Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models

PLoS Comput Biol. 2021 Mar 15;17(3):e1008831. doi: 10.1371/journal.pcbi.1008831. eCollection 2021 Mar.

Abstract

Ensembling combines the predictions made by individual component base models with the goal of achieving a predictive accuracy that is better than that of any one of the constituent member models. Diversity among the base models in terms of predictions is a crucial criterion in ensembling. However, there are practical instances when the available base models produce highly correlated predictions, because they may have been developed within the same research group or may have been built from the same underlying algorithm. We investigated, via a case study on Fusarium head blight (FHB) on wheat in the U.S., whether ensembles of simple yet highly correlated models for predicting the risk of FHB epidemics, all generated from logistic regression, provided any benefit to predictive performance, despite relatively low levels of base model diversity. Three ensembling methods were explored: soft voting, weighted averaging of smaller subsets of the base models, and penalized regression as a stacking algorithm. Soft voting and weighted model averages were generally better at classification than the base models, though not universally so. The performances of stacked regressions were superior to those of the other two ensembling methods we analyzed in this study. Ensembling simple yet correlated models is computationally feasible and is therefore worth pursuing for models of epidemic risk.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Epidemics / statistics & numerical data*
  • Fusarium
  • Models, Statistical*
  • Plant Diseases / statistics & numerical data
  • Triticum / microbiology

Associated data

  • Dryad/10.5061/dryad.fn2z34trv

Grants and funding

This research was supported by the U.S. Wheat & Barley Scab Initiative (https://scabusa.org/), agreements 59-0206-6-015 (EDW) and 59-0206-4-018 (PAP). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.