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Hawkes processes are point process models that have been used to capture self-excitatory behavior in social interactions, neural activity, earthquakes and viral epidemics. They can model the occurrence of the times and locations of events. Here we develop a new class of spatiotemporal Hawkes processes that can capture both triggering and clustering behavior and we provide an efficient method for performing inference. We use a log-Gaussian Cox process (LGCP) as prior for the background rate of the Hawkes process which gives arbitrary flexibility to capture a wide range of underlying background effects (for infectious diseases these are called endemic effects). The Hawkes process and LGCP are computationally expensive due to the former having a likelihood with quadratic complexity in the number of observations and the latter involving inversion of the precision matrix which is cubic in observations. Here we propose a novel approach to perform MCMC sampling for our Hawkes process with LGCP background, using pre-trained Gaussian Process generators which provide direct and cheap access to samples during inference. We show the efficacy and flexibility of our approach in experiments on simulated data and use our methods to uncover the trends in a dataset of reported crimes in the US., Comment: 8 Figures, 27 pages without references, 3 pages of references

Renewal equations are a popular approach used in modelling the number of new infections, i.e., incidence, in an outbreak. We develop a stochastic model of an outbreak based on a time-varying variant of the Crump-Mode-Jagers branching process. This model accommodates a time-varying reproduction number and a time-varying distribution for the generation interval. We then derive renewal-like integral equations for incidence, cumulative incidence and prevalence under this model. We show that the equations for incidence and prevalence are consistent with the so-called back-calculation relationship. We analyse two particular cases of these integral equations, one that arises from a Bellman-Harris process and one that arises from an inhomogeneous Poisson process model of transmission. We also show that the incidence integral equations that arise from both of these specific models agree with the renewal equation used ubiquitously in infectious disease modelling. We present a numerical discretisation scheme to solve these equations, and use this scheme to estimate rates of transmission from serological prevalence of SARS-CoV-2 in the UK and historical incidence data on Influenza, Measles, SARS and Smallpox., Comment: 35 pages, 4 figures, v4: major revision, including a new argument for the equivalence of incidence equations

Updating observations of a signal due to the delays in the measurement process is a common problem in signal processing, with prominent examples in a wide range of fields. An important example of this problem is the nowcasting of COVID-19 mortality: given a stream of reported counts of daily deaths, can we correct for the delays in reporting to paint an accurate picture of the present, with uncertainty? Without this correction, raw data will often mislead by suggesting an improving situation. We present a flexible approach using a latent Gaussian process that is capable of describing the changing auto-correlation structure present in the reporting time-delay surface. This approach also yields robust estimates of uncertainty for the estimated nowcasted numbers of deaths. We test assumptions in model specification such as the choice of kernel or hyper priors, and evaluate model performance on a challenging real dataset from Brazil. Our experiments show that Gaussian process nowcasting performs favourably against both comparable methods, and against a small sample of expert human predictions. Our approach has substantial practical utility in disease modelling -- by applying our approach to COVID-19 mortality data from Brazil, where reporting delays are large, we can make informative predictions on important epidemiological quantities such as the current effective reproduction number., Comment: 26 pages, 31 figures

Successfully training Variational Autoencoders (VAEs) with a hierarchy of discrete latent variables remains an area of active research. Vector-Quantised VAEs are a powerful approach to discrete VAEs, but naive hierarchical extensions can be unstable when training. Leveraging insights from classical methods of inference we introduce \textit{Relaxed-Responsibility Vector-Quantisation}, a novel way to parameterise discrete latent variables, a refinement of relaxed Vector-Quantisation that gives better performance and more stable training. This enables a novel approach to hierarchical discrete variational autoencoders with numerous layers of latent variables (here up to 32) that we train end-to-end. Within hierarchical probabilistic deep generative models with discrete latent variables trained end-to-end, we achieve state-of-the-art bits-per-dim results for various standard datasets. % Unlike discrete VAEs with a single layer of latent variables, we can produce samples by ancestral sampling: it is not essential to train a second autoregressive generative model over the learnt latent representations to then sample from and then decode. % Moreover, that latter approach in these deep hierarchical models would require thousands of forward passes to generate a single sample. Further, we observe different layers of our model become associated with different aspects of the data., Comment: 10 Pages

Infinite-activity completely random measures (CRMs) have become important building blocks of complex Bayesian nonparametric models. They have been successfully used in various applications such as clustering, density estimation, latent feature models, survival analysis or network science. Popular infinite-activity CRMs include the (generalized) gamma process and the (stable) beta process. However, except in some specific cases, exact simulation or scalable inference with these models is challenging and finite-dimensional approximations are often considered. In this work, we propose a general and unified framework to derive both series representations and finite-dimensional approximations of CRMs. Our framework can be seen as an extension of constructions based on size-biased sampling of Poisson point process [Perman1992]. It includes as special cases several known series representations as well as novel ones. In particular, we show that one can get novel series representations for the generalized gamma process and the stable beta process. We also provide some analysis of the truncation error.

We propose a novel class of network models for temporal dyadic interaction data. Our goal is to capture a number of important features often observed in social interactions: sparsity, degree heterogeneity, community structure and reciprocity. We propose a family of models based on self-exciting Hawkes point processes in which events depend on the history of the process. The key component is the conditional intensity function of the Hawkes Process, which captures the fact that interactions may arise as a response to past interactions (reciprocity), or due to shared interests between individuals (community structure). In order to capture the sparsity and degree heterogeneity, the base (non time dependent) part of the intensity function builds on compound random measures following Todeschini et al. (2016). We conduct experiments on a variety of real-world temporal interaction data and show that the proposed model outperforms many competing approaches for link prediction, and leads to interpretable parameters.

We propose a novel statistical model for sparse networks with overlapping community structure. The model is based on representing the graph as an exchangeable point process, and naturally generalizes existing probabilistic models with overlapping block-structure to the sparse regime. Our construction builds on vectors of completely random measures, and has interpretable parameters, each node being assigned a vector representing its level of affiliation to some latent communities. We develop methods for simulating this class of random graphs, as well as to perform posterior inference. We show that the proposed approach can recover interpretable structure from two real-world networks and can handle graphs with thousands of nodes and tens of thousands of edges.