Mixed-Output Gaussian Process Latent Variable Models

This work develops a Bayesian non-parametric approach to signal separation where the signals may vary according to latent variables. Our key contribution is to augment Gaussian Process Latent Variable Models (GPLVMs) to incorporate the case where each data point comprises the weighted sum of a known number of pure component signals, observed across several input locations. Our framework allows the use of a range of priors for the weights of each observation. This flexibility enables us to represent use cases including sum-to-one constraints for estimating fractional makeup, and binary weights for classification. Our contributions are particularly relevant to spectroscopy, where changing conditions may cause the underlying pure component signals to vary from sample to sample. To demonstrate the applicability to both spectroscopy and other domains, we consider several applications: a near-infrared spectroscopy data set with varying temperatures, a simulated data set for identifying flow configuration through a pipe, and a data set for determining the type of rock from its reflectance.

Delayed Feedback in Generalised Linear Bandits Revisited

The stochastic generalised linear bandit is a well-understood model for sequential decision-making problems, with many algorithms achieving near-optimal regret guarantees under immediate feedback. However, in many real world settings, the requirement that the reward is observed immediately is not applicable. In this setting, standard algorithms are no longer theoretically understood. We study the phenomenon of delayed rewards in a theoretical manner by introducing a delay between selecting an action and receiving the reward. Subsequently, we show that an algorithm based on the optimistic principle improves on existing approaches for this setting by eliminating the need for prior knowledge of the delay distribution and relaxing assumptions on the decision set and the delays. This also leads to improving the regret guarantees from $ \widetilde O(\sqrt{dT}\sqrt{d + \mathbb{E}[\tau]})$ to $ \widetilde O(d\sqrt{T} + d^{3/2}\mathbb{E}[\tau])$, where $\mathbb{E}[\tau]$ denotes the expected delay, $d$ is the dimension and $T$ the time horizon and we have suppressed logarithmic terms. We verify our theoretical results through experiments on simulated data.

Variational Bayes for high-dimensional proportional hazards models with applications to gene expression variable selection

We propose a variational Bayesian proportional hazards model for prediction and variable selection regarding high-dimensional survival data. Our method, based on a mean-field variational approximation, overcomes the high computational cost of MCMC whilst retaining the useful features, providing excellent point estimates and offering a natural mechanism for variable selection via posterior inclusion probabilities. The performance of our proposed method is assessed via extensive simulations and compared against other state-of-the-art Bayesian variable selection methods, demonstrating comparable or better performance. Finally, we demonstrate how the proposed method can be used for variable selection on two transcriptomic datasets with censored survival outcomes, where we identify genes with pre-existing biological interpretations.

Delayed Feedback in Episodic Reinforcement Learning

There are many provably efficient algorithms for episodic reinforcement learning. However, these algorithms are built under the assumption that the sequences of states, actions and rewards associated with each episode arrive immediately, allowing policy updates after every interaction with the environment. This assumption is often unrealistic in practice, particularly in areas such as healthcare and online recommendation. In this paper, we study the impact of delayed feedback on several provably efficient algorithms for regret minimisation in episodic reinforcement learning. Firstly, we consider updating the policy as soon as new feedback becomes available. Using this updating scheme, we show that the regret increases by an additive term involving the number of states, actions, episode length and the expected delay. This additive term changes depending on the optimistic algorithm of choice. We also show that updating the policy less frequently can lead to an improved dependency of the regret on the delays.

BART-based inference for Poisson processes

The effectiveness of Bayesian Additive Regression Trees (BART) has been demonstrated in a variety of contexts including non parametric regression and classification. Here we introduce a BART scheme for estimating the intensity of inhomogeneous Poisson Processes. Poisson intensity estimation is a vital task in various applications including medical imaging, astrophysics and network traffic analysis. Our approach enables full posterior inference of the intensity in a nonparametric regression setting. We demonstrate the performance of our scheme through simulation studies on synthetic and real datasets in one and two dimensions, and compare our approach to alternative approaches.

A Bayesian nonparametric test for conditional independence

This article introduces a Bayesian nonparametric method for quantifying the relative evidence in a dataset in favour of the dependence or independence of two variables conditional on a third. The approach uses Polya tree priors on spaces of conditional probability densities, accounting for uncertainty in the form of the underlying distributions in a nonparametric way. The Bayesian perspective provides an inherently symmetric probability measure of conditional dependence or independence, a feature particularly advantageous in causal discovery and not employed by any previous procedure of this type.

Interpreting Deep Neural Networks Through Variable Importance

While the success of deep neural networks (DNNs) is well-established across a variety of domains, our ability to explain and interpret these methods is limited. Unlike previously proposed local methods which try to explain particular classification decisions, we focus on global interpretability and ask a universally applicable question: given a trained model, which features are the most important? In the context of neural networks, a feature is rarely important on its own, so our strategy is specifically designed to leverage partial covariance structures and incorporate variable dependence into feature ranking. Our methodological contributions in this paper are two-fold. First, we propose an effect size analogue for DNNs that is appropriate for applications with highly collinear predictors (ubiquitous in computer vision). Second, we extend the recently proposed "RelATive cEntrality" (RATE) measure (Crawford et al., 2019) to the Bayesian deep learning setting. RATE applies an information theoretic criterion to the posterior distribution of effect sizes to assess feature significance. We apply our framework to three broad application areas: computer vision, natural language processing, and social science.

Large-Scale Kernel Methods for Independence Testing

Representations of probability measures in reproducing kernel Hilbert spaces provide a flexible framework for fully nonparametric hypothesis tests of independence, which can capture any type of departure from independence, including nonlinear associations and multivariate interactions. However, these approaches come with an at least quadratic computational cost in the number of observations, which can be prohibitive in many applications. Arguably, it is exactly in such large-scale datasets that capturing any type of dependence is of interest, so striking a favourable tradeoff between computational efficiency and test performance for kernel independence tests would have a direct impact on their applicability in practice. In this contribution, we provide an extensive study of the use of large-scale kernel approximations in the context of independence testing, contrasting block-based, Nystrom and random Fourier feature approaches. Through a variety of synthetic data experiments, it is demonstrated that our novel large scale methods give comparable performance with existing methods whilst using significantly less computation time and memory.

Bayesian Learning of Kernel Embeddings

Kernel methods are one of the mainstays of machine learning, but the problem of kernel learning remains challenging, with only a few heuristics and very little theory. This is of particular importance in methods based on estimation of kernel mean embeddings of probability measures. For characteristic kernels, which include most commonly used ones, the kernel mean embedding uniquely determines its probability measure, so it can be used to design a powerful statistical testing framework, which includes nonparametric two-sample and independence tests. In practice, however, the performance of these tests can be very sensitive to the choice of kernel and its lengthscale parameters. To address this central issue, we propose a new probabilistic model for kernel mean embeddings, the Bayesian Kernel Embedding model, combining a Gaussian process prior over the Reproducing Kernel Hilbert Space containing the mean embedding with a conjugate likelihood function, thus yielding a closed form posterior over the mean embedding. The posterior mean of our model is closely related to recently proposed shrinkage estimators for kernel mean embeddings, while the posterior uncertainty is a new, interesting feature with various possible applications. Critically for the purposes of kernel learning, our model gives a simple, closed form marginal pseudolikelihood of the observed data given the kernel hyperparameters. This marginal pseudolikelihood can either be optimized to inform the hyperparameter choice or fully Bayesian inference can be used.

Optimism in Reinforcement Learning and Kullback-Leibler Divergence

We consider model-based reinforcement learning in finite Markov De- cision Processes (MDPs), focussing on so-called optimistic strategies. In MDPs, optimism can be implemented by carrying out extended value it- erations under a constraint of consistency with the estimated model tran- sition probabilities. The UCRL2 algorithm by Auer, Jaksch and Ortner (2009), which follows this strategy, has recently been shown to guarantee near-optimal regret bounds. In this paper, we strongly argue in favor of using the Kullback-Leibler (KL) divergence for this purpose. By studying the linear maximization problem under KL constraints, we provide an ef- ficient algorithm, termed KL-UCRL, for solving KL-optimistic extended value iteration. Using recent deviation bounds on the KL divergence, we prove that KL-UCRL provides the same guarantees as UCRL2 in terms of regret. However, numerical experiments on classical benchmarks show a significantly improved behavior, particularly when the MDP has reduced connectivity. To support this observation, we provide elements of com- parison between the two algorithms based on geometric considerations.