# Diffusion Model in Latent Space for Medical Image Segmentation Task

arXiv: https://arxiv.org/abs/2512.01292 · HTML: https://mlsanity.com/paper/2512.01292/

## 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 30 of its 46 references that are in the map.
- First posted on arXiv 1 Dec 2025.

## Placed in

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

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

- [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)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [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)
- [Align your Latents: High-Resolution Video Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2304.08818/) (2023)
- [Generating Diverse High-Fidelity Images with VQ-VAE-2](https://mlsanity.com/paper/1906.00446/) (2019)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [A Survey on Deep Learning in Medical Image Analysis](https://mlsanity.com/paper/1702.05747/) (2017)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Pseudo Numerical Methods for Diffusion Models on Manifolds](https://mlsanity.com/paper/2202.09778/) (2022)
- [Skin Lesion Analysis Toward Melanoma Detection 2018: A Challenge Hosted by the International Skin Imaging Collaboration (ISIC)](https://mlsanity.com/paper/1902.03368/) (2019)
- [Kvasir-SEG: A Segmented Polyp Dataset](https://mlsanity.com/paper/1911.07069/) (2019)
- [SegDiff: Image Segmentation with Diffusion Probabilistic Models](https://mlsanity.com/paper/2112.00390/) (2021)
- [Brain Imaging Generation with Latent Diffusion Models](https://mlsanity.com/paper/2209.07162/) (2022)
- [ResUNet-a: a deep learning framework for semantic segmentation of remotely sensed data](https://mlsanity.com/paper/1904.00592/) (2019)
- [Diffusion Models for Implicit Image Segmentation Ensembles](https://mlsanity.com/paper/2112.03145/) (2021)
- [MedSegDiff: Medical Image Segmentation with Diffusion Probabilistic Model](https://mlsanity.com/paper/2211.00611/) (2022)
- [MedSegDiff-V2: Diffusion based Medical Image Segmentation with Transformer](https://mlsanity.com/paper/2301.11798/) (2023)
- [Generating Diverse Structure for Image Inpainting With Hierarchical VQ-VAE](https://mlsanity.com/paper/2103.10022/) (2021)
- [HyperSeg: Patch-wise Hypernetwork for Real-time Semantic Segmentation](https://mlsanity.com/paper/2012.11582/) (2020)
- [Latent Diffusion for Medical Image Segmentation: End to end learning for fast sampling and accuracy](https://mlsanity.com/paper/2407.12952/) (2024)
- [Aleatoric Uncertainty Medical Image Segmentation Estimation via Flow Matching](https://mlsanity.com/paper/2507.22418/) (2025)

## Abstract (arXiv)

Medical image segmentation is crucial for clinical diagnosis and treatment planning. Traditional methods typically produce a single segmentation mask, failing to capture inherent uncertainty. Recent generative models enable the creation of multiple plausible masks per image, mimicking the collaborative interpretation of several clinicians. However, these approaches remain computationally heavy. We propose MedSegLatDiff, a diffusion based framework that combines a variational autoencoder (VAE) with a latent diffusion model for efficient medical image segmentation. The VAE compresses the input into a low dimensional latent space, reducing noise and accelerating training, while the diffusion process operates directly in this compact representation. We further replace the conventional MSE loss with weighted cross entropy in the VAE mask reconstruction path to better preserve tiny structures such as small nodules. MedSegLatDiff is evaluated on ISIC-2018 (skin lesions), CVC-Clinic (polyps), and LIDC-IDRI (lung nodules). It achieves state of the art or highly competitive Dice and IoU scores while simultaneously generating diverse segmentation hypotheses and confidence maps. This provides enhanced interpretability and reliability compared to deterministic baselines, making the model particularly suitable for clinical deployment.