Self-supervised contrastive learning with random walks for medical image segmentation with limited annotations

Medical image segmentation has seen significant progress through the use of supervised deep learning. Hereby, large annotated datasets were employed to reliably segment anatomical structures. To reduce the requirement for annotated training data, self-supervised pre-training strategies on non-annotated data were designed. Especially contrastive learning schemes operating on dense pixel-wise representations have been introduced as an effective tool. In this work, we expand on this strategy and leverage inherent anatomical similarities in medical imaging data. We apply our approach to the task of semantic segmentation in a semi-supervised setting with limited amounts of annotated volumes. Trained alongside a segmentation loss in one single training stage, a contrastive loss aids to differentiate between salient anatomical regions that conform to the available annotations. Our approach builds upon the work of Jabri et al. (2020), who proposed cyclical contrastive random walks (CCRW) for self-supervision on palindromes of video frames. We adapt this scheme to operate on entries of paired embedded image slices. Using paths of cyclical random walks bypasses the need for negative samples, as commonly used in contrastive approaches, enabling the algorithm to discriminate among relevant salient (anatomical) regions implicitly. Further, a multi-level supervision strategy is employed, ensuring adequate representations of local and global characteristics of anatomical structures. The effectiveness of reducing the amount of required annotations is shown on three MRI datasets. A median increase of 8.01 and 5.90 pp in the Dice Similarity Coefficient (DSC) compared to our baseline could be achieved across all three datasets in the case of one and two available annotated examples per dataset.