# Domain Aware Multi-Task Pretraining of 3D Swin Transformer for T1-weighted Brain MRI

arXiv: https://arxiv.org/abs/2410.00410 · HTML: https://mlsanity.com/paper/2410.00410/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 40 of its 94 references that are in the map.
- First posted on arXiv 1 Oct 2024.

## Builds on (most cited first, 30 of 40)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Quo Vadis, Action Recognition? A New Model and the Kinetics Dataset](https://mlsanity.com/paper/1705.07750/) (2017)
- [Improved Baselines with Momentum Contrastive Learning](https://mlsanity.com/paper/2003.04297/) (2020)
- [Unsupervised Representation Learning by Predicting Image Rotations](https://mlsanity.com/paper/1803.07728/) (2018)
- [Context Encoders: Feature Learning by Inpainting](https://mlsanity.com/paper/1604.07379/) (2016)
- [Unsupervised Learning of Visual Representations by Solving Jigsaw Puzzles](https://mlsanity.com/paper/1603.09246/) (2016)
- [A Survey on Deep Learning in Medical Image Analysis](https://mlsanity.com/paper/1702.05747/) (2017)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Colorful Image Colorization](https://mlsanity.com/paper/1603.08511/) (2016)
- [Unsupervised Visual Representation Learning by Context Prediction](https://mlsanity.com/paper/1505.05192/) (2015)
- [Scaling Vision Transformers](https://mlsanity.com/paper/2106.04560/) (2021)
- [Grad-CAM++: Improved Visual Explanations for Deep Convolutional Networks](https://mlsanity.com/paper/1710.11063/) (2017)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Do Vision Transformers See Like Convolutional Neural Networks?](https://mlsanity.com/paper/2108.08810/) (2021)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Big Self-Supervised Models Advance Medical Image Classification](https://mlsanity.com/paper/2101.05224/) (2021)
- [Med3D: Transfer Learning for 3D Medical Image Analysis](https://mlsanity.com/paper/1904.00625/) (2019)
- [Transformers in Medical Imaging: A Survey](https://mlsanity.com/paper/2201.09873/) (2022)
- [Brain Tumor Segmentation with Deep Neural Networks](https://mlsanity.com/paper/1505.03540/) (2015)

## Built on by (most cited first, 2 of 2)

- [How Much MRI Preprocessing Is Enough? A Cost-Utility Study for Brain MRI Foundation Models](https://mlsanity.com/paper/2606.08164/) (2026)
- [Combining General and Domain-Specific Pretext Tasks for Brain MR Image Segmentation](https://mlsanity.com/paper/2609.30708/) (2026)

## Abstract (arXiv)

The scarcity of annotated medical images is a major bottleneck in developing learning models for medical image analysis. Hence, recent studies have focused on pretrained models with fewer annotation requirements that can be fine-tuned for various downstream tasks. However, existing approaches are mainly 3D adaptions of 2D approaches ill-suited for 3D medical imaging data. Motivated by this gap, we propose novel domain-aware multi-task learning tasks to pretrain a 3D Swin Transformer for brain magnetic resonance imaging (MRI). Our method considers the domain knowledge in brain MRI by incorporating brain anatomy and morphology as well as standard pretext tasks adapted for 3D imaging in a contrastive learning setting. We pretrain our model using large-scale brain MRI data of 13,687 samples spanning several large-scale databases. Our method outperforms existing supervised and self-supervised methods in three downstream tasks of Alzheimer's disease classification, Parkinson's disease classification, and age prediction tasks. The ablation study of the proposed pretext tasks shows the effectiveness of our pretext tasks.