# Benchmarking transferability of SSL pretraining to same and different modality segmentation tasks

arXiv: https://arxiv.org/abs/2605.18491 · HTML: https://mlsanity.com/paper/2605.18491/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 45 of its 64 references that are in the map.
- First posted on arXiv 18 May 2026.

## Builds on (most cited first, 30 of 45)

- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [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)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [Unsupervised Representation Learning by Predicting Image Rotations](https://mlsanity.com/paper/1803.07728/) (2018)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [Contrastive learning of global and local features for medical image segmentation with limited annotations](https://mlsanity.com/paper/2006.10511/) (2020)
- [Do Wide and Deep Networks Learn the Same Things? Uncovering How Neural Network Representations Vary with Width and Depth](https://mlsanity.com/paper/2010.15327/) (2020)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [How Well Do Self-Supervised Models Transfer?](https://mlsanity.com/paper/2011.13377/) (2020)
- [Self-supervised Pretraining of Visual Features in the Wild](https://mlsanity.com/paper/2103.01988/) (2021)
- [DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation](https://mlsanity.com/paper/1506.06448/) (2015)
- [On the Challenges and Perspectives of Foundation Models for Medical Image Analysis](https://mlsanity.com/paper/2306.05705/) (2023)
- [3D Self-Supervised Methods for Medical Imaging](https://mlsanity.com/paper/2006.03829/) (2020)
- [MST: Masked Self-Supervised Transformer for Visual Representation](https://mlsanity.com/paper/2106.05656/) (2021)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT](https://mlsanity.com/paper/2307.01984/) (2023)
- [Self-Supervised Pretraining Improves Self-Supervised Pretraining](https://mlsanity.com/paper/2103.12718/) (2021)
- [Masked Image Modeling Advances 3D Medical Image Analysis](https://mlsanity.com/paper/2204.11716/) (2022)
- [Transferable Visual Words: Exploiting the Semantics of Anatomical Patterns for Self-supervised Learning](https://mlsanity.com/paper/2102.10680/) (2021)
- [What Makes Transfer Learning Work For Medical Images: Feature Reuse & Other Factors](https://mlsanity.com/paper/2203.01825/) (2022)
- [UniMiSS: Universal Medical Self-Supervised Learning via Breaking Dimensionality Barrier](https://mlsanity.com/paper/2112.09356/) (2021)
- [Contrastive Learning with Continuous Proxy Meta-Data for 3D MRI Classification](https://mlsanity.com/paper/2106.08808/) (2021)
- [Are Natural Domain Foundation Models Useful for Medical Image Classification?](https://mlsanity.com/paper/2310.19522/) (2023)

## Abstract (arXiv)

Methods: Nine SSL methods spanning four pretext-task families were pretrained from scratch using the same 10{,}412 3D CT scans (1.89~M 2D axial slices) covering varied disease sites. The pretrained Swin Transformer encoder from each method was integrated into a SwinUNETR-style segmentation network (Swin encoder with a 3D CNN decoder and skip connections) and fine-tuned on nine public segmentation tasks of varying complexity, including large abdominal organs, head-and-neck structures, and tumors from CT and MRI. Performance was assessed using Dice similarity coefficient (DSC). Fine-tuning convergence speed, transferability across modalities (CT-to-MRI), and feature-reuse patterns between few- and many-shot fine tuning were further analyzed using centered kernel alignment. Results: Self-distilled masked image transformer (SMIT), which combines masked image modeling (MIM) with local and global self-distillation, achieved the highest overall segmentation accuracy across the nine tasks, the fastest fine-tuning convergence, and the smallest few-shot-to-many-shot performance gap, indicating the strongest data efficiency. SMIT also showed the most consistent feature-reuse patterns between few- and many-shot fine tuning. MIM-based SimMIM and self-distillation methods (DINO, iBOT) outperformed contrastive learning and rotation prediction, which rely on image-level global representations. Differences between SSL methods were largest in the few-shot setting and narrowed as the size of the labeled fine-tuning dataset increased, indicating that the choice of SSL pretraining matters most under limited annotation budgets.