# Self-supervised learning methods and applications in medical imaging analysis: A survey

arXiv: https://arxiv.org/abs/2109.08685 · HTML: https://mlsanity.com/paper/2109.08685/

## Key facts

- Cited by 77 papers in the map (data through 14 Oct 2026).
- Builds on 80 of its 130 references that are in the map.
- First posted on arXiv 17 Sep 2021.

## Builds on (most cited first, 30 of 80)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [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)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [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)
- [Going Deeper with Convolutions](https://mlsanity.com/paper/1409.4842/) (2014)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Prototypical Networks for Few-shot Learning](https://mlsanity.com/paper/1703.05175/) (2017)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distances](https://mlsanity.com/paper/1306.0895/) (2013)
- [Improved Baselines with Momentum Contrastive Learning](https://mlsanity.com/paper/2003.04297/) (2020)
- [Unsupervised Representation Learning with Deep Convolutional Generative Adversarial Networks](https://mlsanity.com/paper/1511.06434/) (2015)
- [Identity Mappings in Deep Residual Networks](https://mlsanity.com/paper/1603.05027/) (2016)
- [Unsupervised Feature Learning via Non-Parametric Instance-level Discrimination](https://mlsanity.com/paper/1805.01978/) (2018)
- [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)
- [CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison](https://mlsanity.com/paper/1901.07031/) (2019)
- [Unsupervised Learning of Visual Representations by Solving Jigsaw Puzzles](https://mlsanity.com/paper/1603.09246/) (2016)
- [Big Self-Supervised Models are Strong Semi-Supervised Learners](https://mlsanity.com/paper/2006.10029/) (2020)
- [Colorful Image Colorization](https://mlsanity.com/paper/1603.08511/) (2016)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Unsupervised Visual Representation Learning by Context Prediction](https://mlsanity.com/paper/1505.05192/) (2015)
- [Conditional Image Generation with PixelCNN Decoders](https://mlsanity.com/paper/1606.05328/) (2016)
- [Self-supervised Learning: Generative or Contrastive](https://mlsanity.com/paper/2006.08218/) (2020)
- [Data-Efficient Image Recognition with Contrastive Predictive Coding](https://mlsanity.com/paper/1905.09272/) (2019)
- [Self-supervised Visual Feature Learning with Deep Neural Networks: A Survey](https://mlsanity.com/paper/1902.06162/) (2019)

## Built on by (most cited first, 30 of 77)

- [RealGen: Retrieval Augmented Generation for Controllable Traffic Scenarios](https://mlsanity.com/paper/2312.13303/) (2023)
- [WSSS4LUAD: Grand Challenge on Weakly-supervised Tissue Semantic Segmentation for Lung Adenocarcinoma](https://mlsanity.com/paper/2204.06455/) (2022)
- [Review of multimodal machine learning approaches in healthcare](https://mlsanity.com/paper/2402.02460/) (2024)
- [Towards Label-efficient Automatic Diagnosis and Analysis: A Comprehensive Survey of Advanced Deep Learning-based Weakly-supervised, Semi-supervised and Self-supervised Techniques in Histopathological Image Analysis](https://mlsanity.com/paper/2208.08789/) (2022)
- [Segment Anything Model (SAM) for Radiation Oncology](https://mlsanity.com/paper/2306.11730/) (2023)
- [From Denoising Training to Test-Time Adaptation: Enhancing Domain Generalization for Medical Image Segmentation](https://mlsanity.com/paper/2310.20271/) (2023)
- [Self-supervised Learning for Electroencephalogram: A Systematic Survey](https://mlsanity.com/paper/2401.05446/) (2024)
- [LeBenchmark 2.0: a Standardized, Replicable and Enhanced Framework for Self-supervised Representations of French Speech](https://mlsanity.com/paper/2309.05472/) (2023)
- [A Survey of Pathology Foundation Model: Progress and Future Directions](https://mlsanity.com/paper/2504.04045/) (2025)
- [Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation](https://mlsanity.com/paper/2205.00627/) (2022)
- [Global Contrast Masked Autoencoders Are Powerful Pathological Representation Learners](https://mlsanity.com/paper/2205.09048/) (2022)
- [A Review of Predictive and Contrastive Self-supervised Learning for Medical Images](https://mlsanity.com/paper/2302.05043/) (2023)
- [SURDS: Self-Supervised Attention-guided Reconstruction and Dual Triplet Loss for Writer Independent Offline Signature Verification](https://mlsanity.com/paper/2201.10138/) (2022)
- [Data efficient deep learning for medical image analysis: A survey](https://mlsanity.com/paper/2310.06557/) (2023)
- [CSLP-AE: A Contrastive Split-Latent Permutation Autoencoder Framework for Zero-Shot Electroencephalography Signal Conversion](https://mlsanity.com/paper/2311.07788/) (2023)
- [Your contrastive learning problem is secretly a distribution alignment problem](https://mlsanity.com/paper/2502.20141/) (2025)
- [IDEAL: Improved DEnse locAL Contrastive Learning for Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2210.15075/) (2022)
- [Self-Supervised Skeleton-Based Action Representation Learning: A Benchmark and Beyond](https://mlsanity.com/paper/2406.02978/) (2024)
- [Continual Self-supervised Learning Considering Medical Domain Knowledge in Chest CT Images](https://mlsanity.com/paper/2501.04217/) (2025)
- [A Self-supervised Multimodal Deep Learning Approach to Differentiate Post-radiotherapy Progression from Pseudoprogression in Glioblastoma](https://mlsanity.com/paper/2502.03999/) (2025)
- [TopoCL: Topological Contrastive Learning for Medical Imaging](https://mlsanity.com/paper/2603.14647/) (2026)
- [Self-Supervised Learning for Data Scarcity in a Fatigue Damage Prognostic Problem](https://mlsanity.com/paper/2301.08441/) (2023)
- [OTCXR: Rethinking Self-supervised Alignment using Optimal Transport for Chest X-ray Analysis](https://mlsanity.com/paper/2404.11868/) (2024)
- [Image-based Freeform Handwriting Authentication with Energy-oriented Self-Supervised Learning](https://mlsanity.com/paper/2408.09676/) (2024)
- [Adaptation of Foundation Models for Medical Image Analysis: Strategies, Challenges, and Future Directions](https://mlsanity.com/paper/2511.01284/) (2025)
- [Edema Estimation From Facial Images Taken Before and After Dialysis via Contrastive Multi-Patient Pre-Training](https://mlsanity.com/paper/2212.07582/) (2022)
- [Exploring Self-Supervised Representation Learning For Low-Resource Medical Image Analysis](https://mlsanity.com/paper/2303.02245/) (2023)
- [Unleash Model Potential: Bootstrapped Meta Self-supervised Learning](https://mlsanity.com/paper/2308.14267/) (2023)
- [A Survey of the Impact of Self-Supervised Pretraining for Diagnostic Tasks with Radiological Images](https://mlsanity.com/paper/2309.02555/) (2023)
- [A Study on Self-Supervised Pretraining for Vision Problems in Gastrointestinal Endoscopy](https://mlsanity.com/paper/2401.06278/) (2024)

## Abstract (arXiv)

The scarcity of high-quality annotated medical imaging datasets is a major problem that collides with machine learning applications in the field of medical imaging analysis and impedes its advancement. Self-supervised learning is a recent training paradigm that enables learning robust representations without the need for human annotation which can be considered an effective solution for the scarcity of annotated medical data. This article reviews the state-of-the-art research directions in self-supervised learning approaches for image data with a concentration on their applications in the field of medical imaging analysis. The article covers a set of the most recent self-supervised learning methods from the computer vision field as they are applicable to the medical imaging analysis and categorize them as predictive, generative, and contrastive approaches. Moreover, the article covers 40 of the most recent research papers in the field of self-supervised learning in medical imaging analysis aiming at shedding the light on the recent innovation in the field. Finally, the article concludes with possible future research directions in the field.