# A continually expandable foundation model for brain MRI

arXiv: https://arxiv.org/abs/2608.08319 · HTML: https://mlsanity.com/paper/2608.08319/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 49 references that are in the map.
- First posted on arXiv 8 Aug 2026.

## Builds on (most cited first, 22 of 22)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (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)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Overcoming catastrophic forgetting in neural networks](https://mlsanity.com/paper/1612.00796/) (2016)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Overcoming catastrophic forgetting with hard attention to the task](https://mlsanity.com/paper/1801.01423/) (2018)
- [Linear Mode Connectivity in Multitask and Continual Learning](https://mlsanity.com/paper/2010.04495/) (2020)
- [Automated brain extraction of multi-sequence MRI using artificial neural networks](https://mlsanity.com/paper/1901.11341/) (2019)
- [What is Healthy? Generative Counterfactual Diffusion for Lesion Localization](https://mlsanity.com/paper/2207.12268/) (2022)
- [The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)](https://mlsanity.com/paper/2305.17033/) (2023)
- [The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI](https://mlsanity.com/paper/2306.00838/) (2023)
- [An OpenMind for 3D medical vision self-supervised learning](https://mlsanity.com/paper/2412.17041/) (2024)
- [Flow Matching for Medical Image Synthesis: Bridging the Gap Between Speed and Quality](https://mlsanity.com/paper/2503.00266/) (2025)
- [Towards Scalable Language-Image Pre-training for 3D Medical Imaging](https://mlsanity.com/paper/2505.21862/) (2025)
- [Counterfactual Image Synthesis for Discovery of Personalized Predictive Image Markers](https://mlsanity.com/paper/2208.02311/) (2022)
- [Building a General SimCLR Self-Supervised Foundation Model Across Neurological Diseases to Advance 3D Brain MRI Diagnoses](https://mlsanity.com/paper/2509.10620/) (2025)
- [Learning without Isolation: Pathway Protection for Continual Learning](https://mlsanity.com/paper/2505.18568/) (2025)
- [BrainDINO: A Brain MRI Foundation Model for Generalizable Clinical Representation Learning](https://mlsanity.com/paper/2604.27277/) (2026)
- [Predicting survival of glioblastoma from automatic whole-brain and tumor segmentation of MR images](https://mlsanity.com/paper/2109.12334/) (2021)

## Abstract (arXiv)

Brain magnetic resonance imaging (MRI) is central to neuroscience and clinical assessment, but models are commonly developed for individual diseases, populations or imaging protocols. Foundation models promise more general representations, yet they are usually pretrained once and can lose earlier capabilities when updated with new data. Here we show that Alcmaeon, a three-dimensional brain MRI foundation model pretrained without manual labels on more than 425,000 volumes and derived imaging maps, can be expanded sequentially across clinical domains. Alcmaeon combines volumetric encoding and latent diffusion generation with Graph-Blueprint Pruning (GBP), which protects network modules important to earlier domains while leaving the remaining capacity trainable. Across expansion from healthy ageing and neurodegeneration to developmental, psychiatric and tumour imaging, GBP showed less forgetting than sequential adaptation and elastic weight consolidation across voxel-level reconstruction measures, with its largest advantage after adaptation to tumour imaging. The blueprints provided an inspectable record of how model capacity was protected and reused. Representations from different model levels supported image synthesis, disease classification, survival modelling and postoperative prediction, although no single representation was optimal for every task. These findings provide a route towards brain MRI foundation models that can grow with emerging data while retaining earlier capabilities.