Comparing and linking machine learning and semi-mechanistic models for the predictability of endemic measles dynamics

• Authors: Siu Lau, Emory University; Max SY Lau, Emory University; Alex Becker, Princeton University; Wyatt Madden, Emory University; Lance Waller, Emory University; Metcalf CE Jessica, Princeton University; Bryan T Grenfell, Princeton University
• Journal Title: PLoS Computational Biology
• Volume: Volume 18, Number 9 September
• Publisher: (publisher) | 2022-09-01, Pages e1010251-e1010251
• Type of Work: Article | Final Publisher PDF
• Publisher DOI: http://doi.org/10.1371/journal.pcbi.1010251
• Subjects: Biology, Biostatistics; Biology, General
• Keywords: Communicable Diseases; Disease Outbreaks; Epidemics; Humans; Machine Learning; Measles; United States

Abstract

Measles is one the best-documented and most-mechanistically-studied non-linear infectious disease dynamical systems. However, systematic investigation into the comparative performance of traditional mechanistic models and machine learning approaches in forecasting the transmission dynamics of this pathogen are still rare. Here, we compare one of the most widely used semi-mechanistic models for measles (TSIR) with a commonly used machine learning approach (LASSO), comparing performance and limits in predicting short to long term outbreak trajectories and seasonality for both regular and less regular measles outbreaks in England and Wales (E&W) and the United States. First, our results indicate that the proposed LASSO model can efficiently use data from multiple major cities and achieve similar short-to-medium term forecasting performance to semi-mechanistic models for E&W epidemics. Second, interestingly, the LASSO model also captures annual to biennial bifurcation of measles epidemics in E&W caused by susceptible response to the late 1940s baby boom. LASSO may also outperform TSIR for predicting less-regular dynamics such as those observed in major cities in US between 1932–45. Although both approaches capture short-term forecasts, accuracy suffers for both methods as we attempt longer-term predictions in highly irregular, post-vaccination outbreaks in E&W. Finally, we illustrate that the LASSO model can both qualitatively and quantitatively reconstruct mechanistic assumptions, notably susceptible dynamics, in the TSIR model. Our results characterize the limits of predictability of infectious disease dynamics for strongly immunizing pathogens with both mechanistic and machine learning models, and identify connections between these two approaches.