# Medical Transformer: Gated Axial-Attention for Medical Image Segmentation

arXiv: https://arxiv.org/abs/2102.10662 · HTML: https://mlsanity.com/paper/2102.10662/

## Key facts

- Cited by 320 papers in the map (data through 14 Oct 2026).
- Builds on 33 of its 47 references that are in the map.
- First posted on arXiv 21 Feb 2021.

## Builds on (most cited first, 30 of 33)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [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)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [Pyramid Scene Parsing Network](https://mlsanity.com/paper/1612.01105/) (2016)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (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)
- [SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation](https://mlsanity.com/paper/1511.00561/) (2015)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)
- [Self-Attention with Relative Position Representations](https://mlsanity.com/paper/1803.02155/) (2018)
- [CCNet: Criss-Cross Attention for Semantic Segmentation](https://mlsanity.com/paper/1811.11721/) (2018)
- [Semantic Image Segmentation with Deep Convolutional Nets and Fully Connected CRFs](https://mlsanity.com/paper/1412.7062/) (2014)
- [Axial Attention in Multidimensional Transformers](https://mlsanity.com/paper/1912.12180/) (2019)
- [MaX-DeepLab: End-to-End Panoptic Segmentation with Mask Transformers](https://mlsanity.com/paper/2012.00759/) (2020)
- [UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation](https://mlsanity.com/paper/2004.08790/) (2020)
- [Axial-DeepLab: Stand-Alone Axial-Attention for Panoptic Segmentation](https://mlsanity.com/paper/2003.07853/) (2020)
- [TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation](https://mlsanity.com/paper/2102.08005/) (2021)
- [Scaling Neural Machine Translation](https://mlsanity.com/paper/1806.00187/) (2018)
- [Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest](https://mlsanity.com/paper/1603.00275/) (2016)
- [Hierarchical Transformers for Long Document Classification](https://mlsanity.com/paper/1910.10781/) (2019)
- [Multi-scale self-guided attention for medical image segmentation](https://mlsanity.com/paper/1906.02849/) (2019)
- [KiU-Net: Towards Accurate Segmentation of Biomedical Images using Over-complete Representations](https://mlsanity.com/paper/2006.04878/) (2020)
- [Y-Net: Joint Segmentation and Classification for Diagnosis of Breast Biopsy Images](https://mlsanity.com/paper/1806.01313/) (2018)

## Built on by (most cited first, 30 of 320)

- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Multiscale Vision Transformers](https://mlsanity.com/paper/2104.11227/) (2021)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [SegDiff: Image Segmentation with Diffusion Probabilistic Models](https://mlsanity.com/paper/2112.00390/) (2021)
- [Transformers in Medical Imaging: A Survey](https://mlsanity.com/paper/2201.09873/) (2022)
- [TransWeather: Transformer-based Restoration of Images Degraded by Adverse Weather Conditions](https://mlsanity.com/paper/2111.14813/) (2021)
- [UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer](https://mlsanity.com/paper/2109.04335/) (2021)
- [Medical Image Segmentation Review: The success of U-Net](https://mlsanity.com/paper/2211.14830/) (2022)
- [UNeXt: MLP-based Rapid Medical Image Segmentation Network](https://mlsanity.com/paper/2203.04967/) (2022)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [A Unified Survey on Anomaly, Novelty, Open-Set, and Out-of-Distribution Detection: Solutions and Future Challenges](https://mlsanity.com/paper/2110.14051/) (2021)
- [Rendezvous: Attention Mechanisms for the Recognition of Surgical Action Triplets in Endoscopic Videos](https://mlsanity.com/paper/2109.03223/) (2021)
- [DS-TransUNet:Dual Swin Transformer U-Net for Medical Image Segmentation](https://mlsanity.com/paper/2106.06716/) (2021)
- [UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation](https://mlsanity.com/paper/2212.04497/) (2022)
- [LViT: Language meets Vision Transformer in Medical Image Segmentation](https://mlsanity.com/paper/2206.14718/) (2022)
- [Recent advances and clinical applications of deep learning in medical image analysis](https://mlsanity.com/paper/2105.13381/) (2021)
- [HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation](https://mlsanity.com/paper/2207.08518/) (2022)
- [Ambiguous Medical Image Segmentation using Diffusion Models](https://mlsanity.com/paper/2304.04745/) (2023)
- [MedViT: A Robust Vision Transformer for Generalized Medical Image Classification](https://mlsanity.com/paper/2302.09462/) (2023)
- [AutoSAM: Adapting SAM to Medical Images by Overloading the Prompt Encoder](https://mlsanity.com/paper/2306.06370/) (2023)
- [Are we ready for a new paradigm shift? A Survey on Visual Deep MLP](https://mlsanity.com/paper/2111.04060/) (2021)
- [Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review](https://mlsanity.com/paper/2301.03505/) (2023)
- [TransCrowd: weakly-supervised crowd counting with transformers](https://mlsanity.com/paper/2104.09116/) (2021)
- [Large AI Models in Health Informatics: Applications, Challenges, and the Future](https://mlsanity.com/paper/2303.11568/) (2023)
- [TransAttUnet: Multi-level Attention-guided U-Net with Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2107.05274/) (2021)
- [Vision-LSTM: xLSTM as Generic Vision Backbone](https://mlsanity.com/paper/2406.04303/) (2024)
- [Vision Transformers with Patch Diversification](https://mlsanity.com/paper/2104.12753/) (2021)
- [Rethinking Data Augmentation for Single-source Domain Generalization in Medical Image Segmentation](https://mlsanity.com/paper/2211.14805/) (2022)
- [TransDeepLab: Convolution-Free Transformer-based DeepLab v3+ for Medical Image Segmentation](https://mlsanity.com/paper/2208.00713/) (2022)

## Abstract (arXiv)

Over the past decade, Deep Convolutional Neural Networks have been widely adopted for medical image segmentation and shown to achieve adequate performance. However, due to the inherent inductive biases present in the convolutional architectures, they lack understanding of long-range dependencies in the image. Recently proposed Transformer-based architectures that leverage self-attention mechanism encode long-range dependencies and learn representations that are highly expressive. This motivates us to explore Transformer-based solutions and study the feasibility of using Transformer-based network architectures for medical image segmentation tasks. Majority of existing Transformer-based network architectures proposed for vision applications require large-scale datasets to train properly. However, compared to the datasets for vision applications, for medical imaging the number of data samples is relatively low, making it difficult to efficiently train transformers for medical applications. To this end, we propose a Gated Axial-Attention model which extends the existing architectures by introducing an additional control mechanism in the self-attention module. Furthermore, to train the model effectively on medical images, we propose a Local-Global training strategy (LoGo) which further improves the performance. Specifically, we operate on the whole image and patches to learn global and local features, respectively. The proposed Medical Transformer (MedT) is evaluated on three different medical image segmentation datasets and it is shown that it achieves better performance than the convolutional and other related transformer-based architectures. Code: https://github.com/jeya-maria-jose/Medical-Transformer