A Machine Learning-Aided Global Diagnostic and Comparative Tool to Assess Effect of Quarantine Control in COVID-19 Spread

We have developed a globally applicable diagnostic COVID-19 model by augmenting the classical SIR epidemiological model with a neural network module. Our model does not rely upon previous epidemics like SARS/MERS and all parameters are optimized via machine learning algorithms used on publicly available COVID-19 data. The model decomposes the contributions to the infection time series to analyze and compare the role of quarantine control policies used in highly affected regions of Europe, North America, South America, and Asia in controlling the spread of the virus. For all continents considered, our results show a generally strong correlation between strengthening of the quarantine controls as learnt by the model and actions taken by the regions' respective governments. In addition, we have hosted our quarantine diagnosis results for the top 70 affected countries worldwide, on a public platform.

[1]  Sean Gerrish,et al.  Black Box Variational Inference , 2013, AISTATS.

[2]  Carl E. Rasmussen,et al.  Gaussian processes for machine learning , 2005, Adaptive computation and machine learning.

[3]  Pauline van den Driessche,et al.  Reproduction numbers of infectious disease models. , 2017 .

[4]  J A Jacquez,et al.  Reproduction numbers and thresholds in stochastic epidemic models. I. Homogeneous populations. , 1991, Mathematical biosciences.

[5]  S. Lo,et al.  A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster , 2020, The Lancet.

[6]  Jianhong Wu,et al.  Estimation of the Transmission Risk of the 2019-nCoV and Its Implication for Public Health Interventions , 2020, Journal of clinical medicine.

[7]  J. Nieto,et al.  Modeling and forecasting the COVID-19 pandemic in India , 2020, Chaos, Solitons & Fractals.

[8]  Jing Zhao,et al.  Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia , 2020, The New England journal of medicine.

[9]  Vaibhav Dixit,et al.  DiffEqFlux.jl - A Julia Library for Neural Differential Equations , 2019, ArXiv.

[10]  L. Allen,et al.  Comparison of deterministic and stochastic SIS and SIR models in discrete time. , 2000, Mathematical biosciences.

[11]  Chong Wang,et al.  Stochastic variational inference , 2012, J. Mach. Learn. Res..

[12]  G. Leung,et al.  Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study , 2020, The Lancet.

[13]  David Cyranoski,et al.  What China’s coronavirus response can teach the rest of the world , 2020, Nature.

[14]  Shengtai Li,et al.  Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution , 2002, SIAM J. Sci. Comput..

[15]  Masaya M. Saito,et al.  Extension and verification of the SEIR model on the 2009 influenza A (H1N1) pandemic in Japan. , 2013, Mathematical biosciences.

[16]  David M. Blei,et al.  Deep Exponential Families , 2014, AISTATS.

[17]  P. van den Driessche,et al.  Reproduction numbers of infectious disease models , 2017, Infectious Disease Modelling.

[18]  Gerardo Chowell,et al.  Forecasting Epidemics Through Nonparametric Estimation of Time-Dependent Transmission Rates Using the SEIR Model , 2017, Bulletin of Mathematical Biology.

[19]  Dustin Tran,et al.  Variational Gaussian Process , 2015, ICLR.

[20]  S. Lindstrom,et al.  First Case of 2019 Novel Coronavirus in the United States , 2020, The New England journal of medicine.

[21]  Steve R. Waterhouse,et al.  Bayesian Methods for Mixtures of Experts , 1995, NIPS.

[22]  Qun Li Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia , 2020 .

[23]  Daan Wierstra,et al.  Stochastic Backpropagation and Approximate Inference in Deep Generative Models , 2014, ICML.

[24]  Chen Shen,et al.  ข้อสรุปจากบทความ “ผลของมาตรการที่ไม่ใช่ยาในการลดอัตราการตายและความต้องการทรัพยาการทาง สาธารณสุขเนื่องจากโรคโควิด-19” โดย Neil Ferguson และคณะ Review of Ferguson et al ”Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand.” , 2020 .

[25]  Jeffrey D Sachs,et al.  Projecting hospital utilization during the COVID-19 outbreaks in the United States , 2020, Proceedings of the National Academy of Sciences.

[26]  B. Mukhopadhyay,et al.  Analysis of a spatially extended nonlinear SEIS epidemic model with distinct incidence for exposed and infectives , 2008 .

[27]  Michael Y. Li,et al.  Why is it difficult to accurately predict the COVID-19 epidemic? , 2020, Infectious Disease Modelling.

[28]  Max Welling,et al.  Auto-Encoding Variational Bayes , 2013, ICLR.

[29]  M. L. Li,et al.  Forecasting COVID-19 and Analyzing the Effect of Government Interventions , 2020, medRxiv.

[30]  Jessica T Davis,et al.  The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak , 2020, Science.

[31]  R. Dandekar,et al.  A Machine Learning-Aided Global Diagnostic and Comparative Tool to Assess Effect of Quarantine Control in COVID-19 Spread , 2020, Patterns.

[32]  Jon Wakefield,et al.  Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data , 2016, Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.

[33]  Geoffrey E. Hinton,et al.  Keeping the neural networks simple by minimizing the description length of the weights , 1993, COLT '93.

[34]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[35]  R. May,et al.  Infectious Diseases of Humans: Dynamics and Control , 1991, Annals of Internal Medicine.

[36]  M. Baguelin,et al.  Report 3: Transmissibility of 2019-nCoV , 2020 .

[37]  An Pan,et al.  Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China , 2020, medRxiv.

[38]  D. Cummings,et al.  Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions , 2020, medRxiv.

[39]  E. Gibney Whose coronavirus strategy worked best? Scientists hunt most effective policies , 2020, Nature.

[40]  Daryl J. Daley,et al.  Epidemic Modelling: An Introduction , 1999 .

[41]  P. Klepac,et al.  Early dynamics of transmission and control of COVID-19: a mathematical modelling study , 2020, The Lancet Infectious Diseases.

[42]  Delfim F. M. Torres,et al.  Mathematical modeling of COVID-19 transmission dynamics with a case study of Wuhan , 2020, Chaos, Solitons & Fractals.

[43]  W. O. Kermack,et al.  A contribution to the mathematical theory of epidemics , 1927 .

[44]  Yee Whye Teh,et al.  A Fast Learning Algorithm for Deep Belief Nets , 2006, Neural Computation.

[45]  Yoshua Bengio,et al.  Deep Sparse Rectifier Neural Networks , 2011, AISTATS.

[46]  Tara N. Sainath,et al.  Improving deep neural networks for LVCSR using rectified linear units and dropout , 2013, 2013 IEEE International Conference on Acoustics, Speech and Signal Processing.

[47]  Nuno R. Faria,et al.  The effect of human mobility and control measures on the COVID-19 epidemic in China , 2020, Science.

[48]  Dennis Normile,et al.  Coronavirus cases have dropped sharply in South Korea. What’s the secret to its success? , 2020 .

[49]  Ali Ramadhan,et al.  Universal Differential Equations for Scientific Machine Learning , 2020, ArXiv.

[50]  Joel E. Cohen,et al.  Infectious Diseases of Humans: Dynamics and Control , 1992 .

[51]  Michael I. Jordan,et al.  An Introduction to Variational Methods for Graphical Models , 1999, Machine Learning.

[52]  Kurt Hornik,et al.  Approximation capabilities of multilayer feedforward networks , 1991, Neural Networks.

[53]  Habib N. Najm,et al.  Workshop Report on Basic Research Needs for Scientific Machine Learning: Core Technologies for Artificial Intelligence , 2018 .

[54]  Carl A. B. Pearson,et al.  The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: a modelling study , 2020, The Lancet Public Health.

[55]  Haiping Fang,et al.  Modelling the SARS epidemic by a lattice-based Monte-Carlo simulation , 2005, 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference.

[56]  C. Whittaker,et al.  Report 9: Impact of non-pharmaceutical interventions (NPIs) to reduce COVID19 mortality and healthcare demand , 2020 .