# Pretext Matters: An Empirical Study of SSL Methods in Medical Imaging

arXiv: https://arxiv.org/abs/2603.22649 · HTML: https://mlsanity.com/paper/2603.22649/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 26 of its 38 references that are in the map.
- First posted on arXiv 23 Mar 2026.

## Builds on (most cited first, 26 of 26)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [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)
- [Zero-Shot Text-to-Image Generation](https://mlsanity.com/paper/2102.12092/) (2021)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [VideoMAE: Masked Autoencoders are Data-Efficient Learners for Self-Supervised Video Pre-Training](https://mlsanity.com/paper/2203.12602/) (2022)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [data2vec: A General Framework for Self-supervised Learning in Speech, Vision and Language](https://mlsanity.com/paper/2202.03555/) (2022)
- [Self-supervised Visual Feature Learning with Deep Neural Networks: A Survey](https://mlsanity.com/paper/1902.06162/) (2019)
- [LeJEPA: Provable and Scalable Self-Supervised Learning Without the Heuristics](https://mlsanity.com/paper/2511.08544/) (2025)
- [Phikon-v2, A large and public feature extractor for biomarker prediction](https://mlsanity.com/paper/2409.09173/) (2024)
- [USFM: A Universal Ultrasound Foundation Model Generalized to Tasks and Organs towards Label Efficient Image Analysis](https://mlsanity.com/paper/2401.00153/) (2023)
- [Learning by Reconstruction Produces Uninformative Features For Perception](https://mlsanity.com/paper/2402.11337/) (2024)
- [Talking to DINO: Bridging Self-Supervised Vision Backbones with Language for Open-Vocabulary Segmentation](https://mlsanity.com/paper/2411.19331/) (2024)
- [How JEPA Avoids Noisy Features: The Implicit Bias of Deep Linear Self Distillation Networks](https://mlsanity.com/paper/2407.03475/) (2024)
- [USF-MAE: Ultrasound Self-Supervised Foundation Model with Masked Autoencoding](https://mlsanity.com/paper/2510.22990/) (2025)
- [A Fully Open and Generalizable Foundation Model for Ultrasound Clinical Applications](https://mlsanity.com/paper/2509.11752/) (2025)
- [Revisiting Data Augmentation for Ultrasound Images](https://mlsanity.com/paper/2501.13193/) (2025)
- [General Methods Make Great Domain-specific Foundation Models: A Case-study on Fetal Ultrasound](https://mlsanity.com/paper/2506.19552/) (2025)
- [Beyond [cls]: Exploring the true potential of Masked Image Modeling representations](https://mlsanity.com/paper/2412.03215/) (2024)
- [Self-supervised Learning of Echocardiographic Video Representations via Online Cluster Distillation](https://mlsanity.com/paper/2506.11777/) (2025)
- [Self-Supervised Ultrasound-Video Segmentation with Feature Prediction and 3D Localised Loss](https://mlsanity.com/paper/2507.18424/) (2025)
- [CytoFM: The first cytology foundation model](https://mlsanity.com/paper/2504.13402/) (2025)

## Built on by (most cited first, 3 of 3)

- [Which Pretext Task Transfers? Self-Supervised Pretraining Objectives for Lung Ultrasound](https://mlsanity.com/paper/2609.16551/) (2026)
- [UltraBench 2: Towards Robust Evaluation of Vision Foundation Models on Ultrasound](https://mlsanity.com/paper/2609.28610/) (2026)
- [The Predictability Bias of Joint-Embedding Predictive Learning in Medical Imaging](https://mlsanity.com/paper/2610.13237/) (2026)

## Abstract (arXiv)

Though self-supervised learning (SSL) has demonstrated incredible ability to learn robust representations from unlabeled data, the choice of optimal SSL strategy can lead to vastly different performance outcomes in specialized domains. Joint embedding architectures (JEAs) and joint embedding predictive architectures (JEPAs) have shown robustness to noise and strong semantic feature learning compared to pixel reconstruction-based SSL methods, leading to widespread adoption in medical imaging. However, no prior work has systematically investigated which SSL objective is better aligned with the spatial organization of clinically relevant signal. In this work, we empirically investigate how the choice of SSL method impacts the learned representations in medical imaging. We select two representative imaging modalities characterized by unique noise profiles: ultrasound and histopathology. When informative signal is spatially localized, as in histopathology, JEAs are more effective due to their view-invariance objective. In contrast, when diagnostically relevant information is globally structured, such as the macroscopic anatomy present in liver ultrasounds, JEPAs are optimal. These differences are especially evident in the clinical relevance of the learned features, as independently validated by board-certified radiologists and pathologists. Together, our results provide a framework for matching SSL objectives to the structural and noise properties of medical imaging modalities.