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A broad class of stochastic volatility models are defined by systems of stochastic differential equations. While these models have seen widespread success in domains such as finance and statistical climatology, they typically lack an ability to condition on historical data to produce a true posterior distribution. To address this fundamental limitation, we show how to re-cast a class of stochastic volatility models as a hierarchical Gaussian process (GP) model with specialized covariance functions. This GP model retains the inductive biases of the stochastic volatility model while providing the posterior predictive distribution given by GP inference. Within this framework, we take inspiration from well studied domains to introduce a new class of models, Volt and Magpie, that significantly outperform baselines in stock and wind speed forecasting, and naturally extend to the multitask setting., ICML 2022. Code available at https://github.com/g-benton/Volt

Aleatoric uncertainty captures the inherent randomness of the data, such as measurement noise. In Bayesian regression, we often use a Gaussian observation model, where we control the level of aleatoric uncertainty with a noise variance parameter. By contrast, for Bayesian classification we use a categorical distribution with no mechanism to represent our beliefs about aleatoric uncertainty. Our work shows that explicitly accounting for aleatoric uncertainty significantly improves the performance of Bayesian neural networks. We note that many standard benchmarks, such as CIFAR, have essentially no aleatoric uncertainty. Moreover, we show data augmentation in approximate inference has the effect of softening the likelihood, leading to underconfidence and profoundly misrepresenting our honest beliefs about aleatoric uncertainty. Accordingly, we find that a cold posterior, tempered by a power greater than one, often more honestly reflects our beliefs about aleatoric uncertainty than no tempering -- providing an explicit link between data augmentation and cold posteriors. We show that we can match or exceed the performance of posterior tempering by using a Dirichlet observation model, where we explicitly control the level of aleatoric uncertainty, without any need for tempering.

Bayesian optimization (BayesOpt) is a gold standard for query-efficient continuous optimization. However, its adoption for drug design has been hindered by the discrete, high-dimensional nature of the decision variables. We develop a new approach (LaMBO) which jointly trains a denoising autoencoder with a discriminative multi-task Gaussian process head, allowing gradient-based optimization of multi-objective acquisition functions in the latent space of the autoencoder. These acquisition functions allow LaMBO to balance the explore-exploit tradeoff over multiple design rounds, and to balance objective tradeoffs by optimizing sequences at many different points on the Pareto frontier. We evaluate LaMBO on two small-molecule design tasks, and introduce new tasks optimizing \emph{in silico} and \emph{in vitro} properties of large-molecule fluorescent proteins. In our experiments LaMBO outperforms genetic optimizers and does not require a large pretraining corpus, demonstrating that BayesOpt is practical and effective for biological sequence design., ICML 2022. Code available at https://github.com/samuelstanton/lambo

Bayesian optimization is a coherent, ubiquitous approach to decision-making under uncertainty, with applications including multi-arm bandits, active learning, and black-box optimization. Bayesian optimization selects decisions (i.e. objective function queries) with maximal expected utility with respect to the posterior distribution of a Bayesian model, which quantifies reducible, epistemic uncertainty about query outcomes. In practice, subjectively implausible outcomes can occur regularly for two reasons: 1) model misspecification and 2) covariate shift. Conformal prediction is an uncertainty quantification method with coverage guarantees even for misspecified models and a simple mechanism to correct for covariate shift. We propose conformal Bayesian optimization, which directs queries towards regions of search space where the model predictions have guaranteed validity, and investigate its behavior on a suite of black-box optimization tasks and tabular ranking tasks. In many cases we find that query coverage can be significantly improved without harming sample-efficiency., Comment: For code, see https://www.github.com/samuelstanton/conformal-bayesopt.git

While recent work on conjugate gradient methods and Lanczos decompositions have achieved scalable Gaussian process inference with highly accurate point predictions, in several implementations these iterative methods appear to struggle with numerical instabilities in learning kernel hyperparameters, and poor test likelihoods. By investigating CG tolerance, preconditioner rank, and Lanczos decomposition rank, we provide a particularly simple prescription to correct these issues: we recommend that one should use a small CG tolerance ($\epsilon \leq 0.01$) and a large root decomposition size ($r \geq 5000$). Moreover, we show that L-BFGS-B is a compelling optimizer for Iterative GPs, achieving convergence with fewer gradient updates., Comment: ICML 2021 OPTML Workshop

With a better understanding of the loss surfaces for multilayer networks, we can build more robust and accurate training procedures. Recently it was discovered that independently trained SGD solutions can be connected along one-dimensional paths of near-constant training loss. In this paper, we show that there are mode-connecting simplicial complexes that form multi-dimensional manifolds of low loss, connecting many independently trained models. Inspired by this discovery, we show how to efficiently build simplicial complexes for fast ensembling, outperforming independently trained deep ensembles in accuracy, calibration, and robustness to dataset shift. Notably, our approach only requires a few training epochs to discover a low-loss simplex, starting from a pre-trained solution. Code is available at https://github.com/g-benton/loss-surface-simplexes., ICML 2021

The inductive biases of trained neural networks are difficult to understand and, consequently, to adapt to new settings. We study the inductive biases of linearizations of neural networks, which we show to be surprisingly good summaries of the full network functions. Inspired by this finding, we propose a technique for embedding these inductive biases into Gaussian processes through a kernel designed from the Jacobian of the network. In this setting, domain adaptation takes the form of interpretable posterior inference, with accompanying uncertainty estimation. This inference is analytic and free of local optima issues found in standard techniques such as fine-tuning neural network weights to a new task. We develop significant computational speed-ups based on matrix multiplies, including a novel implementation for scalable Fisher vector products. Our experiments on both image classification and regression demonstrate the promise and convenience of this framework for transfer learning, compared to neural network fine-tuning. Code is available at https://github.com/amzn/xfer/tree/master/finite_ntk., Comment: AISTATS 2021

With a principled representation of uncertainty and closed form posterior updates, Gaussian processes (GPs) are a natural choice for online decision making. However, Gaussian processes typically require at least $\mathcal{O}(n^2)$ computations for $n$ training points, limiting their general applicability. Stochastic variational Gaussian processes (SVGPs) can provide scalable inference for a dataset of fixed size, but are difficult to efficiently condition on new data. We propose online variational conditioning (OVC), a procedure for efficiently conditioning SVGPs in an online setting that does not require re-training through the evidence lower bound with the addition of new data. OVC enables the pairing of SVGPs with advanced look-ahead acquisition functions for black-box optimization, even with non-Gaussian likelihoods. We show OVC provides compelling performance in a range of applications including active learning of malaria incidence, and reinforcement learning on MuJoCo simulated robotic control tasks., Comment: NeurIPS 2021

Neural networks appear to have mysterious generalization properties when using parameter counting as a proxy for complexity. Indeed, neural networks often have many more parameters than there are data points, yet still provide good generalization performance. Moreover, when we measure generalization as a function of parameters, we see double descent behaviour, where the test error decreases, increases, and then again decreases. We show that many of these properties become understandable when viewed through the lens of effective dimensionality, which measures the dimensionality of the parameter space determined by the data. We relate effective dimensionality to posterior contraction in Bayesian deep learning, model selection, width-depth tradeoffs, double descent, and functional diversity in loss surfaces, leading to a richer understanding of the interplay between parameters and functions in deep models. We also show that effective dimensionality compares favourably to alternative norm- and flatness- based generalization measures.

A suitable similarity index for comparing learnt neural networks plays an important role in understanding the behaviour of the highly-nonlinear functions, and can provide insights on further theoretical analysis and empirical studies. We define two key steps when comparing models: firstly, the representation abstracted from the learnt model, where we propose to leverage both feature vectors and gradient ones (which are largely ignored in prior work) into designing the representation of a neural network. Secondly, we define the employed similarity index which gives desired invariance properties, and we facilitate the chosen ones with sketching techniques for comparing various datasets efficiently. Empirically, we show that the proposed approach provides a state-of-the-art method for computing similarity of neural networks that are trained independently on different datasets and the tasks defined by the datasets.

We propose SWA-Gaussian (SWAG), a simple, scalable, and general purpose approach for uncertainty representation and calibration in deep learning. Stochastic Weight Averaging (SWA), which computes the first moment of stochastic gradient descent (SGD) iterates with a modified learning rate schedule, has recently been shown to improve generalization in deep learning. With SWAG, we fit a Gaussian using the SWA solution as the first moment and a low rank plus diagonal covariance also derived from the SGD iterates, forming an approximate posterior distribution over neural network weights; we then sample from this Gaussian distribution to perform Bayesian model averaging. We empirically find that SWAG approximates the shape of the true posterior, in accordance with results describing the stationary distribution of SGD iterates. Moreover, we demonstrate that SWAG performs well on a wide variety of tasks, including out of sample detection, calibration, and transfer learning, in comparison to many popular alternatives including MC dropout, KFAC Laplace, SGLD, and temperature scaling., Published at NeurIPS 2019

Bayesian inference was once a gold standard for learning with neural networks, providing accurate full predictive distributions and well calibrated uncertainty. However, scaling Bayesian inference techniques to deep neural networks is challenging due to the high dimensionality of the parameter space. In this paper, we construct low-dimensional subspaces of parameter space, such as the first principal components of the stochastic gradient descent (SGD) trajectory, which contain diverse sets of high performing models. In these subspaces, we are able to apply elliptical slice sampling and variational inference, which struggle in the full parameter space. We show that Bayesian model averaging over the induced posterior in these subspaces produces accurate predictions and well calibrated predictive uncertainty for both regression and image classification., Comment: Published at UAI 2019

Gaussian processes are flexible function approximators, with inductive biases controlled by a covariance kernel. Learning the kernel is the key to representation learning and strong predictive performance. In this paper, we develop functional kernel learning (FKL) to directly infer functional posteriors over kernels. In particular, we place a transformed Gaussian process over a spectral density, to induce a non-parametric distribution over kernel functions. The resulting approach enables learning of rich representations, with support for any stationary kernel, uncertainty over the values of the kernel, and an interpretable specification of a prior directly over kernels, without requiring sophisticated initialization or manual intervention. We perform inference through elliptical slice sampling, which is especially well suited to marginalizing posteriors with the strongly correlated priors typical to function space modelling. We develop our approach for non-uniform, large-scale, multi-task, and multidimensional data, and show promising performance in a wide range of settings, including interpolation, extrapolation, and kernel recovery experiments., Comment: Published at NeurIPS 2019