Detecting Outbreaks Using a Latent Field: Part II -- Scalable Estimation

TL;DR

This paper introduces a Bayesian, spatially-aware method to estimate disease infection-rates from case data, improving outbreak detection and clustering in epidemiological surveillance.

Contribution

It develops a scalable Bayesian approach with Markov random fields and variational inference for estimating infection-rates across multiple regions, enhancing robustness over traditional case-count methods.

Findings

Successfully estimated COVID-19 infection-rates in New Mexico counties.

Detected the Fall 2020 COVID-19 wave using the infection-rate estimates.

Clustered counties with similar epidemiological dynamics.

Abstract

In this paper, we explore whether the infection-rate of a disease can serve as a robust monitoring variable in epidemiological surveillance algorithms. The infection-rate is dependent on population mixing patterns that do not vary erratically day-to-day; in contrast, daily case-counts used in contemporary surveillance algorithms are corrupted by reporting errors. The technical challenge lies in estimating the latent infection-rate from case-counts. Here we devise a Bayesian method to estimate the infection-rate across multiple adjoining areal units, and then use it, via an anomaly detector, to discern a change in epidemiological dynamics. We extend an existing model for estimating the infection-rate in an areal unit by incorporating a Markov random field model, so that we may estimate infection-rates across multiple areal units, while preserving spatial correlations observed in the epidemiological dynamics. To carry out the high-dimensional Bayesian inverse problem, we develop an implementation of mean-field variational inference specific to the infection model and integrate it with the random field model to incorporate correlations across counties. The method is tested on estimating the COVID-19 infection-rates across all 33 counties in New Mexico using data from the summer of 2020, and then employing them to detect the arrival of the Fall 2020 COVID-19 wave. We perform the detection using a temporal algorithm that is applied county-by-county. We also show how the infection-rate field can be used to cluster counties with similar epidemiological dynamics.