Keypoint-Augmented Self-Supervised Learning for Medical Image Segmentation with Limited Annotation

Zhangsihao Yang, Mengwei Ren, Kaize Ding, Guido Gerig, Yalin Wang

Research output: Contribution to journalConference articlepeer-review


Pretraining CNN models (i.e., UNet) through self-supervision has become a powerful approach to facilitate medical image segmentation under low annotation regimes. Recent contrastive learning methods encourage similar global representations when the same image undergoes different transformations, or enforce invariance across different image/patch features that are intrinsically correlated. However, CNN-extracted global and local features are limited in capturing long-range spatial dependencies that are essential in biological anatomy. To this end, we present a keypoint-augmented fusion layer that extracts representations preserving both short- and long-range self-attention. In particular, we augment the CNN feature map at multiple scales by incorporating an additional input that learns long-range spatial self-attention among localized keypoint features. Further, we introduce both global and local self-supervised pretraining for the framework. At the global scale, we obtain global representations from both the bottleneck of the UNet, and by aggregating multiscale keypoint features. These global features are subsequently regularized through image-level contrastive objectives. At the local scale, we define a distance-based criterion to first establish correspondences among keypoints and encourage similarity between their features. Through extensive experiments on both MRI and CT segmentation tasks, we demonstrate the architectural advantages of our proposed method in comparison to both CNN and Transformer-based UNets, when all architectures are trained with randomly initialized weights. With our proposed pretraining strategy, our method further outperforms existing SSL methods by producing more robust self-attention and achieving state-of-the-art segmentation results. The code is available at

Original languageEnglish (US)
JournalAdvances in Neural Information Processing Systems
StatePublished - 2023
Event37th Conference on Neural Information Processing Systems, NeurIPS 2023 - New Orleans, United States
Duration: Dec 10 2023Dec 16 2023

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Information Systems
  • Signal Processing


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