# Anatomically-guided masked autoencoder pre-training for aneurysm detection

arXiv: https://arxiv.org/abs/2502.21244 · HTML: https://mlsanity.com/paper/2502.21244/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 47 references that are in the map.
- First posted on arXiv 28 Feb 2025.

## Builds on (most cited first, 19 of 19)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [ViViT: A Video Vision Transformer](https://mlsanity.com/paper/2103.15691/) (2021)
- [VideoMAE: Masked Autoencoders are Data-Efficient Learners for Self-Supervised Video Pre-Training](https://mlsanity.com/paper/2203.12602/) (2022)
- [ImageNet-21K Pretraining for the Masses](https://mlsanity.com/paper/2104.10972/) (2021)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [Masked Autoencoders As Spatiotemporal Learners](https://mlsanity.com/paper/2205.09113/) (2022)
- [SatMAE: Pre-training Transformers for Temporal and Multi-Spectral Satellite Imagery](https://mlsanity.com/paper/2207.08051/) (2022)
- [Self Pre-training with Masked Autoencoders for Medical Image Classification and Segmentation](https://mlsanity.com/paper/2203.05573/) (2022)
- [nnDetection: A Self-configuring Method for Medical Object Detection](https://mlsanity.com/paper/2106.00817/) (2021)
- [The TopCoW Challenge -- Topology-Aware Circle of Willis Segmentation for CT and MR Angiography](https://mlsanity.com/paper/2312.17670/) (2023)
- [Advancing Volumetric Medical Image Segmentation via Global-Local Masked Autoencoder](https://mlsanity.com/paper/2306.08913/) (2023)
- [Self-Supervised Pre-Training with Contrastive and Masked Autoencoder Methods for Dealing with Small Datasets in Deep Learning for Medical Imaging](https://mlsanity.com/paper/2308.06534/) (2023)
- [Towards automated brain aneurysm detection in TOF-MRA: open data, weak labels, and anatomical knowledge](https://mlsanity.com/paper/2103.06168/) (2021)
- [On the Generalization Ability of Unsupervised Pretraining](https://mlsanity.com/paper/2403.06871/) (2024)
- [Dynamic-Computed Tomography Angiography for Cerebral Vessel Templates and Segmentation](https://mlsanity.com/paper/2502.09893/) (2025)

## Abstract (arXiv)

Intracranial aneurysms are a major cause of morbidity and mortality worldwide, and detecting them manually is a complex, time-consuming task. Albeit automated solutions are desirable, the limited availability of training data makes it difficult to develop such solutions using typical supervised learning frameworks. In this work, we propose a novel pre-training strategy using more widely available unannotated head CT scan data to pre-train a 3D Vision Transformer model prior to fine-tuning for the aneurysm detection task. Specifically, we modify masked auto-encoder (MAE) pre-training in the following ways: we use a factorized self-attention mechanism to make 3D attention computationally viable, we restrict the masked patches to areas near arteries to focus on areas where aneurysms are likely to occur, and we reconstruct not only CT scan intensity values but also artery distance maps, which describe the distance between each voxel and the closest artery, thereby enhancing the backbone's learned representations. Compared with SOTA aneurysm detection models, our approach gains +4-8% absolute Sensitivity at a false positive rate of 0.5. Code and weights will be released.