Identification of snails and parasites of medical importance via convolutional neural network: an application for human schistosomiasis

Liu, Z. Y.-C.; Chamberlin, A. J.; Shome, P.; Jones, I. J.; Riveau, G.; Ndione, R. A.; Bandagny, L.; Jouanard, N.; Van Eck, P.; Ngo, T.; Sokolow, S. H.; De Leo, G. A.

doi:10.1101/713727

bioRxiv · 10.1101/713727

Identification of snails and parasites of medical importance via convolutional neural network: an application for human schistosomiasis

Liu, Z. Y.-C.·Chamberlin, A. J.·Shome, P.·Jones, I. J.·Riveau, G.·Ndione, R. A.·Bandagny, L.·Jouanard, N.·Van Eck, P.·Ngo, T.·Sokolow, S. H.·De Leo, G. A.

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Abstract

Schistosomiasis is a debilitating parasitic disease infecting over 250 million people with nearly 800 million people at risk worldwide, primarily in sub-Saharan Africa. Transmission to humans involves freshwater snails as intermediate hosts, which are particularly prevalent in developing countries where dams and water resource projects have expanded freshwater snail habitat. At our study sites in the lower Senegal River Basin, we have collected more than 5,500 images of the 7 freshwater snail species (grouped into 4 categories) most frequently encountered in this aquatic ecosystem, 5 of which amplify and transmit either urinary or intestinal human schistosomiasis, with the other 2 species responsible for the transmission of less common parasitic diseases of humans and/or livestock. We have also collected over 5,100 images of 11 classes of trematodes, including human and non-human schistosomes. It takes a great deal of training and expertise to accurately classify these organisms morphologically. In recent years, deep convolutional neural networks (CNNs) have proven to be highly efficient for image recognition tasks across many object categories. Here we demonstrate classification capacity for snail and parasite images and test our models performance against 8 highly-trained human parasitologists with experience taxonomically classifying snail and parasite species from the Senegal River Basin in West Africa. We establish and train a single CNN end-to-end directly from images with only pixels and labels as inputs. Applying this state-of-the-art algorithm, we are able to classify images of 4 snail categories with 99.64% accuracy and images of 11 parasite categories with 88.14% accuracy, which rivals highly-trained human parasitologists. The trained algorithm could next be deployed to mobile devices for use in remote field settings by local technicians, and significantly improve monitoring snail and parasite occurrence in the field for disease control purposes.\n\nAuthor SummarySchistosomiasis is a neglected tropical disease (NTD) infecting over 250 million people worldwide. The current approach to mitigate this disease in endemic regions is community or school-based mass drug administration. However, parasites are primarily transmitted through environmental reservoirs where freshwater snails serve as intermediate hosts. People use the contaminated water sources for their daily tasks and get re-infected after drug treatment. Therefore, drug administration alone is not effective for schistosomiasis control in such high transmission settings. Recent studies show that snail population control is essential to reduce disease transmission risks. To discern between parasitic worms of humans in snails and those of other non-human species is a necessary step to precisely quantify transmission risk for human schistosomiasis. However, it takes a great deal of expertise to train lab and field technicians to accurately classify snail and parasite species. Artificial intelligence (AI)-powered computer vision algorithms have recently proven to be highly efficient for image recognition tasks. We have collected thousands of snail and parasite images in Senegal during 2015-2018. Using these images as training data, we developed an AI model that classifies images of 4 snail categories and 11 parasite categories with, in some cases, higher accuracy than well-trained human parasitologists. This model could next be deployed to mobile devices for use in remote field settings to support local technicians to identify transmission hotspots and target control.

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Liu, Z. Y.-C., Chamberlin, A. J., Shome, P., Jones, I. J., Riveau, G., Ndione, R. A., Bandagny, L., Jouanard, N., Van Eck, P., Ngo, T., Sokolow, S. H., De Leo, G. A.. 2019-07-24. Identification of snails and parasites of medical importance via convolutional neural network: an application for human schistosomiasis. https://doi.org/10.1101/713727

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