COVID19 Diagnosis using AutoML from 3D CT scans

Coronavirus is a pandemic that affects the respiratory system causing cough, shortness of breath, and death in severe cases. Polymerase chain reaction (PCR) tests are used to diagnose coronavirus. The false-negative rate of these tests is high, so there needs a supporting method for an accurate diagnosis. CT scan provides a detailed examination of the chest to diagnose COVID, but a single CT scan comprises hundreds of slices. Expert and experienced radiologists and pulmonologists can diagnose COVID from these hundreds of slices, but this is very time-consuming. So an automatic artificial intelligence (AI) based method is required to diagnose coronavirus with high accuracy. Developing this AI-based technique requires a lot of resources and time, but once it is developed, it can significantly help the clinicians. This paper used an Automated machine learning (AutoML) technique that requires fewer resources (optimal architecture trials) and time to develop, resulting in the best diagnosis. The AutoML models are trained on 2D slices instead of 3D CT scans, and the predictions on unknown data (slices of CT scan) are aggregated to form a prediction of 3D CT scan. The aggregation process picked the most occurred case, whether COVID or non-COVID from all CT scan slices and labeled the 3D CT scan accordingly. Different thresholds are also used to label COVID or non-COVID 3D CT scans from 2D slices. The approach resulted in accuracy and F1-score of 89% and 88%, respectively. Implementation is available at github.com/talhaanwarch/mia-covid19