A novel data-driven model for real-time influenza forecasting

We provide data-driven machine learning methods that are capable of making real-time influenza forecasts that integrate the impacts of climatic factors and geographical proximity to achieve better forecasting performance. The key contributions of our approach are both applying deep learning methods and incorporation of environmental and spatio-temporal factors to improve the performance of the influenza forecasting models. We evaluate the method on Influenza Like Illness (ILI) counts and climatic data, both publicly available data sets. Our proposed method outperforms existing known influenza forecasting methods in terms of their Mean Absolute Percentage Error and Root Mean Square Error. The key advantages of the proposed data-driven methods are as following: (1) The deep-learning model was able to effectively capture the temporal dynamics of flu spread in different geographical regions, (2) The extensions to the deep-learning model capture the influence of external variables that include the geographical proximity and climatic variables such as humidity, temperature, precipitation and sun exposure in future stages, (3) The model consistently performs well for both the city scale and the regional scale on the Google Flu Trends (GFT) and Center for Disease Control (CDC) flu counts. The results offer a promising direction in terms of both data-driven forecasting methods and capturing the influence of spatio-temporal and environmental factors for influenza forecasting methods.

[1]  Jürgen Schmidhuber,et al.  Applying LSTM to Time Series Predictable through Time-Window Approaches , 2000, ICANN.

[2]  Raymond Tellier,et al.  Review of Aerosol Transmission of Influenza A Virus , 2006, Emerging infectious diseases.

[3]  Krzysztof Sakrejda,et al.  Case Study in Evaluating Time Series Prediction Models Using the Relative Mean Absolute Error , 2016, The American statistician.

[4]  G. Chowell,et al.  Comparative estimation of the reproduction number for pandemic influenza from daily case notification data , 2007, Journal of The Royal Society Interface.

[5]  D. J. Rogers,et al.  Global Transport Networks and Infectious Disease Spread , 2006, Advances in Parasitology.

[6]  Richard K. Kiang,et al.  Modeling and Predicting Seasonal Influenza Transmission in Warm Regions Using Climatological Parameters , 2010, PloS one.

[7]  Yoshua Bengio,et al.  Learning long-term dependencies with gradient descent is difficult , 1994, IEEE Trans. Neural Networks.

[8]  Herbert W. Hethcote,et al.  The Mathematics of Infectious Diseases , 2000, SIAM Rev..

[9]  Jürgen Schmidhuber,et al.  Long Short-Term Memory , 1997, Neural Computation.

[10]  Charles Elkan,et al.  Learning to Diagnose with LSTM Recurrent Neural Networks , 2015, ICLR.

[11]  Bruno Gonçalves,et al.  Modeling and Predicting Human Infectious Diseases , 2015, Social Phenomena.

[12]  Alicia Karspeck,et al.  Real-Time Influenza Forecasts during the 2012–2013 Season , 2013, Nature Communications.

[13]  S. Lemon,et al.  Classification and regression tree analysis in public health: Methodological review and comparison with logistic regression , 2003, Annals of behavioral medicine : a publication of the Society of Behavioral Medicine.

[14]  Cécile Viboud,et al.  Air Travel and the Spread of Influenza: Important Caveats , 2006, PLoS medicine.

[15]  Carlos Guestrin,et al.  "Why Should I Trust You?": Explaining the Predictions of Any Classifier , 2016, ArXiv.

[16]  Y. Gel,et al.  Influenza Forecasting with Google Flu Trends , 2013, PloS one.

[17]  Jeffrey Shaman,et al.  Absolute humidity modulates influenza survival, transmission, and seasonality , 2009, Proceedings of the National Academy of Sciences.

[18]  Hiroshi Nishiura,et al.  Real-time forecasting of an epidemic using a discrete time stochastic model: a case study of pandemic influenza (H1N1-2009) , 2011, Biomedical engineering online.

[19]  G. Harper,et al.  Airborne micro-organisms: survival tests with four viruses , 1961, Epidemiology and Infection.

[20]  Dit-Yan Yeung,et al.  Convolutional LSTM Network: A Machine Learning Approach for Precipitation Nowcasting , 2015, NIPS.

[21]  Dylan B. George,et al.  Big Data Opportunities for Global Infectious Disease Surveillance , 2013, PLoS medicine.

[22]  Marcus Liwicki,et al.  A novel approach to on-line handwriting recognition based on bidirectional long short-term memory networks , 2007 .

[23]  John Steel,et al.  Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature , 2007, PLoS pathogens.

[24]  Jian Ma,et al.  A neural netwok based approach to detect influenza epidemics using search engine query data , 2010, 2010 International Conference on Machine Learning and Cybernetics.

[25]  Eduardo Sontag,et al.  Turing computability with neural nets , 1991 .

[26]  Andrew W. Senior,et al.  Long short-term memory recurrent neural network architectures for large scale acoustic modeling , 2014, INTERSPEECH.

[27]  Eirini Christaki New technologies in predicting, preventing and controlling emerging infectious diseases , 2015, Virulence.

[28]  Sérgio Matos,et al.  Analysing Twitter and web queries for flu trend prediction , 2014, Theoretical Biology and Medical Modelling.

[29]  Alberto Maria Segre,et al.  The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. during the Influenza A H1N1 Pandemic , 2011, PloS one.

[30]  Jürgen Schmidhuber,et al.  LSTM recurrent networks learn simple context-free and context-sensitive languages , 2001, IEEE Trans. Neural Networks.

[31]  Jeremy Ginsberg,et al.  Detecting influenza epidemics using search engine query data , 2009, Nature.

[32]  Jürgen Schmidhuber,et al.  Learning to Forget: Continual Prediction with LSTM , 2000, Neural Computation.

[33]  Raymond Tellier,et al.  Transmission of influenza A in human beings. , 2007, The Lancet. Infectious diseases.

[34]  Razvan Pascanu,et al.  How to Construct Deep Recurrent Neural Networks , 2013, ICLR.

[35]  John Steel,et al.  Roles of Humidity and Temperature in Shaping Influenza Seasonality , 2014, Journal of Virology.

[36]  PAUL J. WERBOS,et al.  Generalization of backpropagation with application to a recurrent gas market model , 1988, Neural Networks.

[37]  Mevin B. Hooten,et al.  Assessing North American influenza dynamics with a statistical SIRS model. , 2010, Spatial and spatio-temporal epidemiology.

[38]  Robert Fildes,et al.  The evaluation of extrapolative forecasting methods , 1992 .

[39]  Xiangang Li,et al.  Constructing long short-term memory based deep recurrent neural networks for large vocabulary speech recognition , 2014, 2015 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[40]  S B Thacker,et al.  An evaluation of influenza mortality surveillance, 1962-1979. I. Time series forecasts of expected pneumonia and influenza deaths. , 1981, American journal of epidemiology.

[41]  J. Brownstein,et al.  Empirical Evidence for the Effect of Airline Travel on Inter-Regional Influenza Spread in the United States , 2006, PLoS medicine.

[42]  Yunpeng Wang,et al.  Long short-term memory neural network for traffic speed prediction using remote microwave sensor data , 2015 .

[43]  M. Keeling,et al.  Modeling Infectious Diseases in Humans and Animals , 2007 .

[44]  Geoffrey E. Hinton,et al.  Speech recognition with deep recurrent neural networks , 2013, 2013 IEEE International Conference on Acoustics, Speech and Signal Processing.

[45]  M. Wilson,et al.  The traveller and emerging infections: sentinel, courier, transmitter , 2003, Journal of applied microbiology.

[46]  Paola Velardi,et al.  Results from the centers for disease control and prevention’s predict the 2013–2014 Influenza Season Challenge , 2016, BMC Infectious Diseases.

[47]  F. L. Schaffer,et al.  Survival of airborne influenza virus: Effects of propagating host, relative humidity, and composition of spray fluids , 2005, Archives of Virology.

[48]  Christopher M. Fuhrmann,et al.  The Effects of Weather and Climate on the Seasonality of Influenza: What We Know and What We Need to Know , 2010 .

[49]  A. Hall,et al.  Adaptive Switching Circuits , 2016 .

[50]  Mark A. Miller,et al.  Seasonal influenza in the United States, France, and Australia: transmission and prospects for control , 2007, Epidemiology and Infection.

[51]  E. Nsoesie,et al.  A systematic review of studies on forecasting the dynamics of influenza outbreaks , 2013, Influenza and other respiratory viruses.