Predicting diarrhoea outbreaks with climate change

BACKGROUND: Climate change is expected to exacerbate diarrhoea outbreaks across the developing world, most notably in Sub-Saharan countries such as South Africa. In South Africa, diseases related to diarrhoea outbreak is a leading cause of morbidity and mortality. In this study, we modelled the impacts of climate change on diarrhoea with various machine learning (ML) methods to predict daily outbreak of diarrhoea cases in nine South African provinces. METHODS: We applied two deep Learning DL techniques, Convolutional Neural Networks (CNNs) and Long-Short term Memory Networks (LSTMs); and a Support Vector Machine (SVM) to predict daily diarrhoea cases over the different South African provinces by incorporating climate information. Generative Adversarial Networks (GANs) was used to generate synthetic data which was used to augment the available data-set. Furthermore, Relevance Estimation and Value Calibration (REVAC) was used to tune the parameters of the ML methods to optimize the accuracy of their predictions. Sensitivity analysis was also performed to investigate the contribution of the different climate factors to the diarrhoea prediction method. RESULTS: Our results showed that all three ML methods were appropriate for predicting daily diarrhoea cases with respect to the selected climate variables in each South African province. However, the level of accuracy for each method varied across different experiments, with the deep learning methods outperforming the SVM method. Among the deep learning techniques, the CNN method performed best when only real-world data-set was used, while the LSTM method outperformed the other methods when the real-world data-set was augmented with synthetic data. Across the provinces, the accuracy of all three ML methods improved by at least 30 percent when data augmentation was implemented. In addition, REVAC improved the accuracy of the CNN method by about 2.5% in each province. Our parameter sensitivity analysis revealed that the most influential climate variables to be considered when predicting outbreak of diarrhoea in South Africa were precipitation, humidity, evaporation and temperature conditions. CONCLUSIONS: Overall, experiments indicated that the prediction capacity of our DL methods (Convolutional Neural Networks) was found to be superior (with statistical significance) in terms of prediction accuracy across most provinces. This study’s results have important implications for the development of automated early warning systems for diarrhoea (and related disease) outbreaks across the globe.