Simulation-based inference has been popular for amortized Bayesian computation. It is typical to have more than one posterior approximation, from different inference algorithms, different architectures, or simply the randomness of initialization and stochastic gradients. With a consistency guarantee, we present a general posterior stacking framework to make use of all available approximations. Our stacking method is able to combine densities, simulation draws, confidence intervals, and moments, and address the overall precision, calibration, coverage, and bias of the posterior approximation at the same time. We illustrate our method on several benchmark simulations and a challenging cosmological inference task.

Importance weighting is a general way to adjust Monte Carlo integration to account for draws from the wrong distribution, but the resulting estimate can be highly variable when the importance ratios have a heavy right tail. This routinely occurs when there are aspects of the target distribution that are not well captured by the approximating distribution, in which case more stable estimates can be obtained by modifying extreme importance ratios. We present a new method for stabilizing importance weights using a generalized Pareto distribution fit to the upper tail of the distribution of the simulated importance ratios. The method, which empirically performs better than existing methods for stabilizing importance sampling estimates, includes stabilized effective sample size estimates, Monte Carlo error estimates, and convergence diagnostics. The presented Pareto $\hat{k}$ finite sample convergence rate diagnostic is useful for any Monte Carlo estimator.

Variational inference (VI) is a method to approximate the computationally intractable posterior distributions that arise in Bayesian statistics. Typically, VI fits a simple parametric distribution to be close to the target posterior, optimizing an appropriate objective such as the evidence lower bound (ELBO). In this work, we present a new approach to VI. Our method is based on the principle of score matching---namely, that if two distributions are equal then their score functions (i.e., gradients of the log density) are equal at every point on their support. With this principle, we develop score-matching VI, an iterative algorithm that seeks to match the scores between the variational approximation and the exact posterior. At each iteration, score-matching VI solves an inner optimization, one that minimally adjusts the current variational estimate to match the scores at a newly sampled value of the latent variables. We show that when the variational family is a Gaussian, this inner optimization enjoys a closed-form solution, which we call Gaussian score matching VI (GSM-VI). GSM-VI is a ``black box'' variational algorithm in that it only requires a differentiable joint distribution, and as such it can be applied to a wide class of models. We compare GSM-VI to black box variational inference (BBVI), which has similar requirements but instead optimizes the ELBO. We first study how GSM-VI behaves as a function of the problem dimensionality, the condition number of the target covariance matrix (when the target is Gaussian), and the degree of mismatch between the approximating and exact posterior distribution. We then study GSM-VI on a collection of real-world Bayesian inference problems from the posteriorDB database of datasets and models. We find that GSM-VI is faster than BBVI and equally or more accurate. Specifically, over a wide range of target posteriors, GSM-VI requires 10-100x fewer gradient evaluations than BBVI to obtain a comparable quality of approximation.

To check the accuracy of Bayesian computations, it is common to use rank-based simulation-based calibration (SBC). However, SBC has drawbacks: The test statistic is somewhat ad-hoc, interactions are difficult to examine, multiple testing is a challenge, and the resulting p-value is not a divergence metric. We propose to replace the marginal rank test with a flexible classification approach that learns test statistics from data. This measure typically has a higher statistical power than the SBC test and returns an interpretable divergence measure of miscalibration, computed from classification accuracy. This approach can be used with different data generating processes to address simulation-based inference or traditional inference methods like Markov chain Monte Carlo or variational inference. We illustrate an automated implementation using neural networks and statistically-inspired features, and validate the method with numerical and real data experiments.

When working with multimodal Bayesian posterior distributions, Markov chain Monte Carlo (MCMC) algorithms have difficulty moving between modes, and default variational or mode-based approximate inferences will understate posterior uncertainty. And, even if the most important modes can be found, it is difficult to evaluate their relative weights in the posterior. Here we propose an approach using parallel runs of MCMC, variational, or mode-based inference to hit as many modes or separated regions as possible and then combine these using Bayesian stacking, a scalable method for constructing a weighted average of distributions. The result from stacking efficiently samples from multimodal posterior distribution, minimizes cross validation prediction error, and represents the posterior uncertainty better than variational inference, but it is not necessarily equivalent, even asymptotically, to fully Bayesian inference. We present theoretical consistency with an example where the stacked inference approximates the true data generating process from the misspecified model and a non-mixing sampler, from which the predictive performance is better than full Bayesian inference, hence the multimodality can be considered a blessing rather than a curse under model misspecification. We demonstrate practical implementation in several model families: latent Dirichlet allocation, Gaussian process regression, hierarchical regression, horseshoe variable selection, and neural networks.

While it’s always possible to compute a variational approximation to a posterior distribution, it can be difficult to discover problems with this approximation. We propose two diagnostic algorithms to alleviate this problem. The Pareto-smoothed importance sampling (PSIS) diagnostic gives a goodness of fit measurement for joint distributions, while simultaneously improving the error in the estimate. The variational simulation-based calibration (VSBC) assesses the average performance of point estimates.