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This research addresses data scarcity in medical imaging by combining domain-specific brain age prediction with general image inpainting tasks to train more robust foundation models. The proposed multitask self-supervised framework significantly outperforms single-task approaches across multiple sclerosis, stroke, and cortical segmentation benchmarks. By leveraging complementary representations from both specific and general pretext tasks, the study advances the development of generalizable neuroimaging AI models that require fewer manual annotations.
Combining General and Domain-Specific Pretext Tasks for Brain MR Image Segmentation
arXiv:2609.30708v1 Announce Type: cross Abstract: A key challenge in medical image analysis is the scarcity of large annotated datasets for specific populations and diseases. As deep learning models rely heavily on labeled data, effective transfer learning strategies are needed to reduce the dependence on manual annotations. Self-supervised learning has emerged as a promising approach for developing foundation models by enabling the learning of transferable feature representations from large-scale unlabeled medical imaging datasets. In this study, we investigate voxel-level brain age prediction as a domain-specific self-supervised pretext task and compare it with image inpainting, a widely used non-domain-specific alternative. We further propose a multitask self-supervised pretraining framework that jointly optimizes both objectives to learn complementary neuroimaging representations. The pretrained models are evaluated on three downstream magnetic resonance image segmentation tasks: multiple sclerosis lesion segmentation, ischemic stroke lesion segmentation, and cortical brain structure segmentation. Overall, the proposed multitask pretraining framework consistently outperformed the single-task pretrained models and training from scratch across most experimental settings, demonstrating the benefit of combining domain-specific and general self-supervised learning pretext tasks for the development of generalizable neuroimaging foundation models.\ Code Availability: The source code used in this study is publicly available at https://github.com/TasneemN/Combining-General-and-Domain-Specific-Pretext-Tasks-for-Brain-MR-Image-Segmentation/
Abstract:A key challenge in medical image analysis is the scarcity of large annotated datasets for specific populations and diseases. As deep learning models rely heavily on labeled data, effective transfer learning strategies are needed to reduce the dependence on manual annotations. Self-supervised learning has emerged as a promising approach for developing foundation models by enabling the learning of transferable feature representations from large-scale unlabeled medical imaging datasets. In this study, we investigate voxel-level brain age prediction as a domain-specific self-supervised pretext task and compare it with image inpainting, a widely used non-domain-specific alternative. We further propose a multitask self-supervised pretraining framework that jointly optimizes both objectives to learn complementary neuroimaging representations. The pretrained models are evaluated on three downstream magnetic resonance image segmentation tasks: multiple sclerosis lesion segmentation, ischemic stroke lesion segmentation, and cortical brain structure segmentation. Overall, the proposed multitask pretraining framework consistently outperformed the single-task pretrained models and training from scratch across most experimental settings, demonstrating the benefit of combining domain-specific and general self-supervised learning pretext tasks for the development of generalizable neuroimaging foundation models.\ Code Availability: The source code used in this study is publicly available at this https URL
Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI)
arXiv:2609.30708 [cs.CV]
(or arXiv:2609.30708v1 [cs.CV] for this version)
https://doi.org/10.48550/arXiv.2609.30708 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
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