Two-Stage Self-Supervised Contrastive Learning Aided Transformer for Real-Time Medical Image Segmentation
Qayyum, Abdul Razzak, Imran Mazher, Moona Khan, Tariq Ding, Weiping Niederer, Steven
Qayyum, Abdul
Razzak, Imran
Mazher, Moona
Khan, Tariq
Ding, Weiping
Niederer, Steven
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Computational Biology
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Journal article
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Abstract
The availability of large, high-quality annotated datasets in the medical domain poses a substantial challenge in segmentation tasks. To mitigate the reliance on annotated training data, self-supervised pre-training strategies have emerged, particularly employing contrastive learning methods on dense pixel-level representations. In this work, we proposed to capitalize on intrinsic anatomical similarities within medical image data and develop a semantic segmentation framework through a self-supervised fusion network, where the availability of annotated volumes is limited. In a unified training phase, we combine segmentation loss with contrastive loss, enhancing the distinction between significant anatomical regions that adhere to the available annotations. To further improve the segmentation performance, we introduce an efficient parallel transformer module that leverages Multiview multiscale feature fusion and depth-wise features. The proposed transformer architecture, based on multiple encoders, is trained in a self-supervised manner using contrastive loss. Initially, the transformer is trained using an unlabeled dataset. We then fine-tune one encoder using data from the first stage and another encoder using a small set of annotated segmentation masks. These encoder features are subsequently concatenated for the purpose of brain tumor segmentation. The multiencoder-based transformer model yields significantly better outcomes across three medical image segmentation tasks. We validated our proposed solution by fusing images across diverse medical image segmentation challenge datasets, demonstrating its efficacy by outperforming state-of-the-art methodologies.
Citation
A. Qayyum, I. Razzak, M. Mazher, T. Khan, W. Ding, S. Niederer, "Two-Stage Self-Supervised Contrastive Learning Aided Transformer for Real-Time Medical Image Segmentation," IEEE Journal of Biomedical and Health Informatics, vol. 30, no. 2, pp. 1039-1048, 2023, https://doi.org/10.1109/jbhi.2023.3340956.
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IEEE Journal of Biomedical and Health Informatics
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46 Information and Computing Sciences, 4603 Computer Vision and Multimedia Computation, 4611 Machine Learning, Algorithms, Brain, Databases, Factual, Humans, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Supervised Machine Learning
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IEEE