# Self Pre-training with Topology- and Spatiality-aware Masked Autoencoders for 3D Medical Image Segmentation

arXiv: https://arxiv.org/abs/2406.10519 · HTML: https://mlsanity.com/paper/2406.10519/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 46 of its 73 references that are in the map.
- First posted on arXiv 15 Jun 2024.

## Builds on (most cited first, 30 of 46)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [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)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Photo-Realistic Single Image Super-Resolution Using a Generative Adversarial Network](https://mlsanity.com/paper/1609.04802/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Context Encoders: Feature Learning by Inpainting](https://mlsanity.com/paper/1604.07379/) (2016)
- [Unsupervised Learning of Visual Representations by Solving Jigsaw Puzzles](https://mlsanity.com/paper/1603.09246/) (2016)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)
- [VideoMAE: Masked Autoencoders are Data-Efficient Learners for Self-Supervised Video Pre-Training](https://mlsanity.com/paper/2203.12602/) (2022)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Deep Clustering for Unsupervised Learning of Visual Features](https://mlsanity.com/paper/1807.05520/) (2018)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [VLMo: Unified Vision-Language Pre-Training with Mixture-of-Modality-Experts](https://mlsanity.com/paper/2111.02358/) (2021)
- [UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation](https://mlsanity.com/paper/2004.08790/) (2020)
- [Medical Transformer: Gated Axial-Attention for Medical Image Segmentation](https://mlsanity.com/paper/2102.10662/) (2021)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [Split-Brain Autoencoders: Unsupervised Learning by Cross-Channel Prediction](https://mlsanity.com/paper/1611.09842/) (2016)
- [Topology-Preserving Deep Image Segmentation](https://mlsanity.com/paper/1906.05404/) (2019)
- [Colorization as a Proxy Task for Visual Understanding](https://mlsanity.com/paper/1703.04044/) (2017)

## Built on by (most cited first, 6 of 6)

- [Revisiting MAE pre-training for 3D medical image segmentation](https://mlsanity.com/paper/2410.23132/) (2024)
- [TopoCL: Topological Contrastive Learning for Medical Imaging](https://mlsanity.com/paper/2603.14647/) (2026)
- [Integrating Multi-scale and Multi-filtration Topological Features for Medical Image Classification](https://mlsanity.com/paper/2512.07190/) (2025)
- [Learning with Geometric Priors in U-Net Variants for Polyp Segmentation](https://mlsanity.com/paper/2601.17331/) (2026)
- [SPAR: Self-supervised Placement-Aware Representation Learning for Distributed Sensing](https://mlsanity.com/paper/2505.16936/) (2025)
- [Patch-MoE Mamba: A Patch-Ordered Mixture-of-Experts State Space Architecture for Medical Image Segmentation](https://mlsanity.com/paper/2605.17719/) (2026)

## Abstract (arXiv)

Masked Autoencoders (MAEs) have been shown to be effective in pre-training Vision Transformers (ViTs) for natural and medical image analysis problems. By reconstructing missing pixel/voxel information in visible patches, a ViT encoder can aggregate contextual information for downstream tasks. But, existing MAE pre-training methods, which were specifically developed with the ViT architecture, lack the ability to capture geometric shape and spatial information, which is critical for medical image segmentation tasks. In this paper, we propose a novel extension of known MAEs for self pre-training (i.e., models pre-trained on the same target dataset) for 3D medical image segmentation. (1) We propose a new topological loss to preserve geometric shape information by computing topological signatures of both the input and reconstructed volumes, learning geometric shape information. (2) We introduce a pre-text task that predicts the positions of the centers and eight corners of 3D crops, enabling the MAE to aggregate spatial information. (3) We extend the MAE pre-training strategy to a hybrid state-of-the-art (SOTA) medical image segmentation architecture and co-pretrain it alongside the ViT. (4) We develop a fine-tuned model for downstream segmentation tasks by complementing the pre-trained ViT encoder with our pre-trained SOTA model. Extensive experiments on five public 3D segmentation datasets show the effectiveness of our new approach.