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:

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

A list of recent self-supervised learning papers in medical imaging published since 2017.
Papers are collected from peer-reviewed journals and high reputed conferences. However, it might have recent papers on arXiv.
A meta-data is required along 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)
Applied Soft Computing (ASC)
Medical Image Analysis (MedIA)
International Journal of Computer Assisted Radiology and Surgery (IJCARS)
Nature Machine Intelligence (NMI)
Pattern Recognition
Expert Systems with Applications (ESA)
Neurocomputing
Proceedings of Machine Learning Research (PMLR)
Annual Conference on Neural Information Processing Systems (NIPS)
International Conference on Information Processing in Medical Imaging (IPMI)
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
International Conference on Medical Imaging with Deep Learning (MIDL)
IEEE International Symposium on Biomedical Imaging (ISBI)
Joint European Conference on Machine Learning and Knowledge Discovery in Databases (JECMLKDD)
IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
International Workshop on Deep Learning in Medical Image Analysis (DLMIA)

2021

Paper title	Journal/Conference	Category	Paper link	Code link
Multimodal Self-supervised Learning for Medical Image Analysis	IPMI	Predictive	Link	N/A
Self-supervised multimodal reconstruction pre-training for retinal computer-aided diagnosis	ESA	Generative	Link	N/A
MedAug: Contrastive learning leveraging patient metadata improves representations for chest X-ray interpretation	ArXiv	Contrastive	Link	N/A
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	N/A
Big Self-Supervised Models Advance Medical Image Classification	ArXiv	Contrastive	Link	N/A
Self-supervised Multi-task Representation Learning for Sequential Medical Images	JECMLKDD	Multiple-tasks/Multi-tasking	Link	N/A
Self-path: Self-supervision for classification of pathology images with limited annotations	TMI	Multiple-tasks/Multi-tasking	Link	N/A
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.	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	N/A

2020

Paper title	Journal/Conference	Category	Paper link	Code link
Self-Loop Uncertainty: A Novel Pseudo-Label for Semi-supervised Medical Image Segmentation	MICCAI	Predictive	Link	N/A
Rubik’s Cube+: A self-supervised feature learning framework for 3D medical image analysis	MedIA	Predictive	Link	N/A
Self-Supervised Learning Based on Spatial Awareness for Medical Image Analysis	IEEE Access	Predictive	Link	N/A
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	N/A
Multimodal Transfer Learning-based Approaches for Retinal Vascular Segmentation	ArXiv	Generative	Link	N/A
Multi-modal self-supervised pre-training for joint optic disc and cup segmentation in eye fundus images	ICASSP	Generative	Link	N/A
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	N/A
Revisiting rubik’s cube: Self-supervised learning with volume-wise transformation for 3d medical image segmentation	MICCAI	Generative	Link	N/A
Semi-supervised breast cancer histology classification using deep multiple instance learning and contrast predictive coding	ArXiv	Contrastive	Link	N/A
Embedding Task Knowledge into 3D Neural Networks via Self-supervised Learning	ArXiv	Contrastive	Link	N/A
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	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	N/A
A Multi-Task Self-Supervised Learning Framework for Scopy Images	ISBI	Multiple-tasks/Multi-tasking	Link	N/A
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	N/A
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	N/A

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	N/A
Self-supervised Feature Learning for 3D Medical Images by Playing a Rubik’s Cube	MICCAI	Predictive	Link	N/A
Self-supervised learning for medical image analysis using image context restoration	MedIA	Generative	Link	N/A
Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis	MICCAI	Generative	Link	tensorflow
Surrogate Supervision for Medical Image Analysis: Effective Deep Learning From Limited Quantities of Labeled Data	ISBI	Multiple-tasks/Multi-tasking	Link	N/A

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	N/A
Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks	MICCAI	Predictive	Link	N/A

2017

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

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