Merging machine learning and mechanistic models to improve prediction and inference in emerging epidemics

PROJECT SUMMARY
When an outbreak of an established or emerging infectious disease occurs we ask a standard set of questions
that are critical to a lifesaving public health response: Where will future incidence occur? How many cases will
there be? And where can we most effectively intervene? The proposed research is motivated by real world
instances where answering these questions was critical to making practical public health decisions, and current
methods came up short: from deciding if and where to build additional Ebola Treatment Units in the 2014-15
West African Ebola epidemic, to identifying priority districts where oral cholera vaccine should be used in the
2016-17 cholera outbreak in Yemen, to picking locations where sufficient cases might occur to selecting and
prioritizing interventions to slow the spread of COVID-19 worldwide. Forecasts informing such decisions are
typically generated either using an epidemic model that relies on knowledge of the disease transmission
mechanism and epidemic theory or using a statistical model to project the expected number of cases based on
the relationship between covariates and observed counts. However, both approaches are subject to limitations,
particularly early in an epidemic when few cases are observed. This project is based on the overarching
scientific premise that inferences that combine the strengths of mechanistic epidemic models and statistical
covariate models will substantially outperform either approach alone in forecasting and making decisions to
confront emerging infectious disease threats. Specifically, this project aims to (1) Develop a framework to
forecast incidence in ongoing outbreaks that merges mechanistic and machine learning approaches;
(2) Validate the framework using retrospective data and apply the framework to inform decision making
in emerging epidemics; (3) Integrate this inferential forecasting framework into causal decision theory
to optimize critical actions in the public health response to emerging epidemics; and (4) Develop
accessible and extensible tools for forecasting and decision analysis in infectious disease epidemics.
We will validate these approaches using rigorous simulation studies and by applying the proposed approaches
to retrospective data from important recent epidemics (e.g., Ebola, Cholera and COVID-19, as mentioned
above). We will prospectively apply our approach to inform the response to emerging disease threats that
occur during the project period, including the ongoing COVID-19 pandemic. To ensure that the tools developed
are useful, efficient, and user friendly, we will work with international humanitarian organizations responding to
epidemics. Successful completion of these aims will provide a flexible and validated framework for forecasting
and decision making during ongoing epidemics, while allowing for innovation in mechanistic and statistical
approaches. In doing so it will provide tools to optimize responses and reduce morbidity and mortality during
public health crises.