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.Comment: 29 pages, 6 figure

Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures

In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a "null model" of pairwise independence. In simulation studies, as well as for a real data analysis, we show that our approach provides a useful tool for the exploratory nonparametric Bayesian analysis of large multivariate data sets

Considerate Approaches to Achieving Sufficiency for ABC model selection

For nearly any challenging scientific problem evaluation of the likelihood is problematic if not impossible. Approximate Bayesian computation (ABC) allows us to employ the whole Bayesian formalism to problems where we can use simulations from a model, but cannot evaluate the likelihood directly. When summary statistics of real and simulated data are compared --- rather than the data directly --- information is lost, unless the summary statistics are sufficient. Here we employ an information-theoretical framework that can be used to construct (approximately) sufficient statistics by combining different statistics until the loss of information is minimized. Such sufficient sets of statistics are constructed for both parameter estimation and model selection problems. We apply our approach to a range of illustrative and real-world model selection problems

Modelling phylogeny in 16S rRNA gene sequencing datasets using string kernels

Bacterial community composition is measured using 16S rRNA (ribosomal ribonucleic acid) gene sequencing, for which one of the defining characteristics is the phylogenetic relationships that exist between variables. Here, we demonstrate the utility of modelling these relationships in two statistical tasks (the two sample test and host trait prediction) by employing string kernels originally proposed in natural language processing. We show via simulation studies that a kernel two-sample test using the proposed kernels, which explicitly model phylogenetic relationships, is powerful while also being sensitive to the phylogenetic scale of the difference between the two populations. We also demonstrate how the proposed kernels can be used with Gaussian processes to improve predictive performance in host trait prediction. Our method is implemented in the Python package StringPhylo (available at github.com/jonathanishhorowicz/stringphylo)

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

Group Spike and Slab Variational Bayes

We introduce Group Spike-and-slab Variational Bayes (GSVB), a scalable method for group sparse regression. A fast co-ordinate ascent variational inference (CAVI) algorithm is developed for several common model families including Gaussian, Binomial and Poisson. Theoretical guarantees for our proposed approach are provided by deriving contraction rates for the variational posterior in grouped linear regression. Through extensive numerical studies, we demonstrate that GSVB provides state-of-the-art performance, offering a computationally inexpensive substitute to MCMC, whilst performing comparably or better than existing MAP methods. Additionally, we analyze three real world datasets wherein we highlight the practical utility of our method, demonstrating that GSVB provides parsimonious models with excellent predictive performance, variable selection and uncertainty quantification.Comment: 66 pages, 5 figures, 7 table