Traditional approaches to variational inference rely on parametric families of variational distributions, with the choice of family playing a critical role in determining the accuracy of the resulting posterior approximation. Simple mean-field families often lead to poor approximations, while rich families of distributions like normalizing flows can be difficult to optimize and usually do not incorporate the known structure of the target distribution due to their black-box nature. To expand the space of flexible variational families, we revisit Variational Rejection Sampling (VRS) [Grover et al., 2018], which combines a parametric proposal distribution with rejection sampling to define a rich non-parametric family of distributions that explicitly utilizes the known target distribution. By introducing a low-variance reparameterized gradient estimator for the parameters of the proposal distribution, we make VRS an attractive inference strategy for models with continuous latent variables. We argue theoretically and demonstrate empirically that the resulting method--Reparameterized Variational Rejection Sampling (RVRS)--offers an attractive trade-off between computational cost and inference fidelity. In experiments we show that our method performs well in practice and that it is well-suited for black-box inference, especially for models with local latent variables.

Bayesian variable selection is a powerful tool for data analysis, as it offers a principled method for variable selection that accounts for prior information and uncertainty. However, wider adoption of Bayesian variable selection has been hampered by computational challenges, especially in difficult regimes with a large number of covariates P or non-conjugate likelihoods. To scale to the large P regime we introduce an efficient MCMC scheme whose cost per iteration is sublinear in P. In addition we show how this scheme can be extended to generalized linear models for count data, which are prevalent in biology, ecology, economics, and beyond. In particular we design efficient algorithms for variable selection in binomial and negative binomial regression, which includes logistic regression as a special case. In experiments we demonstrate the effectiveness of our methods, including on cancer and maize genomic data.

Variational inference is a powerful paradigm for approximate Bayesian inference with a number of appealing properties, including support for model learning and data subsampling. By contrast MCMC methods like Hamiltonian Monte Carlo do not share these properties but remain attractive since, contrary to parametric methods, MCMC is asymptotically unbiased. For these reasons researchers have sought to combine the strengths of both classes of algorithms, with recent approaches coming closer to realizing this vision in practice. However, supporting data subsampling in these hybrid methods can be a challenge, a shortcoming that we address by introducing a surrogate likelihood that can be learned jointly with other variational parameters. We argue theoretically that the resulting algorithm permits the user to make an intuitive trade-off between inference fidelity and computational cost. In an extensive empirical comparison we show that our method performs well in practice and that it is well-suited for black-box inference in probabilistic programming frameworks.

Bayesian variable selection is a powerful tool for data analysis, as it offers a principled method for variable selection that accounts for prior information and uncertainty. However, wider adoption of Bayesian variable selection has been hampered by computational challenges, especially in difficult regimes with a large number of covariates or non-conjugate likelihoods. Generalized linear models for count data, which are prevalent in biology, ecology, economics, and beyond, represent an important special case. Here we introduce an efficient MCMC scheme for variable selection in binomial and negative binomial regression that exploits Tempered Gibbs Sampling (Zanella and Roberts, 2019) and that includes logistic regression as a special case. In experiments we demonstrate the effectiveness of our approach, including on cancer data with seventeen thousand covariates.

We introduce a simple and scalable method for training Gaussian process (GP) models that exploits cross-validation and nearest neighbor truncation. To accommodate binary and multi-class classification we leverage P\`olya-Gamma auxiliary variables and variational inference. In an extensive empirical comparison with a number of alternative methods for scalable GP regression and classification, we find that our method offers fast training and excellent predictive performance. We argue that the good predictive performance can be traced to the non-parametric nature of the resulting predictive distributions as well as to the cross-validation loss, which provides robustness against model mis-specification.

Bayesian optimization (BO) is a powerful paradigm for efficient optimization of black-box objective functions. High-dimensional BO presents a particular challenge, in part because the curse of dimensionality makes it difficult to define as well as do inference over a suitable class of surrogate models. We argue that Gaussian process surrogate models defined on sparse axis-aligned subspaces offer an attractive compromise between flexibility and parsimony. We demonstrate that our approach, which relies on Hamiltonian Monte Carlo for inference, can rapidly identify sparse subspaces relevant to modeling the unknown objective function, enabling sample-efficient high-dimensional BO. In an extensive suite of experiments comparing to existing methods for high-dimensional BO we demonstrate that our algorithm, Sparse Axis-Aligned Subspace BO (SAASBO), achieves excellent performance on several synthetic and real-world problems without the need to set problem-specific hyperparameters.

Matrix square roots and their inverses arise frequently in machine learning, e.g., when sampling from high-dimensional Gaussians $\mathcal{N}(\mathbf 0, \mathbf K)$ or whitening a vector $\mathbf b$ against covariance matrix $\mathbf K$. While existing methods typically require $O(N^3)$ computation, we introduce a highly-efficient quadratic-time algorithm for computing $\mathbf K^{1/2} \mathbf b$, $\mathbf K^{-1/2} \mathbf b$, and their derivatives through matrix-vector multiplication (MVMs). Our method combines Krylov subspace methods with a rational approximation and typically achieves $4$ decimal places of accuracy with fewer than $100$ MVMs. Moreover, the backward pass requires little additional computation. We demonstrate our method's applicability on matrices as large as $50,\!000 \times 50,\!000$ - well beyond traditional methods - with little approximation error. Applying this increased scalability to variational Gaussian processes, Bayesian optimization, and Gibbs sampling results in more powerful models with higher accuracy.

The combination of inducing point methods with stochastic variational inference has enabled approximate Gaussian Process (GP) inference on large datasets. Unfortunately, the resulting predictive distributions often exhibit substantially underestimated uncertainties. Worse still, in the regression case the predictive variance is typically dominated by observation noise, yielding uncertainty estimates that make little use of the input-dependent function uncertainty that makes GP priors attractive. In this work we propose a simple inference procedure that bypasses posterior approximations and instead directly targets the posterior predictive distribution. In an extensive empirical comparison with a number of alternative inference strategies on univariate and multivariate regression tasks, we find that the resulting predictive distributions exhibit significantly better calibrated uncertainties and higher log likelihoods--often by as much as half a nat or more per datapoint.

We construct flexible likelihoods for multi-output Gaussian process models that leverage neural networks as components. We make use of sparse variational inference methods to enable scalable approximate inference for the resulting class of models. An attractive feature of these models is that they can admit analytic predictive means even when the likelihood is non-linear and the predictive distributions are non-Gaussian. We validate the modeling potential of these models in a variety of experiments in both the supervised and unsupervised setting. We demonstrate that the flexibility of these `neural' likelihoods can improve prediction quality as compared to simpler Gaussian process models and that neural likelihoods can be readily combined with a variety of underlying Gaussian process models, including deep Gaussian processes.

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 suited to the experiment design context by building on ideas from variational inference and mutual information estimation. We show theoretically and empirically that these estimators can provide significant gains in speed and accuracy over previous approaches. We demonstrate the practicality of our approach via a number of experiments, including an adaptive experiment with human participants.