Prior-aware neural network for partially-supervised multi-organ segmentation

Accurate multi-organ abdominal CT segmentation is essential to many clinical applications such as computer-aided intervention. As data annotation requires massive human labor from experienced radiologists, it is common that training data is usually partially-labeled. However, these background labels can be misleading in multi-organ segmentation since the ''background'' usually contains some other organs of interest. To address the background ambiguity in these partially-labeled datasets, we propose Prior-aware Neural Network (PaNN) via explicitly incorporating anatomical priors on abdominal organ sizes, guiding the training process with domain-specific knowledge. More specifically, PaNN assumes that the average organ size distributions in the abdomen should approximate their empirical distributions, a prior statistics obtained from the fully-labeled dataset. As our objective is difficult to be directly optimized using stochastic gradient descent, it is reformulated as a min-max form and optimized via the stochastic primal-dual gradient algorithm. PaNN achieves state-of-the-art performance on the MICCAI2015 challenge ''Multi-Atlas Labeling Beyond the Cranial Vault'', a competition on organ segmentation in the abdomen. We report an average Dice score of 84.97%, surpassing the prior art by a large margin of 3.27%. Code and models will be made publicly available.