# DreaMR: Diffusion-driven Counterfactual Explanation for Functional MRI

arXiv: https://arxiv.org/abs/2307.09547 · HTML: https://mlsanity.com/paper/2307.09547/

## Key facts

- Cited by 14 papers in the map (data through 14 Oct 2026).
- Builds on 44 of its 99 references that are in the map.
- First posted on arXiv 18 Jul 2023.

## Builds on (most cited first, 30 of 44)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Visualizing and Understanding Convolutional Networks](https://mlsanity.com/paper/1311.2901/) (2013)
- [Consistency Models](https://mlsanity.com/paper/2303.01469/) (2023)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [DiffWave: A Versatile Diffusion Model for Audio Synthesis](https://mlsanity.com/paper/2009.09761/) (2020)
- [eDiff-I: Text-to-Image Diffusion Models with an Ensemble of Expert Denoisers](https://mlsanity.com/paper/2211.01324/) (2022)
- [Improving Diffusion Models for Inverse Problems using Manifold Constraints](https://mlsanity.com/paper/2206.00941/) (2022)
- [Diffusion Models for Medical Anomaly Detection](https://mlsanity.com/paper/2203.04306/) (2022)
- [Deep Structural Causal Models for Tractable Counterfactual Inference](https://mlsanity.com/paper/2006.06485/) (2020)
- [Unsupervised Medical Image Translation with Adversarial Diffusion Models](https://mlsanity.com/paper/2207.08208/) (2022)
- [ResViT: Residual vision transformers for multi-modal medical image synthesis](https://mlsanity.com/paper/2106.16031/) (2021)
- [Explainable artificial intelligence (XAI) in deep learning-based medical image analysis](https://mlsanity.com/paper/2107.10912/) (2021)
- [Multi-site fMRI Analysis Using Privacy-preserving Federated Learning and Domain Adaptation: ABIDE Results](https://mlsanity.com/paper/2001.05647/) (2020)
- [Adaptive Diffusion Priors for Accelerated MRI Reconstruction](https://mlsanity.com/paper/2207.05876/) (2022)
- [Disease Prediction using Graph Convolutional Networks: Application to Autism Spectrum Disorder and Alzheimer's Disease](https://mlsanity.com/paper/1806.01738/) (2018)
- [Fast Unsupervised Brain Anomaly Detection and Segmentation with Diffusion Models](https://mlsanity.com/paper/2206.03461/) (2022)
- [Diffusion Visual Counterfactual Explanations](https://mlsanity.com/paper/2210.11841/) (2022)
- [Learning Dynamic Graph Representation of Brain Connectome with Spatio-Temporal Attention](https://mlsanity.com/paper/2105.13495/) (2021)
- [Diffusion Causal Models for Counterfactual Estimation](https://mlsanity.com/paper/2202.10166/) (2022)
- [Diffusion Models for Counterfactual Explanations](https://mlsanity.com/paper/2203.15636/) (2022)
- [Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers](https://mlsanity.com/paper/2105.08059/) (2021)
- [Beyond Trivial Counterfactual Explanations with Diverse Valuable Explanations](https://mlsanity.com/paper/2103.10226/) (2021)
- [What is Healthy? Generative Counterfactual Diffusion for Lesion Localization](https://mlsanity.com/paper/2207.12268/) (2022)
- [Mask, Stitch, and Re-Sample: Enhancing Robustness and Generalizability in Anomaly Detection through Automatic Diffusion Models](https://mlsanity.com/paper/2305.19643/) (2023)
- [CTformer: Convolution-free Token2Token Dilated Vision Transformer for Low-dose CT Denoising](https://mlsanity.com/paper/2202.13517/) (2022)
- [A Comprehensive Survey on Knowledge Distillation of Diffusion Models](https://mlsanity.com/paper/2304.04262/) (2023)

## Built on by (most cited first, 14 of 14)

- [BiomedJourney: Counterfactual Biomedical Image Generation by Instruction-Learning from Multimodal Patient Journeys](https://mlsanity.com/paper/2310.10765/) (2023)
- [Self-Consistent Recursive Diffusion Bridge for Medical Image Translation](https://mlsanity.com/paper/2405.06789/) (2024)
- [I2I-Mamba: Multi-modal medical image synthesis via selective state space modeling](https://mlsanity.com/paper/2405.14022/) (2024)
- [DiffBoost: Enhancing Medical Image Segmentation via Text-Guided Diffusion Model](https://mlsanity.com/paper/2310.12868/) (2023)
- [Learning Fourier-Constrained Diffusion Bridges for MRI Reconstruction](https://mlsanity.com/paper/2308.01096/) (2023)
- [Counterfactual Explanations for Medical Image Classification and Regression using Diffusion Autoencoder](https://mlsanity.com/paper/2408.01571/) (2024)
- [Conditional Diffusion Models are Medical Image Classifiers that Provide Explainability and Uncertainty for Free](https://mlsanity.com/paper/2502.03687/) (2025)
- [Diff-Def: Diffusion-Generated Deformation Fields for Conditional Atlases](https://mlsanity.com/paper/2403.16776/) (2024)
- [Zero-Shot Medical Phrase Grounding with Off-the-shelf Diffusion Models](https://mlsanity.com/paper/2404.12920/) (2024)
- [Back-in-Time Diffusion: Unsupervised Detection of Medical Deepfakes](https://mlsanity.com/paper/2407.15169/) (2024)
- [Learning from the few: Fine-grained approach to pediatric wrist pathology recognition on a limited dataset](https://mlsanity.com/paper/2408.13542/) (2024)
- [An Interpretable Local Editing Model for Counterfactual Medical Image Generation](https://mlsanity.com/paper/2603.00423/) (2026)
- [Multi-Task Adversarial Variational Autoencoder for Estimating Biological Brain Age with Multimodal Neuroimaging](https://mlsanity.com/paper/2411.10100/) (2024)
- [Synthesizing Images on Perceptual Boundaries of ANNs for Uncovering Human Perceptual Variability on Facial Expressions](https://mlsanity.com/paper/2507.14549/) (2025)

## Abstract (arXiv)

Deep learning analyses have offered sensitivity leaps in detection of cognitive states from functional MRI (fMRI) measurements across the brain. Yet, as deep models perform hierarchical nonlinear transformations on their input, interpreting the association between brain responses and cognitive states is challenging. Among common explanation approaches for deep fMRI classifiers, attribution methods show poor specificity and perturbation methods show limited plausibility. While counterfactual generation promises to address these limitations, previous methods use variational or adversarial priors that yield suboptimal sample fidelity. Here, we introduce the first diffusion-driven counterfactual method, DreaMR, to enable fMRI interpretation with high specificity, plausibility and fidelity. DreaMR performs diffusion-based resampling of an input fMRI sample to alter the decision of a downstream classifier, and then computes the minimal difference between the original and counterfactual samples for explanation. Unlike conventional diffusion methods, DreaMR leverages a novel fractional multi-phase-distilled diffusion prior to improve sampling efficiency without compromising fidelity, and it employs a transformer architecture to account for long-range spatiotemporal context in fMRI scans. Comprehensive experiments on neuroimaging datasets demonstrate the superior specificity, fidelity and efficiency of DreaMR in sample generation over state-of-the-art counterfactual methods for fMRI interpretation.