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junyuchen245 / Transformer_for_medical_image_analysis

A collection of papers about Transformer in the field of medical image analysis.
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medical-image-analysis medical-image-processing pytorch tensorflow transformer vision-transformer

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Transformer For Medical Image Analysis

Transformer related papers in medical imaging.

Please check out our survey paper:\ Li, J., Chen, J., Tang, Y., Wang, C., Landman, B. A., & Zhou, S. K. (2023). Transforming medical imaging with Transformers? A comparative review of key properties, current progresses, and future perspectives. Medical image analysis, 102762.

Last updated: 03/17/2022

Image Segmentation

Date First Author Title Modality ND Code Paper
03/10/2022 Lihao Liu PC-SwinMorph: Patch Representation for Unsupervised Medical Image Registration and Segmentation MRI 3D N/A arXiv
03/10/2022 Lei Zhou Self Pre-training with Masked Autoencoders for Medical Image Analysis CT & MRI 3D N/A arXiv
01/30/2022 Jiangyun Li TransBTSV2: Wider Instead of Deeper Transformer for Medical Image Segmentation CT & MRI 3D PyTorch arXiv
01/26/2022 Shiqi Huang RTNet: Relation Transformer Network for Diabetic Retinopathy Multi-lesion Segmentation DR 2D N/A IEEE TMI arXiv
01/04/2022 Ali Hatamizadeh Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images MRI 3D PyTorch arXiv
01/03/2022 Yixuan Wu D-Former: A U-shaped Dilated Transformer for 3D Medical Image Segmentation MRI & CT 3D N/A arXiv
12/17/2021 Yutong Xie Unified 2D and 3D Pre-training for Medical Image Classification and Segmentation X-ray & CT 2D & 3D N/A arXiv
12/09/2021 Xiangde Luo Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer MRI 2D PyTorch arXiv
11/29/2021 Yucheng Tang Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis CT & MRI 3D PyTorch arXiv
11/26/2021 Xiangyu Meng Exploiting full Resolution Feature Context for Liver Tumor and Vessel Segmentation via Fusion Encoder: Application to Liver Tumor and Vessel 3D reconstruction CT 2D N/A arXiv
11/26/2021 Himashi Peiris A Volumetric Transformer for Accurate 3D Tumor Segmentation CT & MRI 3D PyTorch arXiv
11/15/2021 Dong Yang T-AutoML: Automated Machine Learning for Lesion Segmentation using Transformers in 3D Medical Imaging CT 3D N/A ICCV 2021 arXiv
11/08/2021 Hongyi Wang Mixed Transformer U-Net For Medical Image Segmentation CT 2D PyTorch arXiv
09/30/2021 Yunxiang Li GT U-Net: A U-Net Like Group Transformer Network for Tooth Root Segmentation X-ray & Fundus 2D PyTorch MLMI 2021 arXiv
09/15/2021 Xiaohong Huang MISSFormer: An Effective Medical Image Segmentation Transformer CT 2D PyTorch arXiv
09/07/2021 Hong-Yu Zhou nnFormer: Interleaved Transformer for Volumetric Segmentation CT 3D PyTorch arXiv
07/28/2021 Madeleine K. Wyburd TEDS-Net: Enforcing Diffeomorphisms in Spatial Transformers to Guarantee Topology Preservation in Segmentations MRI 2D PyTorch MICCAI 2021 arXiv
07/19/2021 Guoping Xu LeViT-UNet: Make Faster Encoders with Transformer for Medical Image Segmentation CT 2D N/A arXiv
07/12/2021 Bingzhi Chen TransAttUnet: Multi-level Attention-guided U-Net with Transformer for Medical Image Segmentation X-ray & CT ... 2D N/A arXiv
07/12/2021 Chang Yao TransClaw U-Net: Claw U-Net with Transformers for Medical Image Segmentation CT 2D N/A arXiv
07/02/2021 Yunhe Gao UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation CT 2D PyTorch MICCAI 2021 arXiv
06/28/2021 Yuanfeng Ji Multi-Compound Transformer for Accurate Biomedical Image Segmentation Colonoscopy & Pathology ... 2D PyTorch MICCAI 2021 arXiv
06/12/2021 Ailiang Lin DS-TransUNet: Dual Swin Transformer U-Net for Medical Image Segmentation Colonoscopy & Histology ... 2D N/A arXiv
06/02/2021 Shaohua Li Medical Image Segmentation Using Squeeze-and-Expansion Transformers Fundus & Colonoscopy & MRI 2D & 3D PyTorch IJCAI 2021 arXiv
05/12/2021 Hu Cao Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation CT 2D PyTorch arXiv
04/29/2021 Zhuangzhuang Zhang Pyramid Medical Transformer for Medical Image Segmentation Microscopic 2D N/A arXiv
04/28/2021 Eunji Jun Medical Transformer: Universal Brain Encoder for 3D MRI Analysis MRI 3D N/A arXiv
03/18/2021 Ali Hatamizadeh UNETR: Transformers for 3D Medical Image Segmentation CT & MRI 3D PyTorch arXiv
03/10/2021 Olivier Petit U-Net Transformer: Self and Cross Attention for Medical Image Segmentation CT 2D N/A arXiv
03/07/2021 Wenxuan Wang TransBTS: Multimodal Brain Tumor Segmentation Using Transformer MRI 3D PyTorch MICCAI 2021 arXiv
03/05/2021 Boxiang Yun SpecTr: Spectral Transformer for Hyperspectral Pathology Image Segmentation HSI 3D PyTorch arXiv
03/04/2021 Yutong Xie CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation CT 3D PyTorch MICCAI 2021arXiv
02/26/2021 Davood Karimi Convolution-Free Medical Image Segmentation using Transformers CT & MRI 3D N/A arXiv
02/21/2021 Jeya Maria Jose Valanarasu Medical Transformer: Gated Axial-Attention for Medical Image Segmentation Ultrasound & Microscopic 2D PyTorch MICCAI 2021 arXiv
02/16/2021 Yundong Zhang TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation Colonoscopy 2D N/A arXiv
02/08/2021 Jieneng Chen TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation CT & MRI 2D PyTorch arXiv
02/08/2021 Walter Hugo Lopez Pinaya Unsupervised Brain Anomaly Detection and Segmentation with Transformers MRI 2D N/A MIDL 2021 arXiv
<!--- 11/16/2019 Debesh Jha ResUNet++: An Advanced Architecture for Medical Image Segmentation Colonoscopy 2D TensorFlow PyTorch IEEE ISM 2019arXiv -->

Image Registration

Date First Author Title Modality ND Code Paper
03/10/2022 Lihao Liu PC-SwinMorph: Patch Representation for Unsupervised Medical Image Registration and Segmentation MRI 3D N/A arXiv
11/19/2021 Junyu Chen TransMorph: Transformer for unsupervised medical image registration MRI & CT 3D PyTorch arXiv
09/25/2021 Yungeng Zhang Learning Dual Transformer Network for Diffeomorphic Registration MRI 3D N/A MICCAI 2021 Springer
04/13/2021 Junyu Chen ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration MRI 3D PyTorch MIDL 2021 arXiv

Image Classification & Detection

Date First Author Title Modality ND Code Paper
03/12/2022 Heqin Zhu DATR: Domain-adaptive transformer for multi-domain landmark detection X-Ray 2D N/A arXiv
03/10/2022 Lei Zhou Self Pre-training with Masked Autoencoders for Medical Image Analysis CT & MRI 3D N/A arXiv
02/13/2022 Sangjoon Park AI can evolve without labels: self-evolving vision transformer for chest X-ray diagnosis through knowledge distillation X-ray 2D Unknown arXiv
12/17/2021 Yutong Xie Unified 2D and 3D Pre-training for Medical Image Classification and Segmentation X-ray & CT 2D & 3D N/A arXiv
10/27/2021 Behnaz Gheflati Vision Transformer for Classification of Breast Ultrasound Images Ultrasound 2D N/A arXiv
08/20/2021 Christos Matsoukas Is it Time to Replace CNNs with Transformers for Medical Images? Mammograms... 2D PyTorch ICCV 2021 WorkshoparXiv
06/02/2021 Zhuchen Shao TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classication Pathology 2D N/A arXiv
05/23/2021 Zhiqiang Shen COTR: Convolution in Transformer Network for End to End Polyp Detection Colonoscopy 2D N/A arXiv
04/28/2021 Eunji Jun Medical Transformer: Universal Brain Encoder for 3D MRI Analysis MRI 3D N/A arXiv
03/10/2021 Yin Dai TransMed: Transformers Advance Multi-modal Medical Image Classification MRI 3D N/A arXiv

Image Denoising

Date First Author Title Modality ND Code Paper
09/23/2021 Achleshwar Luthra & Harsh Sulakhe Eformer: Edge Enhancement based Transformer for Medical Image Denoising CT 2D N/A ICCV 2021 arXiv
06/08/2021 Dayang Wang TED-net: Convolution-free T2T Vision Transformer-based Encoder-decoder Dilation network for Low-dose CT Denoising CT 2D N/A MLMI 2021 arXiv
02/28/2021 Zhicheng Zhang TransCT: Dual-path Transformer for Low Dose Computed Tomography CT 2D N/A MICCAI 2021 arXiv

Image Synthesis

Date First Author Title Modality ND Code Paper
10/13/2021 Lingke Kong Breaking the Dilemma of Medical Image-to-image Translation MRI 3D PyTorch NeurIPS 2021 arXiv
10/12/2021 Nicolae-Catalin Ristea CyTran: Cycle-Consistent Transformers for Non-Contrast to Contrast CT Translation CT 3D N/A arXiv
06/30/2021 Onat Dalmaz ResViT: Residual vision transformers for multi-modal medical image synthesis MRI & CT 3D PyTorch NeurIPS 2021 WorkshoparXiv
05/28/2021 Xuzhe Zhang PTNet: A High-Resolution Infant MRI Synthesizer Based on Transformer MRI 2D N/A arXiv

Image Reconstruction

Date First Author Title Modality ND Code Paper
01/23/2022 Pengfei Guo ReconFormer: Accelerated MRI Reconstruction Using Recurrent Transformer MRI 2D PyTorch arXiv
11/03/2021 Alper Güngör TranSMS: Transformers for Super-Resolution Calibration in Magnetic Particle Imaging MPI 2D N/A arXiv
05/21/2021 Yilmaz Korkmaz Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers MRI 3D TensorFlow MLMIR 2021 arXiv

Transformer fundamental papers

Date First Author Title Code Paper
03/25/2021 Ze Liu Swin Transformer: Hierarchical Vision Transformer using Shifted Windows PyTorch arXiv
10/22/2020 Alexey Dosovitskiy An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale JAX PyTorch ICLR 2020 arXiv
12/06/2017 Ashish Vaswani Attention Is All You Need TensorFlow NIPS 2017 arXiv