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

We propose a novel data-driven machine learning method using long short-term memory (LSTM)-based multi-stage forecasting for influenza forecasting. The novel aspects of the method include the following: 1) the introduction of LSTM method to capture the temporal dynamics of seasonal flu and 2) a technique to capture the influence of external variables that includes the geographical proximity and climatic variables such as humidity, temperature, precipitation, and sun exposure. The proposed model is compared against two state-of-the-art techniques using two publicly available datasets. Our proposed method performs better than the existing well-known influenza forecasting methods. The results offer a promising direction in terms of both using the data-driven forecasting methods and capturing the influence of spatio-temporal and environmental factors to improve influenza forecasting.

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

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

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

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

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

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

[7]  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.

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

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

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

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

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

[13]  Martín Abadi,et al.  TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems , 2016, ArXiv.

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

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

[16]  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.

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

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

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

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

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

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

[23]  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.

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

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

[26]  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.

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

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

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

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

[31]  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.

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

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

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

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

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

[37]  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 .

[38]  Rakesh Agarwal,et al.  Fast Algorithms for Mining Association Rules , 1994, VLDB 1994.

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

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

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

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

[43]  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.

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

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

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

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

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

[49]  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).

[50]  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.

[51]  Juan Gabriel Brida Symbolic Time Series Analysis and Economic Regimes , 2000 .

[52]  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.

[53]  J. Shaman,et al.  Forecasting seasonal outbreaks of influenza , 2012, Proceedings of the National Academy of Sciences.

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

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

[56]  Eamonn J. Keogh,et al.  A symbolic representation of time series, with implications for streaming algorithms , 2003, DMKD '03.