Fast and Accurate Forecasting of COVID-19 Deaths Using the SIkJ$\alpha$ Model

Forecasting the effect of COVID-19 is essential to design policies that may prepare us to handle the pandemic. Many methods have already been proposed, particularly, to forecast reported cases and deaths at country-level and state-level. Many of these methods are based on traditional epidemiological model which rely on simulations or Bayesian inference to simultaneously learn many parameters at a time. This makes them prone to over-fitting and slow execution. We propose an extension to our model SIkJα to forecast deaths and show that it can consider the effect of many complexities of the epidemic process and yet be simplified to a few parameters that are learned using fast linear regressions. We also present an evaluation of our method against seven approaches currently being used by the CDC, based on their two weeks forecast at various times during the pandemic. We demonstrate that our method achieves better root mean squared error compared to these seven approaches during majority of the evaluation period. Further, on a 2 core desktop machine, our approach takes only 3.18s to tune hyper-parameters, learn parameters and generate 100 days of forecasts of reported cases and deaths for all the states in the US. The total execution time for 184 countries is 11.83s and for all the US counties (> 3000) is 101.03s.

[1]  Pierre Magal,et al.  The parameter identification problem for SIR epidemic models: identifying unreported cases , 2018, Journal of mathematical biology.

[2]  L. Wang,et al.  Epidemic Model Guided Machine Learning for COVID-19 Forecasts in the United States , 2020, medRxiv.

[3]  Viktor K. Prasanna,et al.  Data-driven Identification of Number of Unreported Cases for COVID-19: Bounds and Limitations , 2020, ArXiv.

[4]  Luís M A Bettencourt,et al.  The estimation of the effective reproductive number from disease outbreak data. , 2009, Mathematical biosciences and engineering : MBE.

[5]  Viktor K. Prasanna,et al.  Learning to Forecast and Forecasting to Learn from the COVID-19 Pandemic , 2020, ArXiv.

[6]  P. Blinder,et al.  A seven-day cycle in COVID-19 infection and mortality rates: Are inter-generational social interactions on the weekends killing susceptible people? , 2020, medRxiv.

[7]  Hannah R. Meredith,et al.  A scenario modeling pipeline for COVID-19 emergency planning , 2020, Scientific Reports.

[8]  Meg Miller,et al.  2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository , 2020 .

[9]  M. Li,et al.  Global dynamics of a SEIR model with varying total population size. , 1999, Mathematical Biosciences.

[10]  Yueying Wang,et al.  Spatiotemporal Dynamics, Nowcasting and Forecasting of COVID-19 in the United States , 2020, 2004.14103.

[11]  S. Pei,et al.  Initial Simulation of SARS-CoV2 Spread and Intervention Effects in the Continental US , 2020, medRxiv.

[12]  E L Ionides,et al.  Inference for nonlinear dynamical systems , 2006, Proceedings of the National Academy of Sciences.

[13]  M. Pascual,et al.  Inapparent infections and cholera dynamics , 2008, Nature.

[14]  G. Webb,et al.  Identifying the number of unreported cases in SIR epidemic models. , 2020, Mathematical medicine and biology : a journal of the IMA.

[15]  Jeffrey L. Anderson An Ensemble Adjustment Kalman Filter for Data Assimilation , 2001 .

[16]  B. Finkenstädt,et al.  Statistical Inference in a Stochastic Epidemic SEIR Model with Control Intervention: Ebola as a Case Study , 2006, Biometrics.

[17]  Nicholas G. Polson,et al.  Tracking Epidemics With Google Flu Trends Data and a State-Space SEIR Model , 2012, Journal of the American Statistical Association.