Awesome Self-Supervised Learning in Medical Imaging

This repository is mainly dedicated for listing the recent research advancements in the application of Self-Supervised-Learning in medical images computing field. Inspired by awesome-self-supervised-learning

What is self-supervised learning?

Self-Supervised learning (SSL) is a hybrid learning approach that combines both supervised and unsupervised learning simultaneously. More clearly, SSL is an approach that aims at learning semantically useful features for a certain task by generating supervisory signal from a pool of unlabeled data without the need for human annotation. These representations is then used for subsequent tasks where the amount of labeled data is limited.

Self-Supervised Learning pipelines in computer vision

Why Self-Supervised learning in medical imaging ?

• Unlabeled medical imaging data is a abundant, but human annotated data is scarce.
• building a large enough human annotated medical imaging datasets is:
  1. Expensive.
  2. Time consuming.
  3. Requires experienced personnel.
  4. Prone to patients’ privacy preserving issues.

This repository is a continuation of our survey in the field, please read and consider citing it in your work:

@article{shurrab2022self,
  title={Self-supervised learning methods and applications in medical imaging analysis: A survey},
  author={Shurrab, Saeed and Duwairi, Rehab},
  journal={PeerJ Computer Science},
  volume={8},
  pages={e1045},
  year={2022},
  publisher={PeerJ Inc.}
}

Call for Contribution

Please help contribute this list by contacting me or add pull request

Markdown format: height

- Paper Name. 
  [[pdf]](link) 
  [[code]](link)
  - Author 1, Author 2, and Author 3. *Conference Year*

Criteria

1. A list of recent self-supervised learning papers in medical imaging published since 2017.

2. Papers are collected from peer-reviewed journals and high reputed conferences. However, it might have recent papers on arXiv.

3. A meta-data is required along with the paper, e.g. category.

List of Journals / Conferences (J/C):

• IEEE Access
• IEEE Transaction on Medical Imaging (IEEE-TMI)
• IEEE Transaction on Biomedical Engineering (IEEE-TBME)
• IEEE Journal of Biomedical and Health Informatics (IEEE-JBHI)
• IEEE Transactions on Image Processing (IEEE-TIP)
• Applied Soft Computing (ASC)
• Computer in Biology and Medicine (CBM)
• Computerized Medical Imaging and Graphics (CMIG)
• Medical Image Analysis (MedIA)
• Machine Learning with Applications (MLwA)
• International Journal of Computer Assisted Radiology and Surgery (IJCARS)
• Nature Machine Intelligence (NMI)
• Pattern Recognition
• Expert Systems with Applications (ESA)
• Neurocomputing
• Diagnostics
• Computer Vision and Pattern Recognition (CVPR)
• Proceedings of Machine Learning Research (PMLR)
• International Conference on Machine Learning (ICML)
• IEEE International Symposium on Biomedical Imaging (ISBI)
• International Conference on Learning Representations (ICLR)
• Proceedings of the AAAI Conference on Artificial Intelligence (AAAI)
• Annual Conference on Neural Information Processing Systems (NIPS)
• International Conference on Medical Imaging with Deep Learning (MIDL)
• International Workshop on Deep Learning in Medical Image Analysis (DLMIA)
• International Conference on Information Processing in Medical Imaging (IPMI)
• IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
• Joint European Conference on Machine Learning and Knowledge Discovery in Databases (JECMLKDD)
• International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)

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2022

Paper title	Journal/Conference	Category	Paper link	Code link
COVID-19 Infection Segmentation and Severity Assessment Using a Self-Supervised Learning Approach	Diagnostics	Multiple-tasks/Multi-tasking	Link	NA
Contrastive Learning with Continuous Proxy Meta-data for 3D MRI Classification	MICCAI	Contrastive	Link	pytorch
How Transferable are Self-supervised Features in Medical Image Classification Tasks?	PMLR	Contrastive	Link	NA
Towards Better Understanding and Better Generalization of Low-shot Classification in Histology Images with Contrastive Learning	ICLR	Contrastive	Link	pytorch
Intra- and Inter-Slice Contrastive Learning for Point Supervised OCT Fluid Segmentation	IEEE-TIP	Contrastive	Link	pytorch
Multimodal image encoding pre-training for diabetic retinopathy grading	CBM	Generative	Link	NA
Self-supervised Learning for Few-shot Medical Image Segmentation	IEEE-TMI	NA	Link	pytorch
Self supervised contrastive learning for digital histopathology	MLwA	Contrastive	Link	pytorch
DeepSMILE: Contrastive self-supervised pre-training benefits MSI and HRD classification directly from H&E whole-slide images in colorectal and breast cancer	MedIA	Contrastive	Link	DLUP, VISSL, pytorch
Deep Contrastive Learning Based Tissue Clustering for Annotation-free Histopathology Image Analysis	CMIG	Contrastive	Link	NA
ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics	CVPR	Contrastive	Link	pytorch
Self-Supervised Learning Methods for Label-Efficient Dental Caries Classification	Diagnostics	Contrastive	Link	NA

2021

Paper title	Journal/Conference	Category	Paper link	Code link
Transferable Visual Words: Exploiting the Semantics of Anatomical Patterns for Self-Supervised Learning	IEEE-TMI	Multiple-tasks/Multi-tasking	Link	tensorflow pytorch
Towards Fine-grained Visual Representations by Combining Contrastive Learning with Image Reconstruction and Attention-weighted Pooling	ICML	Multiple-tasks/Multi-tasking	Link	tensorflow
How Transferable are Self-supervised Features in Medical Image Classification Tasks?	PMLR	Contrastive	Link	NA
Multimodal Self-supervised Learning for Medical Image Analysis	IPMI	Predictive	Link	NA
Self-supervised multimodal reconstruction pre-training for retinal computer-aided diagnosis	ESA	Generative	Link	NA
MedAug: Contrastive learning leveraging patient metadata improves representations for chest X-ray interpretation	ArXiv	Contrastive	Link	NA
COVID-19 Prognosis via Self-Supervised Representation Learning and Multi-Image Prediction	ArXiv	Contrastive	Link	pytorch
Momentum contrastive learning for few-shot COVID-19 diagnosis from chest CT images	Pattern Recognition	Contrastive	Link	NA
Big Self-Supervised Models Advance Medical Image Classification	ArXiv	Contrastive	Link	NA
Self-supervised Multi-task Representation Learning for Sequential Medical Images	JECMLKDD	Multiple-tasks/Multi-tasking	Link	NA
Self-path: Self-supervision for classification of pathology images with limited annotations	IEEE-TMI	Multiple-tasks/Multi-tasking	Link	NA
Twin self-supervision based semi-supervised learning (TS-SSL): Retinal anomaly classification in SD-OCT images	Neurocomputing	Multiple-tasks/Multi-tasking	Link	tensorflow
Rotation-oriented collaborative self-supervised learning for retinal disease diagnosis.	IEEE-TMI	Multiple-tasks/Multi-tasking	Link	tensorflow
Volumetric white matter tract segmentation with nested self-supervised learning using sequential pretext tasks	MedIA	Multiple-tasks/Multi-tasking	Link	NA

2020

Paper title	Journal/Conference	Category	Paper link	Code link
Auto-GAN: Self-Supervised Collaborative Learning for Medical Image Synthesis	AAAI	Generative	Link	NA
Self-Loop Uncertainty: A Novel Pseudo-Label for Semi-supervised Medical Image Segmentation	MICCAI	Predictive	Link	NA
Rubik’s Cube+: A self-supervised feature learning framework for 3D medical image analysis	MedIA	Predictive	Link	NA
Self-Supervised Learning Based on Spatial Awareness for Medical Image Analysis	IEEE Access	Predictive	Link	NA
Self-supervised Skull Reconstruction in Brain CT Images with Decompressive Craniectomy	MICCAI	Generative	Link	pytorch
Learning the retinal anatomy from scarce annotated data using self-supervised multimodal reconstruction	ASC	Generative	Link	NA
Multimodal Transfer Learning-based Approaches for Retinal Vascular Segmentation	ArXiv	Generative	Link	NA
Multi-modal self-supervised pre-training for joint optic disc and cup segmentation in eye fundus images	ICASSP	Generative	Link	NA
Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy	NMI	Generative	Link	tensorflow
Leveraging Self-supervised Denoising for Image Segmentation	ISBI	Generative	Link	tensorflow
Self-Supervised Pretraining with DICOM metadata in Ultrasound Imaging	PMLR	Generative	Link	NA
Revisiting rubik’s cube: Self-supervised learning with volume-wise transformation for 3d medical image segmentation	MICCAI	Generative	Link	NA
Semi-supervised breast cancer histology classification using deep multiple instance learning and contrast predictive coding	ArXiv	Contrastive	Link	NA
Embedding Task Knowledge into 3D Neural Networks via Self-supervised Learning	ArXiv	Contrastive	Link	NA
PGL: Prior-Guided Local Self-supervised Learning for 3D Medical Image Segmentation	ArXiv	Contrastive	Link	pytorch
Self-Supervised Feature Learning via Exploiting Multi-Modal Data for Retinal Disease Diagnosis	IEEE-TMI	Contrastive	Link	pytorch
MoCo Pretraining Improves Representation and Transferability of Chest X-ray Models	PMLR	Contrastive	Link	pytorch
Contrastive learning of global and local features for medical image segmentation with limited annotations	ArXiv	Contrastive	Link	tensorflow
Self-Supervised Representation Learning for Ultrasound Video	ISBI	Multiple-tasks/Multi-tasking	Link	NA
A Multi-Task Self-Supervised Learning Framework for Scopy Images	ISBI	Multiple-tasks/Multi-tasking	Link	NA
3D Self-Supervised Methods for Medical Imaging--update references	NIPS	Multiple-tasks/Multi-tasking	Link	tensorflow
Retinal Image Classification by Self-Supervised Fuzzy Clustering Network	IEEE Access	Multiple-tasks/Multi-tasking	Link	NA
Learning semantics-enriched representation via self-discovery, self-classification, and self-restoration	MICCAI	Multiple-tasks/Multi-tasking	Link	pytorch
SAR: Scale-Aware Restoration Learning for 3D Tumor Segmentation	ArXiv	Multiple-tasks/Multi-tasking	Link	NA

2019

Paper title	Journal/Conference	Category	Paper link	Code link
Self-Supervised Learning for Cardiac MR Image Segmentation by Anatomical Position Prediction	MICCAI	Predictive	Link	NA
Self-supervised Feature Learning for 3D Medical Images by Playing a Rubik’s Cube	MICCAI	Predictive	Link	NA
Self-supervised learning for medical image analysis using image context restoration	MedIA	Generative	Link	NA
Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis	MICCAI	Generative	Link	tensorflow & pytorch
Surrogate Supervision for Medical Image Analysis: Effective Deep Learning From Limited Quantities of Labeled Data	ISBI	Multiple-tasks/Multi-tasking	Link	NA

2018

Paper title	Journal/Conference	Category	Paper link	Code link
Exploiting the potential of unlabeled endoscopic video data with self-supervised learning	IJCARS	Generative	Link	NA
Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks	MICCAI	Predictive	Link	NA

2017

Paper title	Journal/Conference	Category	Paper link	Code link
Self-supervised Learning for Spinal MRIs	DLMIA	Contrastive	Link	NA
Self supervised deep representation learning for fine-grained body part recognition	ISBI	Predictive	Link	NA