%A Tessmer,Heidi L.
%A Ito,Kimihito
%A Omori,Ryosuke
%D 2018
%J Frontiers in Microbiology
%C
%F
%G English
%K Basic Reproduction Number,respiratory virus,infectious disease epidemiology,machine learning,Approximate Bayesian Computation,mathematical model
%Q
%R 10.3389/fmicb.2018.00343
%W
%L
%N 343
%M
%P
%7
%8 2018-March-02
%9 Original Research
%+ Ryosuke Omori,Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University,Japan,omori@czc.hokudai.ac.jp
%+ Ryosuke Omori,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency,Japan,omori@czc.hokudai.ac.jp
%#
%! Likelihood-free methods for the estimation of epidemiological dynamics of respiratory viruses
%*
%<
%T Can Machines Learn Respiratory Virus Epidemiology?: A Comparative Study of Likelihood-Free Methods for the Estimation of Epidemiological Dynamics
%U https://www.frontiersin.org/article/10.3389/fmicb.2018.00343
%V 9
%0 JOURNAL ARTICLE
%@ 1664-302X
%X To estimate and predict the transmission dynamics of respiratory viruses, the estimation of the basic reproduction number, R_{0}, is essential. Recently, approximate Bayesian computation methods have been used as likelihood free methods to estimate epidemiological model parameters, particularly R_{0}. In this paper, we explore various machine learning approaches, the multi-layer perceptron, convolutional neural network, and long-short term memory, to learn and estimate the parameters. Further, we compare the accuracy of the estimates and time requirements for machine learning and the approximate Bayesian computation methods on both simulated and real-world epidemiological data from outbreaks of influenza A(H1N1)pdm09, mumps, and measles. We find that the machine learning approaches can be verified and tested faster than the approximate Bayesian computation method, but that the approximate Bayesian computation method is more robust across different datasets.