Improving probabilistic infectious disease forecasting through coherence

Epicasting: An Ensemble Wavelet Neural Network for forecasting epidemics

Infectious diseases remain among the top contributors to human illness and death worldwide, among which many diseases produce epidemic waves of infection. The lack of specific drugs and ready-to-use vaccines to prevent most of these epidemics worsens the situation. These force public health officials and policymakers to rely on early warning systems generated by accurate and reliable epidemic forecasters. Accurate forecasts of epidemics can assist stakeholders in tailoring countermeasures, such as vaccination campaigns, staff scheduling, and resource allocation, to the situation at hand, which could translate to reductions in the impact of a disease. Unfortunately, most of these past epidemics exhibit nonlinear and non-stationary characteristics due to their spreading fluctuations based on seasonal-dependent variability and the nature of these epidemics. We analyze various epidemic time series datasets using a maximal overlap discrete wavelet transform (MODWT) based autoregressive neural network and call it Ensemble Wavelet Neural Network (EWNet) model. MODWT techniques effectively characterize non-stationary behavior and seasonal dependencies in the epidemic time series and improve the nonlinear forecasting scheme of the autoregressive neural network in the proposed ensemble wavelet network framework. From a nonlinear time series viewpoint, we explore the asymptotic stationarity of the proposed EWNet model to show the asymptotic behavior of the associated Markov Chain. We also theoretically investigate the effect of learning stability and the choice of hidden neurons in the proposal. From a practical perspective, we compare our proposed EWNet framework with twenty-two statistical, machine learning, and deep learning models for fifteen real-world epidemic datasets with three test horizons using four key performance indicators. Experimental results show that the proposed EWNet is highly competitive compared to the state-of-the-art epidemic forecasting methods.

Multiscale influenza forecasting

Influenza forecasting in the United States (US) is complex and challenging due to spatial and temporal variability, nested geographic scales of interest, and heterogeneous surveillance participation. Here we present Dante, a multiscale influenza forecasting model that learns rather than prescribes spatial, temporal, and surveillance data structure and generates coherent forecasts across state, regional, and national scales. We retrospectively compare Dante's short-term and seasonal forecasts for previous flu seasons to the Dynamic Bayesian Model (DBM), a leading competitor. Dante outperformed DBM for nearly all spatial units, flu seasons, geographic scales, and forecasting targets. Dante's sharper and more accurate forecasts also suggest greater public health utility. Dante placed 1st in the Centers for Disease Control and Prevention's prospective 2018/19 FluSight challenge in both the national and regional competition and the state competition. The methodology underpinning Dante can be used in other seasonal disease forecasting contexts having nested geographic scales of interest.

Forecasting influenza-like illness trends in Cameroon using Google Search Data

Although acute respiratory infections are a leading cause of mortality in sub-Saharan Africa, surveillance of diseases such as influenza is mostly neglected. Evaluating the usefulness of influenza-like illness (ILI) surveillance systems and developing approaches for forecasting future trends is important for pandemic preparedness. We applied and compared a range of robust statistical and machine learning models including random forest (RF) regression, support vector machines (SVM) regression, multivariable linear regression and ARIMA models to forecast 2012 to 2018 trends of reported ILI cases in Cameroon, using Google searches for influenza symptoms, treatments, natural or traditional remedies as well as, infectious diseases with a high burden (i.e., AIDS, malaria, tuberculosis). The R2 and RMSE (Root Mean Squared Error) were statistically similar across most of the methods, however, RF and SVM had the highest average R2 (0.78 and 0.88, respectively) for predicting ILI per 100,000 persons at the country level. This study demonstrates the need for developing contextualized approaches when using digital data for disease surveillance and the usefulness of search data for monitoring ILI in sub-Saharan African countries.