COVID-19 seroprevalence estimation and forecasting in the USA from ensemble machine learning models using a stacking strategy

Abstract

The COVID-19 pandemic exposed the importance of research on the spread of epidemic diseases. In this paper, we apply Artificial Intelligence and statistics techniques to build prediction models to estimate the SARS-CoV-2 seroprevalence in the United States, using multiple estimates of COVID-19 prevalence and other explanatory variables. We propose the use of stacking techniques based on multiple model building techniques (Linear and Beta Regression, Genetic Programming and Neural Networks) to obtain Predictive Ensemble Models. There has been extensive research on this field, but there has not been in-depth research on the application of stacking methods to estimate and forecast seroprevalence in the USA specifically. This paper provides a novel comparison of the behaviour and performance of different building techniques for stacking ensemble models and presents which methods are better for different scenarios. We find that Genetic Programming and Neural Networks are the best models with trained data within single states, and when multiple states are considered Genetic Programming is still better than the Regression models, but Neural Networks fail to estimate the seroprevalence accurately. Another novelty of our work is the use of cross-state validation to evaluate the models with new data, as well as temporal forecasting. Depending on how the data is processed, Linear Regression performs very well with cross-state validation and temporal forecasting, and Genetic Programming is very accurate with the former while Neural Networks work better with the latter.