# A Neuroimaging Simulation Framework for Developing and Evaluating Causal AI

arXiv: https://arxiv.org/abs/2606.28684 · HTML: https://mlsanity.com/paper/2606.28684/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 39 references that are in the map.
- First posted on arXiv 27 Jun 2026.

## Builds on (most cited first, 17 of 17)

- [DAGs with NO TEARS: Continuous Optimization for Structure Learning](https://mlsanity.com/paper/1803.01422/) (2018)
- [DAG-GNN: DAG Structure Learning with Graph Neural Networks](https://mlsanity.com/paper/1904.10098/) (2019)
- [SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining](https://mlsanity.com/paper/2107.09559/) (2021)
- [Causality matters in medical imaging](https://mlsanity.com/paper/1912.08142/) (2019)
- [CausalGAN: Learning Causal Implicit Generative Models with Adversarial Training](https://mlsanity.com/paper/1709.02023/) (2017)
- [DAGMA: Learning DAGs via M-matrices and a Log-Determinant Acyclicity Characterization](https://mlsanity.com/paper/2209.08037/) (2022)
- [Causal Machine Learning: A Survey and Open Problems](https://mlsanity.com/paper/2206.15475/) (2022)
- [CausalWorld: A Robotic Manipulation Benchmark for Causal Structure and Transfer Learning](https://mlsanity.com/paper/2010.04296/) (2020)
- [Causal Machine Learning for Healthcare and Precision Medicine](https://mlsanity.com/paper/2205.11402/) (2022)
- [A Survey on Causal Discovery: Theory and Practice](https://mlsanity.com/paper/2305.10032/) (2023)
- [gCastle: A Python Toolbox for Causal Discovery](https://mlsanity.com/paper/2111.15155/) (2021)
- [CausalVAE: Structured Causal Disentanglement in Variational Autoencoder](https://mlsanity.com/paper/2004.08697/) (2020)
- [pgmpy: A Python Toolkit for Bayesian Networks](https://mlsanity.com/paper/2304.08639/) (2023)
- [From Identifiable Causal Representations to Controllable Counterfactual Generation: A Survey on Causal Generative Modeling](https://mlsanity.com/paper/2310.11011/) (2023)
- [Towards objective and systematic evaluation of bias in artificial intelligence for medical imaging](https://mlsanity.com/paper/2311.02115/) (2023)
- [MACAW: A Causal Generative Model for Medical Imaging](https://mlsanity.com/paper/2412.02900/) (2024)
- [Evaluation of 3D Counterfactual Brain MRI Generation](https://mlsanity.com/paper/2508.02880/) (2025)

## Abstract (arXiv)

Causally linking disease-related factors to image-derived biomarkers provides a powerful pathway to understanding disease mechanisms. Despite growing interest in applying causal artificial intelligence (AI) approaches for this task, these methods still need to be adapted for complex medical images, and especially, neuroimaging. However, the lack of ground-truth data presents a barrier to development. To bridge this gap, we developed and tested a method for generating synthetic neuroimages, which adhere to a user-specified causal structure describing the non-image to image variable relationships, permitting the creation of ground-truth neuroimaging datasets. In the simulated T1-weighted magnetic resonance images, anatomical variability is modeled by sampling from a subspace estimated from real data and deforming a template image to create unique simulated subjects. Causal relationships are encoded via precise volumetric changes of any region-of-interest without unwanted global artifacts. We achieved relative volume errors of 0.3-2.66% for the targeted regions-of-interest and demonstrate their statistically significant causal relationships, while maintaining mean absolute errors for non-target brain regions between 0.034-0.397ml. An initial evaluation of causal discovery methods exposes their limited ability to suppress spurious connections, highlighting the need for image-appropriate methods. Our framework is the first to enable the generation of realistic synthetic 3D neuroimages with explicit causal control that can serve as the missing ground-truth data necessary for the objective benchmarking and development of causal AI methods.