Development of machine learning models for object identification of parasite eggs using microscopy

University essay from Uppsala universitet/Signaler och system

Abstract: Over one billion people in developing countries are afflicted by parasitic infections caused by soil-transmitted helminths. These infections are treatable with cheap and safe medicine that is widely available. However, diagnosis of these infections has proven to be a bottleneck by the fact that it is time-consuming, requires expensive equipment and trained personnel to be consistent and accurate. This study aimed to investigate the viability and performance of five machine learning models and a 'modular neural network' approach to localize and classify the following parasite eggs in microscopic images: Ascaris lumbricoides, Trichuris trichuria, Hookworm and Schistosoma mansoni. These models were implemented and evaluated on the Nvidia Jetson AGX Xavier to establish that they fulfilled the specifications of 95\% specificity and sensitivity, but also a speed requirement of 40000 images per 24 hours. The results show that R-FCN ResNet101 was the best model produced in this study, which performed the best on average. However, it did not fulfill the specifications entirely but is still considered a success due to being an improvement to the current implementation at Etteplan. Evaluation of the modular neural network approach would require further investigation to verify the performance of the system, but the results indicate it could be a possible improvement to the off-the-shelf machine learning models. To conclude, the study showed that the data and data infrastructure provided by Etteplan has proven to be a very powerful tool in training machine learning models to classify and localize parasite eggs in stool samples. However, expansion of the data to reduce the imbalance between the representations of the classes but also include more patient information could improve the training and evaluation process of the models.

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