mlsanityData to 7 Oct 2026

Equitable modelling of brain imaging by counterfactual augmentation with morphologically constrained 3D deep generative models

arXiv 2111.14923 ↗First posted 29 Nov 2021cs.CV cs.LGcited by 36

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Abstract (arXiv)

We describe Countersynth, a conditional generative model of diffeomorphic deformations that induce label-driven, biologically plausible changes in volumetric brain images. The model is intended to synthesise counterfactual training data augmentations for downstream discriminative modelling tasks where fidelity is limited by data imbalance, distributional instability, confounding, or underspecification, and exhibits inequitable performance across distinct subpopulations. Focusing on demographic attributes, we evaluate the quality of synthesized counterfactuals with voxel-based morphometry, classification and regression of the conditioning attributes, and the Fr'echet inception distance. Examining downstream discriminative performance in the context of engineered demographic imbalance and confounding, we use UK Biobank magnetic resonance imaging data to benchmark CounterSynth augmentation against current solutions to these problems. We achieve state-of-the-art improvements, both in overall fidelity and equity. The source code for CounterSynth is available online.

Key facts. Cited by 36 papers in the map (data through 7 Oct 2026). Builds on 46 of its 117 references that are in the map. First posted on arXiv 29 Nov 2021.

Builds on

46 of 117 references.

References · 46

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Citing papers per year: 2022: 3; 2023: 6; 2024: 7; 2025: 13; 2026: 7.

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  1. 2023Deep Learning Approaches for Data Augmentation in Medical Imaging: A Reviewcited by 48
  2. 2023Fast Diffusion-Based Counterfactuals for Shortcut Removal and Generationcited by 41
  3. 2024Enhancing Spatiotemporal Disease Progression Models via Latent Diffusion and Prior Knowledgecited by 35
  4. 2022Addressing Fairness Issues in Deep Learning-Based Medical Image Analysis: A Systematic Reviewcited by 27
  5. 2024TADM: Temporally-Aware Diffusion Model for Neurodegenerative Progression on Brain MRIcited by 18
  6. 2025Brain Latent Progression: Individual-based Spatiotemporal Disease Progression on 3D Brain MRIs via Latent Diffusioncited by 17
  7. 2024A Practical Guide to Sample-based Statistical Distances for Evaluating Generative Models in Sciencecited by 14
  8. 2024Latent Drifting in Diffusion Models for Counterfactual Medical Image Synthesiscited by 13
  9. 2025CF-Seg: Counterfactuals meet Segmentationcited by 10
  10. 2025Synthesizing Individualized Aging Brains in Health and Disease with Generative Models and Parallel Transportcited by 9
  11. 2023Multiscale Metamorphic VAE for 3D Brain MRI Synthesiscited by 8
  12. 2025Learning Patient-Specific Disease Dynamics with Latent Flow Matching for Longitudinal Imaging Generationcited by 8
24 more
  1. 2026FlowLet: Conditional 3D Brain MRI Synthesis using Wavelet Flow Matchingcited by 5
  2. 20223D Brain and Heart Volume Generative Models: A Surveycited by 4
  3. 2023A Unified Framework for Generative Data Augmentation: A Comprehensive Surveycited by 4
  4. 2024Synthetic Data for Robust Stroke Segmentationcited by 4
  5. 2024Deep Generative Classification of Blood Cell Morphologycited by 4
  6. 2022Representational Ethical Model Calibrationcited by 3
  7. 2024IdenBAT: Disentangled Representation Learning for Identity-Preserved Brain Age Transformationcited by 3
  8. 2025Temporally-Aware Diffusion Model for Brain Progression Modelling with Bidirectional Temporal Regularisationcited by 3
  9. 2025Neural Autoregressive Modeling of Brain Agingcited by 2
  10. 2026Anatomically Guided Latent Diffusion for Brain MRI Progression Modelingcited by 2
  11. 2023Deep Variational Lesion-Deficit Mappingcited by 1
  12. 2023A Quantitatively Interpretable Model for Alzheimer's Disease Prediction Using Deep Counterfactualscited by 1
  13. 2025MambaControl: Anatomy Graph-Enhanced Mamba ControlNet with Fourier Refinement for Diffusion-Based Disease Trajectory Predictioncited by 1
  14. 2025Integrating Anatomical Priors into a Causal Diffusion Modelcited by 1
  15. 2025Cycle Diffusion Model for Counterfactual Image Generationcited by 1
  16. 2025Forecasting Future Anatomies: Longitudinal Brain Mri-to-Mri Predictioncited by 1
  17. 2026Cortex-Grounded Diffusion Models for Brain Image Generationcited by 1
  18. 2025Generating Novel Brain Morphology by Deforming Learned Templatescited by 0
  19. 2025MRExtrap: Longitudinal Aging of Brain MRIs using Linear Modeling in Latent Spacecited by 0
  20. 2025AD-DAE: Alzheimer's Disease Progression Modeling with Unpaired Longitudinal MRI using Diffusion Auto-Encoderscited by 0
  21. 2026CLIMB: Controllable Longitudinal Brain Image Generation using Mamba-based Latent Diffusion Model and Gaussian-aligned Autoencodercited by 0
  22. 2026SMART: A Flexible, Interpretable, and Scalable Spatio-temporal Brain Atlas from High-Resolution Imaging Datacited by 0
  23. 2026Progression as Latent Drift: Generative Forecasting of Slow-Evolving Pathologiescited by 0
  24. 2026MedDiME: Efficient Latent Diffusion with Adaptive Masking for Medical Counterfactual Generationcited by 0