Uncertainty estimates as data selection criteria to boost omni-supervised learning

© Springer Nature Switzerland AG 2020. For many medical applications, large quantities of imaging data are routinely obtained but it can be difficult and time-consuming to obtain high-quality labels for that data. We propose a novel uncertainty-based method to improve the performance of segmentation networks when limited manual labels are available in a large dataset. We estimate segmentation uncertainty on unlabeled data using test-time augmentation and test-time dropout. We then use uncertainty metrics to select unlabeled samples for further training in a semi-supervised learning framework. Compared to random data selection, our method gives a significant boost in Dice coefficient for semi-supervised volume segmentation on the EADC-ADNI/HARP MRI dataset and the large-scale INTERGROWTH-21st ultrasound dataset. Our results show a greater performance boost on the ultrasound dataset, suggesting that our method is most useful with data of lower or more variable quality.