Correcting class imbalances with self-training for improved universal lesion detection and tagging

Universal lesion detection and tagging (ULDT) in CT studies is critical for tumor burden assessment and tracking the progression of lesion status (growth/shrinkage) over time. However, a lack of fully annotated data hinders the development of effective ULDT approaches. Prior work used the DeepLesion dataset (4,427 patients, 10,594 studies, 32,120 CT slices, 32,735 lesions, 8 body part labels) for algorithmic development, but this dataset is not completely annotated and contains class imbalances. To address these issues, in this work, we developed a self-training pipeline for ULDT. A VFNet model was trained on a limited 11.5% subset of DeepLesion (bounding boxes + tags) to detect and classify lesions in CT studies. Then, it identified and incorporated novel lesion candidates from a larger unseen data subset into its training set, and self-trained itself over multiple rounds. Multiple self-training experiments were conducted with different threshold policies to select predicted lesions with higher quality and cover the class imbalances. We discovered that direct self-training improved the sensitivities of over-represented lesion classes at the expense of under-represented classes. However, upsampling the lesions mined during self-training along with a variable threshold policy yielded a 6.5% increase in sensitivity at 4 FP in contrast to self-training without class balancing (72% vs 78.5%) and a 11.7% increase compared to the same self-training policy without upsampling (66.8% vs 78.5%). Furthermore, we show that our results either improved or maintained the sensitivity at 4FP for all 8 lesion classes.