Data-Driven Malaria Prevalence Prediction in Large Densely-Populated Urban Holoendemic sub-Saharan West Africa: Harnessing Machine Learning Approaches and 22-years of Prospectively Collected Data

Plasmodium falciparum malaria still poses one of the greatest threats to human life with over 200 million cases globally leading to half-million deaths annually. Of these, 90% of cases and of the mortality occurs in sub-Saharan Africa, mostly among children. Although malaria prediction systems are central to the 2016-2030 malaria Global Technical Strategy, currently these are inadequate at capturing and estimating the burden of disease in highly endemic countries. We developed and validated a computational system that exploits the predictive power of current Machine Learning approaches on 22-years of prospective data from the high-transmission holoendemic malaria urban-densely-populated sub-Saharan West-Africa metropolis of Ibadan. Our dataset of >9x104 screened study participants attending our clinical and community services from 1996 to 2017 contains monthly prevalence, temporal, environmental and host features. Our Locality-specific Elastic-Net based Malaria Prediction System (LEMPS) achieves good generalization performance, both in magnitude and direction of the prediction, when tasked to predict monthly prevalence on previously unseen validation data (MAE<=6x10-2, MSE<=7x10-3) within a range of (+0.1 to -0.05) error-tolerance which is relevant and usable for aiding decision-support in a holoendemic setting. LEMPS is well-suited for malaria prediction, where there are multiple features which are correlated with one another, and trading-off between regularization-strength L1-norm and L2-norm allows the system to retain stability. Data-driven systems are critical for regionally-adaptable surveillance, management of control strategies and resource allocation across stretched healthcare systems.

Deep Learning Enhanced Extended Depth-of-Field for Thick Blood-Film Malaria High-Throughput Microscopy

Fast accurate diagnosis of malaria is still a global health challenge for which automated digital-pathology approaches could provide scalable solutions amenable to be deployed in low-to-middle income countries. Here we address the problem of Extended Depth-of-Field (EDoF) in thick blood film microscopy for rapid automated malaria diagnosis. High magnification oil-objectives (100x) with large numerical aperture are usually preferred to resolve the fine structural details that help separate true parasites from distractors. However, such objectives have a very limited depth-of-field requiring the acquisition of a series of images at different focal planes per field of view (FOV). Current EDoF techniques based on multi-scale decompositions are time consuming and therefore not suited for high-throughput analysis of specimens. To overcome this challenge, we developed a new deep learning method based on Convolutional Neural Networks (EDoF-CNN) that is able to rapidly perform the extended depth-of-field while also enhancing the spatial resolution of the resulting fused image. We evaluated our approach using simulated low-resolution z-stacks from Giemsa-stained thick blood smears from patients presenting with Plasmodium falciparum malaria. The EDoF-CNN allows speed-up of our digital-pathology acquisition platform and significantly improves the quality of the EDoF compared to the traditional multi-scaled approaches when applied to lower resolution stacks corresponding to acquisitions with fewer focal planes, large camera pixel binning or lower magnification objectives (larger FOV). We use the parasite detection accuracy of a deep learning model on the EDoFs as a concrete, task-specific measure of performance of this approach.