# Unsupervised Anatomical Feature Learning via Diffusion Models: Enhanced Medical Image Segmentation with Denoising Diffusion Probabilistic Models

arXiv: https://arxiv.org/abs/2608.25693 · HTML: https://mlsanity.com/paper/2608.25693/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 35 of its 62 references that are in the map.
- First posted on arXiv 26 Aug 2026.

## Placed in

- Diffusion models / [Medical imaging and segmentation](https://mlsanity.com/diffusion/medical-imaging-and-segmentation/)

## Builds on (most cited first, 30 of 35)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Improved Baselines with Momentum Contrastive Learning](https://mlsanity.com/paper/2003.04297/) (2020)
- [A Survey on Deep Learning in Medical Image Analysis](https://mlsanity.com/paper/1702.05747/) (2017)
- [Diffusion Models in Vision: A Survey](https://mlsanity.com/paper/2209.04747/) (2022)
- [Self-supervised Visual Feature Learning with Deep Neural Networks: A Survey](https://mlsanity.com/paper/1902.06162/) (2019)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [Label-Efficient Semantic Segmentation with Diffusion Models](https://mlsanity.com/paper/2112.03126/) (2021)
- [Score-based diffusion models for accelerated MRI](https://mlsanity.com/paper/2110.05243/) (2021)
- [SegDiff: Image Segmentation with Diffusion Probabilistic Models](https://mlsanity.com/paper/2112.00390/) (2021)
- [Diffusion Models for Medical Image Analysis: A Comprehensive Survey](https://mlsanity.com/paper/2211.07804/) (2022)
- [Diffusion Model-Based Image Editing: A Survey](https://mlsanity.com/paper/2402.17525/) (2024)
- [A Survey on Self-supervised Learning: Algorithms, Applications, and Future Trends](https://mlsanity.com/paper/2301.05712/) (2023)
- [MultiResUNet : Rethinking the U-Net Architecture for Multimodal Biomedical Image Segmentation](https://mlsanity.com/paper/1902.04049/) (2019)
- [Medical Image Segmentation Review: The success of U-Net](https://mlsanity.com/paper/2211.14830/) (2022)
- [MedSegDiff: Medical Image Segmentation with Diffusion Probabilistic Model](https://mlsanity.com/paper/2211.00611/) (2022)
- [U-Net and its variants for medical image segmentation: theory and applications](https://mlsanity.com/paper/2011.01118/) (2020)
- [DS-TransUNet:Dual Swin Transformer U-Net for Medical Image Segmentation](https://mlsanity.com/paper/2106.06716/) (2021)
- [CA-Net: Comprehensive Attention Convolutional Neural Networks for Explainable Medical Image Segmentation](https://mlsanity.com/paper/2009.10549/) (2020)
- [Diffusion Probabilistic Models beat GANs on Medical Images](https://mlsanity.com/paper/2212.07501/) (2022)
- [PET image denoising based on denoising diffusion probabilistic models](https://mlsanity.com/paper/2209.06167/) (2022)
- [AbdomenAtlas-8K: Annotating 8,000 CT Volumes for Multi-Organ Segmentation in Three Weeks](https://mlsanity.com/paper/2305.09666/) (2023)
- [Residual Attention U-Net for Automated Multi-Class Segmentation of COVID-19 Chest CT Images](https://mlsanity.com/paper/2004.05645/) (2020)

## Abstract (arXiv)

Acquiring pixel-level annotations for medical image segmentation is a severe bottleneck. Traditional U-Net architectures, while effective, learn local texture patterns and lack awareness of global anatomical structures, leading to boundary delineation failures in low-data regimes. This research paper proposes utilizing unsupervised Denoising Diffusion Probabilistic Models (DDPMs) to extract anatomical features. We train a DDPM on 21 unlabeled abdominal CT scans to learn structural representations, transferring the encoder weights to a downstream segmentation task evaluated on the BTCV multi-organ dataset. Diffusion pretraining significantly improved liver segmentation: Dice increased from 0.75±0.36 to 0.93±0.16 (p < 5.33×10-26, 0.529 Cohen's d), Average Surface Distance (ASD) decreased by 66%, and 95th-percentile Hausdorff Distance (HD95) reduced by 45%. For kidney segmentation, Dice improved from 0.90±0.19 to 0.95±0.10 (p < 4.01×10-11). Multi-organ pooled performance showed a 68% variance reduction and a 74% improvement in boundary precision (Dice 0.95±0.07). Crucially, frozen encoder models retained > 80% of fine-tuned performance without exposure to segmentation labels, proving the existence of learned anatomical priors. In low-data scenarios, diffusion-pretrained models maintained robust performance with only 50% (Dice: 0.92 liver, 0.94 kidney), 25%, and even 10% (Dice: 0.89 liver, 0.71 kidney) of labeled data. Using unlabeled images for diffusion-based pretraining successfully embeds robust anatomical features prior to human supervision, transforming U-Nets into anatomy-aware systems.