Small Area Estimation of Case Growths for Timely COVID-19 Outbreak Detection

The COVID-19 pandemic has exerted a profound impact on the global economy and continues to exact a significant toll on human lives. The COVID-19 case growth rate stands as a key epidemiological parameter to estimate and monitor for effective detection and containment of the resurgence of outbreaks. A fundamental challenge in growth rate estimation and hence outbreak detection is balancing the accuracy-speed tradeoff, where accuracy typically degrades with shorter fitting windows. In this paper, we develop a machine learning (ML) algorithm, which we call Transfer Learning Generalized Random Forest (TLGRF), that balances this accuracy-speed tradeoff. Specifically, we estimate the instantaneous COVID-19 exponential growth rate for each U.S. county by using TLGRF that chooses an adaptive fitting window size based on relevant day-level and county-level features affecting the disease spread. Through transfer learning, TLGRF can accurately estimate case growth rates for counties with small sample sizes. Out-of-sample prediction analysis shows that TLGRF outperforms established growth rate estimation methods. Furthermore, we conducted a case study based on outbreak case data from the state of Colorado and showed that the timely detection of outbreaks could have been improved by up to 224% using TLGRF when compared to the decisions made by Colorado's Department of Health and Environment (CDPHE). To facilitate implementation, we have developed a publicly available outbreak detection tool for timely detection of COVID-19 outbreaks in each U.S. county, which received substantial attention from policymakers.

Estimating County-Level COVID-19 Exponential Growth Rates Using Generalized Random Forests

Rapid and accurate detection of community outbreaks is critical to address the threat of resurgent waves of COVID-19. A practical challenge in outbreak detection is balancing accuracy vs. speed. In particular, while estimation accuracy improves with longer fitting windows, speed degrades. This paper presents a machine learning framework to balance this tradeoff using generalized random forests (GRF), and applies it to detect county level COVID-19 outbreaks. This algorithm chooses an adaptive fitting window size for each county based on relevant features affecting the disease spread, such as changes in social distancing policies. Experiment results show that our method outperforms any non-adaptive window size choices in 7-day ahead COVID-19 outbreak case number predictions.