# Attentive Symmetric Autoencoder for Brain MRI Segmentation

arXiv: https://arxiv.org/abs/2209.08887 · HTML: https://mlsanity.com/paper/2209.08887/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 31 references that are in the map.
- First posted on arXiv 19 Sep 2022.

## Builds on (most cited first, 18 of 18)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour](https://mlsanity.com/paper/1706.02677/) (2017)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Masked Feature Prediction for Self-Supervised Visual Pre-Training](https://mlsanity.com/paper/2112.09133/) (2021)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [3D Self-Supervised Methods for Medical Imaging](https://mlsanity.com/paper/2006.03829/) (2020)
- [Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge](https://mlsanity.com/paper/1904.00682/) (2019)
- [Multimodal Self-Supervised Learning for Medical Image Analysis](https://mlsanity.com/paper/1912.05396/) (2019)
- [Revisiting Rubik's Cube: Self-supervised Learning with Volume-wise Transformation for 3D Medical Image Segmentation](https://mlsanity.com/paper/2007.08826/) (2020)
- [Fully Convolutional Network Ensembles for White Matter Hyperintensities Segmentation in MR Images](https://mlsanity.com/paper/1802.05203/) (2018)

## Built on by (most cited first, 8 of 8)

- [nnMamba: 3D Biomedical Image Segmentation, Classification and Landmark Detection with State Space Model](https://mlsanity.com/paper/2402.03526/) (2024)
- [FreMIM: Fourier Transform Meets Masked Image Modeling for Medical Image Segmentation](https://mlsanity.com/paper/2304.10864/) (2023)
- [ASC: Appearance and Structure Consistency for Unsupervised Domain Adaptation in Fetal Brain MRI Segmentation](https://mlsanity.com/paper/2310.14172/) (2023)
- [Self-Supervised Alignment Learning for Medical Image Segmentation](https://mlsanity.com/paper/2406.15699/) (2024)
- [Visual-Attribute Prompt Learning for Progressive Mild Cognitive Impairment Prediction](https://mlsanity.com/paper/2310.14158/) (2023)
- [Structure-aware Semantic Discrepancy and Consistency for 3D Medical Image Self-supervised Learning](https://mlsanity.com/paper/2507.02581/) (2025)
- [A Survey of the Impact of Self-Supervised Pretraining for Diagnostic Tasks with Radiological Images](https://mlsanity.com/paper/2309.02555/) (2023)
- [Leveraging Semantic Asymmetry for Precise Gross Tumor Volume Segmentation of Nasopharyngeal Carcinoma in Planning CT](https://mlsanity.com/paper/2411.18290/) (2024)

## Abstract (arXiv)

Self-supervised learning methods based on image patch reconstruction have witnessed great success in training auto-encoders, whose pre-trained weights can be transferred to fine-tune other downstream tasks of image understanding. However, existing methods seldom study the various importance of reconstructed patches and the symmetry of anatomical structures, when they are applied to 3D medical images. In this paper we propose a novel Attentive Symmetric Auto-encoder (ASA) based on Vision Transformer (ViT) for 3D brain MRI segmentation tasks. We conjecture that forcing the auto-encoder to recover informative image regions can harvest more discriminative representations, than to recover smooth image patches. Then we adopt a gradient based metric to estimate the importance of each image patch. In the pre-training stage, the proposed auto-encoder pays more attention to reconstruct the informative patches according to the gradient metrics. Moreover, we resort to the prior of brain structures and develop a Symmetric Position Encoding (SPE) method to better exploit the correlations between long-range but spatially symmetric regions to obtain effective features. Experimental results show that our proposed attentive symmetric auto-encoder outperforms the state-of-the-art self-supervised learning methods and medical image segmentation models on three brain MRI segmentation benchmarks.