Deep Learning-Based Total Kidney Volume Segmentation in Autosomal Dominant Polycystic Kidney Disease Using Attention, Cosine Loss, and Sharpness Aware Minimization

Abstract

Early detection of the autosomal dominant polycystic kidney disease (ADPKD) is crucial as it is one of the most common causes of end-stage renal disease (ESRD) and kidney failure. The total kidney volume (TKV) can be used as a biomarker to quantify disease progression. The TKV calculation requires accurate delineation of kidney volumes, which is usually performed manually by an expert physician. However, this is time-consuming and automated segmentation is warranted. Furthermore, the scarcity of large annotated datasets hinders the development of deep learning solutions. In this work, we address this problem by implementing three attention mechanisms into the U-Net to improve TKV estimation. Additionally, we implement a cosine loss function that works well on image classification tasks with small datasets. Lastly, we apply a technique called sharpness aware minimization (SAM) that helps improve the generalizability of networks. Our results show significant improvements (p-value < 0.05) over the reference kidney segmentation U-Net. We show that the attention mechanisms and/or the cosine loss with SAM can achieve a dice score (DSC) of 0.918, a mean symmetric surface distance (MSSD) of 1.20 mm with the mean TKV difference of −1.72%, and R2 of 0.96 while using only 100 MRI datasets for training and testing. Furthermore, we tested four ensembles and obtained improvements over the best individual network, achieving a DSC and MSSD of 0.922 and 1.09 mm, respectively.