# UNesT: Local Spatial Representation Learning with Hierarchical Transformer for Efficient Medical Segmentation

arXiv: https://arxiv.org/abs/2209.14378 · HTML: https://mlsanity.com/paper/2209.14378/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 45 of its 74 references that are in the map.
- First posted on arXiv 28 Sep 2022.

## Builds on (most cited first, 30 of 45)

- [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)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [Identity Mappings in Deep Residual Networks](https://mlsanity.com/paper/1603.05027/) (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)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Instance Normalization: The Missing Ingredient for Fast Stylization](https://mlsanity.com/paper/1607.08022/) (2016)
- [Scaling Vision Transformers](https://mlsanity.com/paper/2106.04560/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Transformer in Transformer](https://mlsanity.com/paper/2103.00112/) (2021)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [Medical Transformer: Gated Axial-Attention for Medical Image Segmentation](https://mlsanity.com/paper/2102.10662/) (2021)
- [On the Relationship between Self-Attention and Convolutional Layers](https://mlsanity.com/paper/1911.03584/) (2019)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation](https://mlsanity.com/paper/2102.08005/) (2021)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [Local Relation Networks for Image Recognition](https://mlsanity.com/paper/1904.11491/) (2019)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [Polyp-PVT: Polyp Segmentation with Pyramid Vision Transformers](https://mlsanity.com/paper/2108.06932/) (2021)
- [DS-TransUNet:Dual Swin Transformer U-Net for Medical Image Segmentation](https://mlsanity.com/paper/2106.06716/) (2021)
- [Self-Supervised Learning with Swin Transformers](https://mlsanity.com/paper/2105.04553/) (2021)
- [MISSFormer: An Effective Medical Image Segmentation Transformer](https://mlsanity.com/paper/2109.07162/) (2021)
- [Nested Hierarchical Transformer: Towards Accurate, Data-Efficient and Interpretable Visual Understanding](https://mlsanity.com/paper/2105.12723/) (2021)

## Built on by (most cited first, 1 of 1)

- [CLIP-Driven Universal Model for Organ Segmentation and Tumor Detection](https://mlsanity.com/paper/2301.00785/) (2023)

## Abstract (arXiv)

Transformer-based models, capable of learning better global dependencies, have recently demonstrated exceptional representation learning capabilities in computer vision and medical image analysis. Transformer reformats the image into separate patches and realizes global communication via the self-attention mechanism. However, positional information between patches is hard to preserve in such 1D sequences, and loss of it can lead to sub-optimal performance when dealing with large amounts of heterogeneous tissues of various sizes in 3D medical image segmentation. Additionally, current methods are not robust and efficient for heavy-duty medical segmentation tasks such as predicting a large number of tissue classes or modeling globally inter-connected tissue structures. To address such challenges and inspired by the nested hierarchical structures in vision transformer, we proposed a novel 3D medical image segmentation method (UNesT), employing a simplified and faster-converging transformer encoder design that achieves local communication among spatially adjacent patch sequences by aggregating them hierarchically. We extensively validate our method on multiple challenging datasets, consisting of multiple modalities, anatomies, and a wide range of tissue classes, including 133 structures in the brain, 14 organs in the abdomen, 4 hierarchical components in the kidneys, inter-connected kidney tumors and brain tumors. We show that UNesT consistently achieves state-of-the-art performance and evaluate its generalizability and data efficiency. Particularly, the model achieves whole brain segmentation task complete ROI with 133 tissue classes in a single network, outperforming prior state-of-the-art method SLANT27 ensembled with 27 networks.