The sigma-point filters, such as the UKF, which exploit numerical quadrature to obtain an additional order of accuracy in the moment transformation step, are popular alternatives to the ubiquitous EKF. The classical quadrature rules used in the sigma-point filters are motivated via polynomial approximation of the integrand, however in the applied context these assumptions cannot always be justified. As a result, quadrature error can introduce bias into estimated moments, for which there is no compensatory mechanism in the classical sigma-point filters. This can lead in turn to estimates and predictions that are poorly calibrated. In this article, we investigate the Bayes-Sard quadrature method in the context of sigma-point filters, which enables uncertainty due to quadrature error to be formalised within a probabilistic model. Our first contribution is to derive the well-known classical quadratures as special cases of the Bayes-Sard quadrature method. Then a general-purpose moment transform is developed and utilised in the design of novel sigma-point filters, so that uncertainty due to quadrature error is explicitly quantified. Numerical experiments on a challenging tracking example with misspecified initial conditions show that the additional uncertainty quantification built into our method leads to better-calibrated state estimates with improved RMSE.

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has led to the intriguing discovery that individual cell profiles can reflect the imprint of time or dynamic processes. However, synthesizing this information to reconstruct dynamic biological phenomena from data that are noisy, heterogenous, and sparse---and from processes that may unfold asynchronously---poses a complex computational and statistical challenge. Here, we develop a full generative model for probabilistically reconstructing trees of cellular differentiation from single-cell RNA-seq data. Specifically, we extend the framework of the classical Dirichlet diffusion tree to simultaneously infer branch topology and latent cell states along continuous trajectories over the full tree. In tandem, we construct a novel Markov chain Monte Carlo sampler that interleaves Metropolis-Hastings and message passing to leverage model structure for efficient inference. Finally, we demonstrate that these techniques can recover latent trajectories from simulated single-cell transcriptomes. While this work is motivated by cellular differentiation, we derive a tractable model that provides flexible densities for any data (coupled with an appropriate noise model) that arise from continuous evolution along a latent nonparametric tree.

Recently, techniques for applying convolutional neural networks to graph-structured data have emerged. Graph convolutional neural networks (GCNNs) have been used to address node and graph classification and matrix completion. Although the performance has been impressive, the current implementations have limited capability to incorporate uncertainty in the graph structure. Almost all GCNNs process a graph as though it is a ground-truth depiction of the relationship between nodes, but often the graphs employed in applications are themselves derived from noisy data or modelling assumptions. Spurious edges may be included; other edges may be missing between nodes that have very strong relationships. In this paper we adopt a Bayesian approach, viewing the observed graph as a realization from a parametric family of random graphs. We then target inference of the joint posterior of the random graph parameters and the node (or graph) labels. We present the Bayesian GCNN framework and develop an iterative learning procedure for the case of assortative mixed-membership stochastic block models. We present the results of experiments that demonstrate that the Bayesian formulation can provide better performance when there are very few labels available during the training process.

Assessing the fairness of a decision making system with respect to a protected class, such as gender or race, is challenging when class membership labels are unavailable. Probabilistic models for predicting the protected class based on observable proxies, such as surname and geolocation for race, are sometimes used to impute these missing labels for compliance assessments. Empirically, these methods are observed to exaggerate disparities, but the reason why is unknown. In this paper, we decompose the biases in estimating outcome disparity via threshold-based imputation into multiple interpretable bias sources, allowing us to explain when over- or underestimation occurs. We also propose an alternative weighted estimator that uses soft classification, and show that its bias arises simply from the conditional covariance of the outcome with the true class membership. Finally, we illustrate our results with numerical simulations and a public dataset of mortgage applications, using geolocation as a proxy for race. We confirm that the bias of threshold-based imputation is generally upward, but its magnitude varies strongly with the threshold chosen. Our new weighted estimator tends to have a negative bias that is much simpler to analyze and reason about.

Ensembles of neural networks (NNs) have long been used to estimate predictive uncertainty; a small number of NNs are trained from different initialisations and sometimes on differing versions of the dataset. The variance of the ensemble's predictions is interpreted as its epistemic uncertainty. The appeal of ensembling stems from being a collection of regular NNs - this makes them both scalable and easily implementable. They have achieved strong empirical results in recent years, often presented as a practical alternative to more costly Bayesian NNs (BNNs). The departure from Bayesian methodology is of concern since the Bayesian framework provides a principled, widely-accepted approach to handling uncertainty. In this extended abstract we derive and implement a modified NN ensembling scheme, which provides a consistent estimator of the Bayesian posterior in wide NNs - regularising parameters about values drawn from a prior distribution.

This technical report describes the multi-label classification (MLC) search space in the MEKA software, including the traditional/meta MLC algorithms, and the traditional/meta/pre-processing single-label classification (SLC) algorithms. The SLC search space is also studied because is part of MLC search space as several methods use problem transformation methods to create a solution (i.e., a classifier) for a MLC problem. This was done in order to understand better the MLC algorithms. Finally, we propose a grammar that formally expresses this understatement.

Variational inference (VI) has become the method of choice for fitting many modern probabilistic models. However, practitioners are faced with a fragmented literature that offers a bewildering array of algorithmic options. First, the variational family. Second, the granularity of the updates e.g. whether the updates are local to each data point and employ message passing or global. Third, the method of optimization (bespoke or blackbox, closed-form or stochastic updates, etc.). This paper presents a new framework, termed Partitioned Variational Inference (PVI), that explicitly acknowledges these algorithmic dimensions of VI, unifies disparate literature, and provides guidance on usage. Crucially, the proposed PVI framework allows us to identify new ways of performing VI that are ideally suited to challenging learning scenarios including federated learning (where distributed computing is leveraged to process non-centralized data) and continual learning (where new data and tasks arrive over time and must be accommodated quickly). We showcase these new capabilities by developing communication-efficient federated training of Bayesian neural networks and continual learning for Gaussian process models with private pseudo-points. The new methods significantly outperform the state-of-the-art, whilst being almost as straightforward to implement as standard VI.

The typical pipeline for a supervised machine learning project involves firstly the collection of a significant sample of labelled examples typically referred to as training data. Depending on whether the labels are continuous or categorical, the supervised learning task is known as regression or classification respectively. Next, once the training data is sufficiently clean and complete, it is used to directly build a predictive model using the machine learning algorithm of choice. The predictive model is then used to label new unlabelled examples, and if the labels of the new examples are known a priori by the user (but not used by the learning algorithm) then the predictive accuracy of the model can be evaluated. Different models can therefore be directly compared. In the usual case, the training data is "real", i.e. the model is learned directly from labelled examples that were collected specifically for that purpose. However, quite frequently, modifications are made to the training data after it is collected. For example, it is standard practice to remove outlier examples and normalise numeric values. Moreover, the machine learning algorithm itself may specify modifications to the training data.

This work presents an approach to automatically induction for non-greedy decision trees constructed from neural network architecture. This construction can be used to transfer weights when growing or pruning a decision tree, allowing non-greedy decision tree algorithms to automatically learn and adapt to the ideal architecture. In this work, we examine the underpinning ideas within ensemble modelling and Bayesian model averaging which allow our neural network to asymptotically approach the ideal architecture through weights transfer. Experimental results demonstrate that this approach improves models over fixed set of hyperparameters for decision tree models and decision forest models.

This article is the rejoinder for the paper "Probabilistic Integration: A Role in Statistical Computation?" to appear in Statistical Science with discussion [Briol et al., 2015]. We would first like to thank the reviewers and many of our colleagues who helped shape this paper, the editor for selecting our paper for discussion, and of course all of the discussants for their thoughtful, insightful and constructive comments. In this rejoinder, we respond to some of the points raised by the discussants and comment further on the fundamental questions underlying the paper: - Should Bayesian ideas be used in numerical analysis? Numerical analysis is concerned with the approximation of typically high or infinite-dimensional mathematical quantities using discretisations of the space on which these are defined. Different discretisation schemes lead to different numerical algorithms, whose stability and convergence properties need to be carefully assessed.