As is well known, both sampling from the posterior and computing the mean of the posterior in Gaussian process regression reduces to solving a large linear system of equations. We study the use of stochastic gradient descent for solving this linear system, and show that when done right---by which we mean using specific insights from the optimisation and kernel communities---stochastic gradient descent is highly effective. To that end, we introduce a particularly simple stochastic dual descent algorithm, explain its design in an intuitive manner and illustrate the design choices through a series of ablation studies. Further experiments demonstrate that our new method is highly competitive. In particular, our evaluations on the UCI regression tasks and on Bayesian optimisation set our approach apart from preconditioned conjugate gradients and variational Gaussian process approximations. Moreover, our method places Gaussian process regression on par with state-of-the-art graph neural networks for molecular binding affinity prediction.

Correctly capturing the symmetry transformations of data can lead to efficient models with strong generalization capabilities, though methods incorporating symmetries often require prior knowledge. While recent advancements have been made in learning those symmetries directly from the dataset, most of this work has focused on the discriminative setting. In this paper, we take inspiration from group theoretic ideas to construct a generative model that explicitly aims to capture the data's approximate symmetries. This results in a model that, given a prespecified broad set of possible symmetries, learns to what extent, if at all, those symmetries are actually present. Our model can be seen as a generative process for data augmentation. We provide a simple algorithm for learning our generative model and empirically demonstrate its ability to capture symmetries under affine and color transformations, in an interpretable way. Combining our symmetry model with standard generative models results in higher marginal test-log-likelihoods and improved data efficiency.

Scaling hyperparameter optimisation to very large datasets remains an open problem in the Gaussian process community. This paper focuses on iterative methods, which use linear system solvers, like conjugate gradients, alternating projections or stochastic gradient descent, to construct an estimate of the marginal likelihood gradient. We discuss three key improvements which are applicable across solvers: (i) a pathwise gradient estimator, which reduces the required number of solver iterations and amortises the computational cost of making predictions, (ii) warm starting linear system solvers with the solution from the previous step, which leads to faster solver convergence at the cost of negligible bias, (iii) early stopping linear system solvers after a limited computational budget, which synergises with warm starting, allowing solver progress to accumulate over multiple marginal likelihood steps. These techniques provide speed-ups of up to $72\times$ when solving to tolerance, and decrease the average residual norm by up to $7\times$ when stopping early.

Gaussian processes are a powerful framework for quantifying uncertainty and for sequential decision-making but are limited by the requirement of solving linear systems. In general, this has a cubic cost in dataset size and is sensitive to conditioning. We explore stochastic gradient algorithms as a computationally efficient method of approximately solving these linear systems: we develop low-variance optimization objectives for sampling from the posterior and extend these to inducing points. Counterintuitively, stochastic gradient descent often produces accurate predictions, even in cases where it does not converge quickly to the optimum. We explain this through a spectral characterization of the implicit bias from non-convergence. We show that stochastic gradient descent produces predictive distributions close to the true posterior both in regions with sufficient data coverage, and in regions sufficiently far away from the data. Experimentally, stochastic gradient descent achieves state-of-the-art performance on sufficiently large-scale or ill-conditioned regression tasks. Its uncertainty estimates match the performance of significantly more expensive baselines on a large-scale Bayesian~optimization~task.

Coupling normalizing flows allow for fast sampling and density evaluation, making them the tool of choice for probabilistic modeling of physical systems. However, the standard coupling architecture precludes endowing flows that operate on the Cartesian coordinates of atoms with the SE(3) and permutation invariances of physical systems. This work proposes a coupling flow that preserves SE(3) and permutation equivariance by performing coordinate splits along additional augmented dimensions. At each layer, the flow maps atoms' positions into learned SE(3) invariant bases, where we apply standard flow transformations, such as monotonic rational-quadratic splines, before returning to the original basis. Crucially, our flow preserves fast sampling and density evaluation, and may be used to produce unbiased estimates of expectations with respect to the target distribution via importance sampling. When trained on the DW4, LJ13, and QM9-positional datasets, our flow is competitive with equivariant continuous normalizing flows and diffusion models, while allowing sampling more than an order of magnitude faster. Moreover, to the best of our knowledge, we are the first to learn the full Boltzmann distribution of alanine dipeptide by only modeling the Cartesian positions of its atoms. Lastly, we demonstrate that our flow can be trained to approximately sample from the Boltzmann distribution of the DW4 and LJ13 particle systems using only their energy functions.

The linearised Laplace method for estimating model uncertainty has received renewed attention in the Bayesian deep learning community. The method provides reliable error bars and admits a closed-form expression for the model evidence, allowing for scalable selection of model hyperparameters. In this work, we examine the assumptions behind this method, particularly in conjunction with model selection. We show that these interact poorly with some now-standard tools of deep learning–stochastic approximation methods and normalisation layers–and make recommendations for how to better adapt this classic method to the modern setting. We provide theoretical support for our recommendations and validate them empirically on MLPs, classic CNNs, residual networks with and without normalisation layers, generative autoencoders and transformers.

Algorithmic transparency entails exposing system properties to various stakeholders for purposes that include understanding, improving, and contesting predictions. Until now, most research into algorithmic transparency has predominantly focused on explainability. Explainability attempts to provide reasons for a machine learning model's behavior to stakeholders. However, understanding a model's specific behavior alone might not be enough for stakeholders to gauge whether the model is wrong or lacks sufficient knowledge to solve the task at hand. In this paper, we argue for considering a complementary form of transparency by estimating and communicating the uncertainty associated with model predictions. First, we discuss methods for assessing uncertainty. Then, we characterize how uncertainty can be used to mitigate model unfairness, augment decision-making, and build trustworthy systems. Finally, we outline methods for displaying uncertainty to stakeholders and recommend how to collect information required for incorporating uncertainty into existing ML pipelines. This work constitutes an interdisciplinary review drawn from literature spanning machine learning, visualization/HCI, design, decision-making, and fairness. We aim to encourage researchers and practitioners to measure, communicate, and use uncertainty as a form of transparency.

The Bayesian paradigm has the potential to solve core issues of deep neural networks such as poor calibration and data inefficiency. Alas, scaling Bayesian inference to large weight spaces often requires restrictive approximations. In this work, we show that it suffices to perform inference over a small subset of model weights in order to obtain accurate predictive posteriors. The other weights are kept as point estimates. This subnetwork inference framework enables us to use expressive, otherwise intractable, posterior approximations over such subsets. In particular, we implement subnetwork linearized Laplace as a simple, scalable Bayesian deep learning method: We first obtain a MAP estimate of all weights and then infer a full-covariance Gaussian posterior over a subnetwork using the linearized Laplace approximation. We propose a subnetwork selection strategy that aims to maximally preserve the model’s predictive uncertainty. Empirically, our approach compares favorably to ensembles and less expressive posterior approximations over full networks.

Existing methods for estimating uncertainty in deep learning tend to require multiple forward passes, making them unsuitable for applications where computational resources are limited. To solve this, we perform probabilistic reasoning over the depth of neural networks. Different depths correspond to subnetworks which share weights and whose predictions are combined via marginalisation, yielding model uncertainty. By exploiting the sequential structure of feed-forward networks, we are able to both evaluate our training objective and make predictions with a single forward pass. We validate our approach on real-world regression and image classification tasks. Our approach provides uncertainty calibration, robustness to dataset shift, and accuracies competitive with more computationally expensive baselines.

Learning representations that disentangle the underlying factors of variability in data is an intuitive way to achieve generalization in deep models. In this work, we address the scenario where generative factors present a multimodal distribution due to the existence of class distinction in the data. We propose N-VAE, a model which is capable of separating factors of variation which are exclusive to certain classes from factors that are shared among classes. This model implements an explicitly compositional latent variable structure by defining a class-conditioned latent space and a shared latent space. We show its usefulness for detecting and disentangling class-dependent generative factors as well as its capacity to generate artificial samples which contain characteristics unseen in the training data.