Tensor decomposition for infectious disease incidence data

Research output: Contribution to journalArticle

Abstract

Many demographic and ecological processes generate seasonal and other periodicities. Seasonality in infectious disease transmission can result from climatic forces such as temperature and humidity; variation in contact rates as a result of migration or school calendar; or temporary surges in birth rates. Seasonal drivers of acute immunizing infections can also drive longer-term fluctuations. Tensor decomposition has been used in many disciplines to uncover dominant trends in multi-dimensional data. We introduce tensors as a novel method for decomposing oscillatory infectious disease time series. We illustrate the reliability of the method by applying it to simulated data. We then present decompositions of measles data from England and Wales. This paper leverages simulations as well as much-studied data to illustrate the power of tensor decomposition to uncover dominant epidemic signals as well as variation in space and time. We then use tensor decomposition to uncover new findings and demonstrate the potential power of the method for disease incidence data. In particular, we are able to distinguish between annual and biennial signals across locations and shifts in these signals over time. Tensor decomposition is able to isolate variation in disease seasonality as a result of variation in demographic rates. The method allows us to discern variation in the strength of such signals by space and population size. Tensors provide an opportunity for a concise approach to uncovering heterogeneity in disease transmission across space and time in large datasets.

Original languageEnglish (US)
JournalMethods in Ecology and Evolution
DOIs
StateAccepted/In press - 2020

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Ecological Modeling

Keywords

  • demography
  • disease dynamics
  • measles
  • signal processing
  • tensor
  • wavelet

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