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Francis Akinkunmi

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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

Jun 18, 2019
Biobele J. Brown, Alexander A. Przybylski, Petru Manescu, Fabio Caccioli, Gbeminiyi Oyinloye, Muna Elmi, Michael J. Shaw, Vijay Pawar, Remy Claveau, John Shawe-Taylor, Mandayam A. Srinivasan, Nathaniel K. Afolabi, Adebola E. Orimadegun, Wasiu A. Ajetunmobi, Francis Akinkunmi, Olayinka Kowobari, Kikelomo Osinusi, Felix O. Akinbami, Samuel Omokhodion, Wuraola A. Shokunbi, Ikeoluwa Lagunju, Olugbemiro Sodeinde, Delmiro Fernandez-Reyes

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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.

* 40 pages, 10 figures 
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