Discovering dynamic patterns from infectious disease data using dynamic mode decomposition

International Health
Joshua L Proctor, Philip A Eckhoff

Abstract

The development and application of quantitative methods to understand disease dynamics and plan interventions is becoming increasingly important in the push toward eradication of human infectious diseases, exemplified by the ongoing effort to stop the spread of poliomyelitis. Dynamic mode decomposition (DMD) is a recently developed method focused on discovering coherent spatial-temporal modes in high-dimensional data collected from complex systems with time dynamics. The algorithm has a number of advantages including a rigorous connection to the analysis of nonlinear systems, an equation-free architecture, and the ability to efficiently handle high-dimensional data. We demonstrate the method on three different infectious disease sets including Google Flu Trends data, pre-vaccination measles in the UK, and paralytic poliomyelitis wild type-1 cases in Nigeria. For each case, we describe the utility of the method for surveillance and resource allocation. We demonstrate how DMD can aid in the analysis of spatial-temporal disease data. DMD is poised to be an effective and efficient computational analysis tool for the study of infectious disease.

References

Nov 21, 2008·Nature·Jeremy GinsbergLarry Brilliant
Mar 15, 2014·Science·David LazerAlessandro Vespignani
Jun 5, 2014·BMC Medicine·Alexander M Upfill-BrownGuillaume Chabot-Couture

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Citations

Nov 4, 2015·Journal of Neuroscience Methods·Bingni W BruntonJ Nathan Kutz
Mar 4, 2015·International Health·Philip A Eckhoff, Andrew J Tatem
Nov 6, 2018·PLoS Computational Biology·Keisuke FujiiYoshinobu Kawahara
Nov 16, 2019·Scientific Reports·Keisuke FujiiYoshinobu Kawahara
Apr 23, 2019·Proceedings. Mathematical, Physical, and Engineering Sciences·N M ManganJ L Proctor
Jan 20, 2018·Physical Review. E·Naoya TakeishiTakehisa Yairi
Mar 5, 2020·Science and Technology of Advanced Materials·Itsushi SakataMasato Okada
Oct 19, 2020·International Journal for Numerical Methods in Biomedical Engineering·Jinxiang XiHaibo Dong
Jan 1, 2018·SIAM Journal on Applied Dynamical Systems·Joshua L ProctoryJ Nathan Kutzx
Mar 4, 2021·Chaos·Marvyn Gulina, Alexandre Mauroy
Aug 10, 2021·Engineering with Computers·Gabriel F BarrosAlvaro L G A Coutinho

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Software Mentioned

Google Trends
Flu Trends tool
Google Flu Trends
DMD
Google search

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