. The nonlinear smoother model outperforms previously developed linear methods, and scales to much larger systems than previous methods based on sequential Monte Carlo approaches.

Bayesian optimization has recently emerged as a popular method for the sample-efficient optimization of expensive black-box functions. However, the application to high-dimensional problems with several thousand observations remains challenging, and on difficult problems Bayesian optimization is often not competitive with other paradigms. In this paper we take the view that this is due to the implicit homogeneity of the global probabilistic models and an overemphasized exploration that results from global acquisition. This motivates the design of a local probabilistic approach for global optimization of large-scale high-dimensional problems. We propose the TuRBO algorithm that fits a collection of local models and performs a principled global allocation of samples across these models via an implicit bandit approach. A comprehensive evaluation demonstrates that TuRBO outperforms state-of-the-art methods from machine learning and operations research on problems spanning reinforcement learning, robotics, and the natural sciences.

Asynchronous event sequences are the basis of many applications throughout different industries. In this work, we tackle the task of predicting the next event (given a history), and how this prediction changes with the passage of time. Since at some time points (e.g. predictions far into the future) we might not be able to predict anything with confidence, capturing uncertainty in the predictions is crucial. We present two new architectures, WGP-LN and FD-Dir, modelling the evolution of the distribution on the probability simplex with time-dependent logistic normal and Dirichlet distributions. In both cases, the combination of RNNs with either Gaussian process or function decomposition allows to express rich temporal evolution of the distribution parameters, and naturally captures uncertainty. Experiments on class prediction, time prediction and anomaly detection demonstrate the high performances of our models on various datasets compared to other approaches.

We consider black box optimization of an unknown function in the nonparametric Gaussian process setting when the noise in the observed function values can be heavy tailed. This is in contrast to existing literature that typically assumes sub-Gaussian noise distributions for queries. Under the assumption that the unknown function belongs to the Reproducing Kernel Hilbert Space (RKHS) induced by a kernel, we first show that an adaptation of the well-known GP-UCB algorithm with reward truncation enjoys sublinear $\tilde{O}(T^{\frac{2 + \alpha}{2(1+\alpha)}})$ regret even with only the $(1+\alpha)$-th moments, $\alpha \in (0,1]$, of the reward distribution being bounded ($\tilde{O}$ hides logarithmic factors). However, for the common squared exponential (SE) and Mat\'{e}rn kernels, this is seen to be significantly larger than a fundamental $\Omega(T^{\frac{1}{1+\alpha}})$ lower bound on regret. We resolve this gap by developing novel Bayesian optimization algorithms, based on kernel approximation techniques, with regret bounds matching the lower bound in order for the SE kernel. We numerically benchmark the algorithms on environments based on both synthetic models and real-world data sets.

Bayesian optimal experimental design (BOED) is a principled framework for making efficient use of limited experimental resources. Unfortunately, its applicability is hampered by the difficulty of obtaining accurate estimates of the expected information gain (EIG) of an experiment. To address this, we introduce several classes of fast EIG estimators by building on ideas from amortized variational inference. We show theoretically and empirically that these estimators can provide significant gains in speed and accuracy over previous approaches. We further demonstrate the practicality of our approach on a number of end-to-end experiments.

A multi-layer deep Gaussian process (DGP) model is a hierarchical composition of GP models with a greater expressive power. Exact DGP inference is intractable, which has motivated the recent development of deterministic and stochastic approximation methods. Unfortunately, the deterministic approximation methods yield a biased posterior belief while the stochastic one is computationally costly. This paper presents an implicit posterior variational inference (IPVI) framework for DGPs that can ideally recover an unbiased posterior belief and still preserve time efficiency. Inspired by generative adversarial networks, our IPVI framework achieves this by casting the DGP inference problem as a two-player game in which a Nash equilibrium, interestingly, coincides with an unbiased posterior belief. This consequently inspires us to devise a best-response dynamics algorithm to search for a Nash equilibrium (i.e., an unbiased posterior belief). Empirical evaluation shows that IPVI outperforms the state-of-the-art approximation methods for DGPs.

Bayesian inference in state-space models is challenging due to high-dimensional state trajectories. A viable approach is particle Markov chain Monte Carlo (PMCMC), combining MCMC and sequential Monte Carlo to form ``exact approximations'' to otherwise-intractable MCMC methods. The performance of the approximation is limited to that of the exact method. We focus on particle Gibbs (PG) and particle Gibbs with ancestor sampling (PGAS), improving their performance beyond that of the ideal Gibbs sampler (which they approximate) by marginalizing out one or more parameters. This is possible when the parameter(s) has a conjugate prior relationship with the complete data likelihood. Marginalization yields a non-Markov model for inference, but we show that, in contrast to the general case, the methods still scale linearly in time. While marginalization can be cumbersome to implement, recent advances in probabilistic programming have enabled its automation. We demonstrate how the marginalized methods are viable as efficient inference backends in probabilistic programming, and demonstrate with examples in ecology and epidemiology.

Recent work in variational inference (VI) has used ideas from Monte Carlo estimation to obtain tighter lower bounds on the log-likelihood to be used as objectives for VI. However, there is not a systematic understanding of how optimizing different objectives relates to approximating the posterior distribution. Developing such a connection is important if the ideas are to be applied to inference—i.e., applications that require an approximate posterior and not just an approximation of the log-likelihood. Given a VI objective defined by a Monte Carlo estimator of the likelihood, we use a "divide and couple" procedure to identify augmented proposal and target distributions so that the gap between the VI objective and the log-likelihood is equal to the divergence between these distributions. Thus, after maximizing the VI objective, the augmented variational distribution may be used to approximate the posterior distribution.

Sampling from log-concave distributions is a well researched problem that has many applications in statistics and machine learning. We study the distributions of the form $p^{*}\propto\exp(-f(x))$, where $f:\mathbb{R}^{d}\rightarrow\mathbb{R}$ has an $L$-Lipschitz gradient and is $m$-strongly convex. In our paper, we propose a Markov chain Monte Carlo (MCMC) algorithm based on the underdamped Langevin diffusion (ULD). It can achieve $\epsilon\cdot D$ error (in 2-Wasserstein distance) in $\tilde{O}\left(\kappa^{7/6}/\epsilon^{1/3}+\kappa/\epsilon^{2/3}\right)$ steps, where $D\overset{\mathrm{def}}{=}\sqrt{\frac{d}{m}}$ is the effective diameter of the problem and $\kappa\overset{\mathrm{def}}{=}\frac{L}{m}$ is the condition number. Our algorithm performs significantly faster than the previously best known algorithm for solving this problem, which requires $\tilde{O}\left(\kappa^{1.5}/\epsilon\right)$ steps \cite{chen2019optimal,dalalyan2018sampling}. Moreover, our algorithm can be easily parallelized to require only $O(\kappa\log\frac{1}{\epsilon})$ parallel steps. To solve the sampling problem, we propose a new framework to discretize stochastic differential equations. We apply this framework to discretize and simulate ULD, which converges to the target distribution $p^{*}$. The framework can be used to solve not only the log-concave sampling problem, but any problem that involves simulating (stochastic) differential equations.

Gibbs sampling is a Markov chain Monte Carlo method that is often used for learning and inference on graphical models. Minibatching, in which a small random subset of the graph is used at each iteration, can help make Gibbs sampling scale to large graphical models by reducing its computational cost. In this paper, we propose a new auxiliary-variable minibatched Gibbs sampling method, {\it Poisson-minibatching Gibbs}, which both produces unbiased samples and has a theoretical guarantee on its convergence rate. In comparison to previous minibatched Gibbs algorithms, Poisson-minibatching Gibbs supports fast sampling from continuous state spaces and avoids the need for a Metropolis-Hastings correction on discrete state spaces. We demonstrate the effectiveness of our method on multiple applications and in comparison with both plain Gibbs and previous minibatched methods.

We propose a new algorithm---Stochastic Proximal Langevin Algorithm (SPLA)---for sampling from a log concave distribution. Our method is a generalization of the Langevin algorithm to potentials expressed as the sum of one stochastic smooth term and multiple stochastic nonsmooth terms. In each iteration, our splitting technique only requires access to a stochastic gradient of the smooth term and a stochastic proximal operator for each of the nonsmooth terms. We establish nonasymptotic sublinear and linear convergence rates under convexity and strong convexity of the smooth term, respectively, expressed in terms of the KL divergence and Wasserstein distance. We illustrate the efficiency of our sampling technique through numerical simulations on a Bayesian learning task.

Sampling with Markov chain Monte Carlo methods typically amounts to discretizing some continuous-time dynamics with numerical integration. In this paper, we establish the convergence rate of sampling algorithms obtained by discretizing smooth It\^o diffusions exhibiting fast $2$-Wasserstein contraction, based on local deviation properties of the integration scheme. In particular, we study a sampling algorithm constructed by discretizing the overdamped Langevin diffusion with the method of stochastic Runge-Kutta. For strongly convex potentials that are smooth up to a certain order, its iterates converge to the target distribution in $2$-Wasserstein distance in $\tilde{\mathcal{O}}(d\epsilon^{-2/3})$ iterations. This improves upon the best-known rate for strongly log-concave sampling based on the overdamped Langevin equation using only the gradient oracle without adjustment. Additionally, we extend our analysis of stochastic Runge-Kutta methods to uniformly dissipative diffusions with possibly non-convex potentials and show they achieve better rates compared to the Euler-Maruyama scheme on the dependence on tolerance $\epsilon$. Numerical studies show that these algorithms lead to better stability and lower asymptotic errors.