# Promptable Counterfactual Diffusion Model for Unified Brain Tumor Segmentation and Generation with MRIs

arXiv: https://arxiv.org/abs/2407.12678 · HTML: https://mlsanity.com/paper/2407.12678/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 11 of its 17 references that are in the map.
- First posted on arXiv 17 Jul 2024.

## Placed in

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

## Builds on (most cited first, 11 of 11)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [FiLM: Visual Reasoning with a General Conditioning Layer](https://mlsanity.com/paper/1709.07871/) (2017)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (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)
- [What is Healthy? Generative Counterfactual Diffusion for Lesion Localization](https://mlsanity.com/paper/2207.12268/) (2022)

## Built on by (most cited first, 4 of 4)

- [Diffusion Counterfactual Generation with Semantic Abduction](https://mlsanity.com/paper/2506.07883/) (2025)
- [Direct Distributional Optimization for Provable Alignment of Diffusion Models](https://mlsanity.com/paper/2502.02954/) (2025)
- [DMCIE: Diffusion Model with Concatenation of Inputs and Errors to Improve the Accuracy of the Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2507.00983/) (2025)
- [ReCoSeg++:Extended Residual-Guided Cross-Modal Diffusion for Brain Tumor Segmentation](https://mlsanity.com/paper/2508.01058/) (2025)

## Abstract (arXiv)

Brain tumor analysis in Magnetic Resonance Imaging (MRI) is crucial for accurate diagnosis and treatment planning. However, the task remains challenging due to the complexity and variability of tumor appearances, as well as the scarcity of labeled data. Traditional approaches often address tumor segmentation and image generation separately, limiting their effectiveness in capturing the intricate relationships between healthy and pathological tissue structures. We introduce a novel promptable counterfactual diffusion model as a unified solution for brain tumor segmentation and generation in MRI. The key innovation lies in our mask-level prompting mechanism at the sampling stage, which enables guided generation and manipulation of specific healthy or unhealthy regions in MRI images. Specifically, the model's architecture allows for bidirectional inference, which can segment tumors in existing images and generate realistic tumor structures in healthy brain scans. Furthermore, we present a two-step approach for tumor generation and position transfer, showcasing the model's versatility in synthesizing realistic tumor structures. Experiments on the BRATS2021 dataset demonstrate that our method outperforms traditional counterfactual diffusion approaches, achieving a mean IoU of 0.653 and mean Dice score of 0.785 for tumor segmentation, outperforming the 0.344 and 0.475 of conventional counterfactual diffusion model. Our work contributes to improving brain tumor detection and segmentation accuracy, with potential implications for data augmentation and clinical decision support in neuro-oncology. The code is available at https://github.com/arcadelab/counterfactual_diffusion.