# Self-Supervised Learning for Organs At Risk and Tumor Segmentation with Uncertainty Quantification

arXiv: https://arxiv.org/abs/2305.02491 · HTML: https://mlsanity.com/paper/2305.02491/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 30 references that are in the map.
- First posted on arXiv 4 May 2023.

## Builds on (most cited first, 17 of 17)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [A Survey of Uncertainty in Deep Neural Networks](https://mlsanity.com/paper/2107.03342/) (2021)
- [Do Vision Transformers See Like Convolutional Neural Networks?](https://mlsanity.com/paper/2108.08810/) (2021)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Deeper Depth Prediction with Fully Convolutional Residual Networks](https://mlsanity.com/paper/1606.00373/) (2016)
- [UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation](https://mlsanity.com/paper/2004.08790/) (2020)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [Organ at Risk Segmentation for Head and Neck Cancer using Stratified Learning and Neural Architecture Search](https://mlsanity.com/paper/2004.08426/) (2020)
- [We Know Where We Don't Know: 3D Bayesian CNNs for Credible Geometric Uncertainty](https://mlsanity.com/paper/1910.10793/) (2019)

## Built on by (most cited first, 2 of 2)

- [Uncertainty-Guided Cross Attention Ensemble Mean Teacher for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/2412.15380/) (2024)
- [Uncertainty-Guided Coarse-to-Fine Tumor Segmentation with Anatomy-Aware Post-Processing](https://mlsanity.com/paper/2504.12215/) (2025)

## Abstract (arXiv)

In this study, our goal is to show the impact of self-supervised pre-training of transformers for organ at risk (OAR) and tumor segmentation as compared to costly fully-supervised learning. The proposed algorithm is called Monte Carlo Transformer based U-Net (MC-Swin-U). Unlike many other available models, our approach presents uncertainty quantification with Monte Carlo dropout strategy while generating its voxel-wise prediction. We test and validate the proposed model on both public and one private datasets and evaluate the gross tumor volume (GTV) as well as nearby risky organs' boundaries. We show that self-supervised pre-training approach improves the segmentation scores significantly while providing additional benefits for avoiding large-scale annotation costs.