Sequential Monte Carlo approximations of Wasserstein--Fisher--Rao gradient flows

We consider the problem of sampling from a probability distribution $\pi$. It is well known that this can be written as an optimisation problem over the space of probability distribution in which we aim to minimise the Kullback--Leibler divergence from $\pi$. We consider several partial differential equations (PDEs) whose solution is a minimiser of the Kullback--Leibler divergence from $\pi$ and connect them to well-known Monte Carlo algorithms. We focus in particular on PDEs obtained by considering the Wasserstein--Fisher--Rao geometry over the space of probabilities and show that these lead to a natural implementation using importance sampling and sequential Monte Carlo. We propose a novel algorithm to approximate the Wasserstein--Fisher--Rao flow of the Kullback--Leibler divergence which empirically outperforms the current state-of-the-art. We study tempered versions of these PDEs obtained by replacing the target distribution with a geometric mixture of initial and target distribution and show that these do not lead to a convergence speed up.

Connections between sequential Bayesian inference and evolutionary dynamics

It has long been posited that there is a connection between the dynamical equations describing evolutionary processes in biology and sequential Bayesian learning methods. This manuscript describes new research in which this precise connection is rigorously established in the continuous time setting. Here we focus on a partial differential equation known as the Kushner-Stratonovich equation describing the evolution of the posterior density in time. Of particular importance is a piecewise smooth approximation of the observation path from which the discrete time filtering equations, which are shown to converge to a Stratonovich interpretation of the Kushner-Stratonovich equation. This smooth formulation will then be used to draw precise connections between nonlinear stochastic filtering and replicator-mutator dynamics. Additionally, gradient flow formulations will be investigated as well as a form of replicator-mutator dynamics which is shown to be beneficial for the misspecified model filtering problem. It is hoped this work will spur further research into exchanges between sequential learning and evolutionary biology and to inspire new algorithms in filtering and sampling.

PULASki: Learning inter-rater variability using statistical distances to improve probabilistic segmentation

In the domain of medical imaging, many supervised learning based methods for segmentation face several challenges such as high variability in annotations from multiple experts, paucity of labelled data and class imbalanced datasets. These issues may result in segmentations that lack the requisite precision for clinical analysis and can be misleadingly overconfident without associated uncertainty quantification. We propose the PULASki for biomedical image segmentation that accurately captures variability in expert annotations, even in small datasets. Our approach makes use of an improved loss function based on statistical distances in a conditional variational autoencoder structure (Probabilistic UNet), which improves learning of the conditional decoder compared to the standard cross-entropy particularly in class imbalanced problems. We analyse our method for two structurally different segmentation tasks (intracranial vessel and multiple sclerosis (MS) lesion) and compare our results to four well-established baselines in terms of quantitative metrics and qualitative output. Empirical results demonstrate the PULASKi method outperforms all baselines at the 5\% significance level. The generated segmentations are shown to be much more anatomically plausible than in the 2D case, particularly for the vessel task. Our method can also be applied to a wide range of multi-label segmentation tasks and and is useful for downstream tasks such as hemodynamic modelling (computational fluid dynamics and data assimilation), clinical decision making, and treatment planning.