Hierarchical Self-supervised Learning for Medical Image Segmentation Based on Multi-domain Data Aggregation

A large labeled dataset is a key to the success of supervised deep learning, but for medical image segmentation, it is highly challenging to obtain sufficient annotated images for model training. In many scenarios, unannotated images are abundant and easy to acquire. Self-supervised learning (SSL) has shown great potentials in exploiting raw data information and representation learning. In this paper, we propose Hierarchical Self-Supervised Learning (HSSL), a new self-supervised framework that boosts medical image segmentation by making good use of unannotated data. Unlike the current literature on task-specific self-supervised pretraining followed by supervised fine-tuning, we utilize SSL to learn task-agnostic knowledge from heterogeneous data for various medical image segmentation tasks. Specifically, we first aggregate a dataset from several medical challenges, then pre-train the network in a self-supervised manner, and finally fine-tune on labeled data. We develop a new loss function by combining contrastive loss and classification loss, and pre-train an encoder-decoder architecture for segmentation tasks. Our extensive experiments show that multi-domain joint pretraining benefits downstream segmentation tasks and outperforms single-domain pre-training significantly. Compared to learning from scratch, our method yields better performance on various tasks (e.g., +0.69% to +18.60% in Dice with 5% of annotated data). With limited amounts of training data, our method can substantially bridge the performance gap with respect to denser annotations (e.g., 10% vs. 100% annotations).