Detecting pulmonary Coccidioidomycosis with deep convolutional neural networks

• Published in: Machine learning with applications 2021-09, Vol.5, p.100040, Article 100040
• Main Authors: Ott, Jordan, Bruyette, David, Arbuckle, Cody, Balsz, Dylan, Hecht, Silke, Shubitz, Lisa, Baldi, Pierre
• Format: Article
• Language: English
• ISSN: 2666-8270; 2666-8270
• DOI: 10.1016/j.mlwa.2021.100040

Coccidioidomycosis is the most common systemic mycosis in dogs in the southwestern United States. With warming climates, affected areas and number of cases are expected to increase in the coming years, escalating also the chances of transmission to humans. As a result, developing methods for automating the detection of the disease is important, as this will help doctors and veterinarians more easily identify and diagnose positive cases. We apply machine learning models to provide accurate and interpretable predictions of Coccidioidomycosis. We assemble a set of radiographic images and use it to train and test state-of-the-art convolutional neural networks to detect Coccidioidomycosis. These methods are relatively inexpensive to train and very fast at inference time. We demonstrate the successful application of this approach to detect the disease with an Area Under the Curve (AUC) above 0.99 using 10-fold cross-validation. We also use the classification model to identify regions of interest and localize the disease in the radiographic images, as illustrated through visual heatmaps. This proof-of-concept study establishes the feasibility of very accurate and rapid automated detection of Valley Fever in radiographic images. [Display omitted] •The dataset in this study contains 1,174 radiographic images.•We automate the detection of Valley Fever in canines with deep learning models.•The classification models employed in this study achieve an AUC of 0.99.•These networks have the ability to localize the disease in images.•The proposed approach is show to be fast, accurate, and meaningfully interpretable.