Multiple lines of evidence strongly suggest that infection hotspots, where a single individual infects many others, play a key role in the transmission dynamics of COVID-19. However, most of the existing epidemiological models fail to capture this aspect by neither representing the sites visited by individuals explicitly nor characterizing disease transmission as a function of individual mobility patterns. In this work, we introduce a temporal point process modeling framework that specifically represents visits to the sites where individuals get in contact and infect each other. Under our model, the number of infections caused by an infectious individual naturally emerges to be overdispersed. Using an efficient sampling algorithm, we demonstrate how to estimate the transmission rate of infectious individuals at the sites they visit and in their households using Bayesian optimization and longitudinal case data. Simulations using fine-grained and publicly available demographic data and site locations from Bern, Switzerland showcase the flexibility of our framework. To facilitate research and analyses of other cities and regions, we release an open-source implementation of our framework.

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Bayesian structure learning allows inferring Bayesian network structure from data while reasoning about the epistemic uncertainty-a key element towards enabling active causal discovery and designing interventions in real world systems. In this work, we propose a general, fully differentiable framework for Bayesian structure learning (DiBS) that operates in the continuous space of a latent probabilistic graph representation. Building on recent advances in variational inference, we use DiBS to devise an efficient method for approximating posteriors over structural models. Contrary to existing work, DiBS is agnostic to the form of the local conditional distributions and allows for joint posterior inference of both the graph structure and the conditional distribution parameters. This makes our method directly applicable to posterior inference of nonstandard Bayesian network models, e.g., with nonlinear dependencies encoded by neural networks. In evaluations on simulated and real-world data, DiBS significantly outperforms related approaches to joint posterior inference.

The ongoing COVID-19 pandemic let to efforts to develop and deploy digital contact tracing systems to expedite contact tracing and risk notification. Unfortunately, the success of these systems has been limited, partly owing to poor interoperability with manual contact tracing, low adoption rates, and a societally sensitive trade-off between utility and privacy. In this work, we introduce a new privacy-preserving and inclusive system for epidemic risk assessment and notification that aims to address these limitations. Rather than capturing pairwise encounters between user devices as done by existing systems, our system captures encounters between user devices and beacons placed in strategic locations where infection clusters may originate. Epidemiological simulations using an agent-based model demonstrate that, by utilizing location and environmental information and interoperating with manual contact tracing, our system can increase the accuracy of contact tracing actions and may help reduce epidemic spread already at low adoption.

During the ongoing COVID-19 pandemic, there have been burgeoning efforts to develop and deploy smartphone apps to expedite contact tracing and risk notification. Unfortunately, the success of these apps has been limited, partly owing to poor interoperability with manual contact tracing, low adoption rates, and a societally sensitive trade-off between utility and privacy. In this work, we introduce a new privacy-preserving and inclusive system for epidemic risk assessment and notification that aims to address the above limitations. Rather than capturing pairwise encounters between smartphones as done by existing apps, our system captures encounters between inexpensive, zero-maintenance, small devices carried by users, and beacons placed in strategic locations where infection clusters are most likely to originate. Epidemiological simulations using an agent-based model demonstrate several beneficial properties of our system. By achieving bidirectional interoperability with manual contact tracing, our system can help control disease spread already at low adoption. By utilizing the location and environmental information provided by the beacons, our system can provide significantly higher sensitivity and specificity than existing app-based systems. In addition, our simulations also suggest that it is sufficient to deploy beacons in a small fraction of strategic locations for our system to achieve high utility.