Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.
Awesome Lists | Featured Topics | Projects
https://github.com/xmindflow/Awesome-Transformer-in-Medical-Imaging

[MedIA Journal] An ultimately comprehensive paper list of Vision Transformer/Attention, including papers, codes, and related websites
https://github.com/xmindflow/Awesome-Transformer-in-Medical-Imaging
List: Awesome-Transformer-in-Medical-Imaging
attention-mechanism awesome-list computer-vision deep-learning medical-image-segmentation segmentation transformer transformers vision-transformer vit
Last synced: 3 months ago
JSON representation
[MedIA Journal] An ultimately comprehensive paper list of Vision Transformer/Attention, including papers, codes, and related websites
Host: GitHub
URL: https://github.com/xmindflow/Awesome-Transformer-in-Medical-Imaging
Owner: xmindflow
License: gpl-3.0
Created: 2022-03-13T23:15:41.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2023-11-10T07:19:51.000Z (12 months ago)
Last Synced: 2024-05-21T03:12:54.385Z (6 months ago)
Topics: attention-mechanism, awesome-list, computer-vision, deep-learning, medical-image-segmentation, segmentation, transformer, transformers, vision-transformer, vit
Homepage:
Size: 354 KB
Stars: 140
Watchers: 2
Forks: 18
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project

ultimate-awesome - Awesome-Transformer-in-Medical-Imaging - [MedIA Journal] An ultimately comprehensive paper list of Vision Transformer/Attention, including papers, codes, and related websites. (Other Lists / PowerShell Lists)
README

        # Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review

[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/hee9joon/Awesome-Diffusion-Models) 

[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)

:fire::fire:This is a collection of awesome articles about Transformer models in medical imaging :fire::fire:

:loudspeaker: Our review paper published on MedIA: [Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review](https://www.sciencedirect.com/science/article/abs/pii/S1361841523002608) :heart:

:loudspeaker: Our review paper published on arXiv: [Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review](https://arxiv.org/abs/2301.03505.pdf) :heart:

#### Citation

```

@article{azad2023advances,

  title={Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review},

  author={Azad, Reza and Kazerouni, Amirhossein and Heidari, Moein and Aghdam, Ehsan Khodapanah and Molaei, Amirali and Jia, Yiwei and Jose, Abin and Roy, Rijo and Merhof, Dorit},

  journal={Medical Image Analysis},

  volume = {91},

  pages={103000},

  year={2024},

  issn = {1361-8415},

  publisher={Elsevier}

}

```

## Contents

- [Taxonomy](#taxonomy)

- [Papers](#papers)

  

  - [Image Classification](#image-classification)

  - [Image Segmentation](#image-segmentation)

  - [Image Reconstruction](#image-reconstruction)

  - [Image Synthesizing](#image-synthesizing)

  - [Object Detection](#object-detection)

  - [Image Registration](#image-registration)

  - [Report Generation](#report-generation)

## Taxonomy

![Transformers](https://user-images.githubusercontent.com/61879630/211773884-160e3917-c0f4-45cf-947e-e7fa84b2892e.png)

## Papers

### Image Classification

**HATNet: An End-to-End Holistic Attention Network for Diagnosis of Breast Biopsy Images** 


*Sachin Mehta, Ximing Lu, Donald Weaver, Joann G. Elmore, Hannaneh Hajishirzi, Linda Shapiro*


[25th Jul, 2020] [MedIA Journal, 2022] \

[[PDF](https://arxiv.org/abs/2007.13007)] [[GitHub](https://github.com/sacmehta/HATNet)]

**A graph-transformer for whole slide image classification** 


*Yi Zheng, Rushin H. Gindra, Emily J. Green, Eric J. Burks, Margrit Betke, Jennifer E. Beane, Vijaya B. Kolachalama*


[19th May, 2022] [TMI Journal, 2022] \

[[PDF](https://arxiv.org/abs/2205.09671)] [[GitHub](https://github.com/vkola-lab/tmi2022)]

**RadioTransformer: A Cascaded Global-Focal Transformer for Visual Attention-guided Disease Classification** 


*Moinak Bhattacharya, Shubham Jain, Prateek Prasanna*


[23rd Feb., 2022] [ECCV, 2022] \

[[PDF](https://arxiv.org/abs/2202.11781)]

**Federated Split Vision Transformer for COVID-19 CXR Diagnosis using Task-Agnostic Training** 


*Sangjoon Park, Gwanghyun Kim, Jeongsol Kim, Boah Kim, Jong Chul Ye*


[2nd Nov., 2021] [NeurIPS, 2021] \

[[PDF](https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwijh4Dj5Kb8AhUnRvEDHZWQByUQFnoECA8QAQ&url=https%3A%2F%2Fopenreview.net%2Fpdf%3Fid%3DGgikq6Tdxch&usg=AOvVaw2FRmFAEyk1osGtkMa8nXWL)] 

**Vision transformer for classification of breast ultrasound images** 


*Behnaz Gheflati, Hassan Rivaz*


[27th Oct., 2021] [EMBC, 2022] \

[[PDF](https://arxiv.org/abs/2110.14731)]

**MIL-VT: Multiple Instance Learning Enhanced Vision Transformer for Fundus Image Classification** 


*Shuang Yu, Kai Ma, Qi Bi, Cheng Bian, Munan Ning, Nanjun He, Yuexiang Li, Hanruo Liu, Yefeng Zheng*


[21st Sep., 2021] [MICCAI, 2021] \

[[PDF](https://link.springer.com/chapter/10.1007/978-3-030-87237-3_5)] [[GitHub](https://github.com/greentreeys/MIL-VT)] 

**3DMeT: 3D Medical Image Transformer for Knee Cartilage Defect Assessment** 


*Sheng Wang, Zixu Zhuang, Kai Xuan, Dahong Qian, Zhong Xue, Jia Xu, Ying Liu, Yiming Chai, Lichi Zhang, Qian Wang, Dinggang Shen*


[21st Sep., 2021] [MICCAI Workshop, 2021] \

[[PDF](https://link.springer.com/chapter/10.1007/978-3-030-87589-3_36)]

**COVID-Transformer: Interpretable COVID-19 Detection Using Vision Transformer for Healthcare** 


*Debaditya Shome, T. Kar, Sachi Nandan Mohanty, Prayag Tiwari, Khan Muhammad, Abdullah AlTameem, Yazhou Zhang, Abdul Khader Jilani Saudagar*


[23rd Sep., 2021] [International Journal of Environmental Research and Public Health, 2021] \

[[PDF](https://www.mdpi.com/1660-4601/18/21/11086)] [[GitHub](https://github.com/DebadityaShome/COVID-Transformer)] 

**Is it Time to Replace CNNs with Transformers for Medical Images?** 


*Christos Matsoukas, Johan Fredin Haslum, Magnus Söderberg, Kevin Smith*


[20th Aug., 2021] [ICCV Workshop, 2021] \

[[PDF](https://arxiv.org/abs/2108.09038)] [[GitHub](https://github.com/ChrisMats/medical_transformers)] 

**Vision Transformer for femur fracture classification** 


*Leonardo Tanzi, Andrea Audisio, Giansalvo Cirrincione, Alessandro Aprato, Enrico Vezzetti*


[7th Aug., 2021] [Injury Journal, 2022] \

[[PDF](https://arxiv.org/abs/2108.03414)]

**xViTCOS: Explainable Vision Transformer Based COVID-19 Screening Using Radiography** 


*Arnab Kumar Mondal, Arnab Bhattacharjee, Parag Singla, A. P. Prathosh*


[7th Jul., 2021] [IEEE Journal of Translational Engineering in Health and Medicine, 2021] \

[[PDF](https://www.techrxiv.org/articles/preprint/xViTCOS_Explainable_Vision_Transformer_Based_COVID-19_Screening_Using_Radiography/14912367/1)] [[Github](https://github.com/arnabkmondal/xViTCOS)] 

**COVID-VIT: Classification of COVID-19 from CT chest images based on vision transformer models** 


*Xiaohong Gao, Yu Qian, Alice Gao*


[4th Jul., 2021] [NextComp, 2022] \

[[PDF](https://arxiv.org/abs/2107.01682)] [[GitHub](https://github.com/xiaohong1/COVID-ViT)] 

**TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification** 


*Zhuchen Shao, Hao Bian, Yang Chen, Yifeng Wang, Jian Zhang, Xiangyang Ji, Yongbing Zhang*


[2nd Jun., 2021] [NeurIPS, 2021] \

[[PDF](https://openreview.net/pdf?id=LKUfuWxajHc)] [[GitHub](https://github.com/szc19990412/TransMIL)] 

**Lesion-Aware Transformers for Diabetic Retinopathy Grading** 


*Rui Sun, Yihao Li, Tianzhu Zhang, Zhendong Mao, Feng Wu, Yongdong Zhang*


[1st Jun., 2021] [CVPR, 2021] \

[[PDF](http://openaccess.thecvf.com//content/CVPR2021/papers/Sun_Lesion-Aware_Transformers_for_Diabetic_Retinopathy_Grading_CVPR_2021_paper.pdf)]

**POCFormer: A Lightweight Transformer Architecture for Detection of COVID-19 Using Point of Care Ultrasound** 


*Shehan Perera, Srikar Adhikari, Alper Yilmaz*


[20th May, 2021] [ICIP, 2022] \

[[PDF](https://arxiv.org/abs/2105.09913)]

**Automatic diagnosis of covid-19 using a tailored transformer-like network** 


*Chengeng Liu, Qingshan Yin*


[21st Apr., 2021] [CISAT, 2021] \

[[PDF](https://iopscience.iop.org/article/10.1088/1742-6596/2010/1/012175/pdf)] 

**Vision Transformer for COVID-19 CXR Diagnosis using Chest X-ray Feature Corpus** 


*Sangjoon Park, Gwanghyun Kim, Yujin Oh, Joon Beom Seo, Sang Min Lee, Jin Hwan Kim, Sungjun Moon, Jae-Kwang Lim, Jong Chul Ye*


[12th Mar., 2021] [arXiv, 2021] \

[[PDF](https://arxiv.org/abs/2103.07055)]

**TransMed: Transformers Advance Multi-modal Medical Image Classification** 


*Yin Dai, Yifan Gao*


[10th Mar., 2021] [Diagnostics, 2021] \

[[PDF](https://arxiv.org/abs/2103.05940)]

---

### Image Segmentation

**TransDeepLab: Convolution-Free Transformer-based DeepLab v3+ for Medical Image Segmentation** 


*Reza Azad, Moein Heidari, Moein Shariatnia, Ehsan Khodapanah Aghdam, Sanaz Karimijafarbigloo, Ehsan Adeli, Dorit Merhof*


[1st Aug., 2022] [MICCAI Workshop, 2022] \

[[PDF]](https://arxiv.org/abs/2208.00713) [[GitHub](https://github.com/rezazad68/transdeeplab)]

**HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation**


*Moein Heidari, Amirhossein Kazerouni, Milad Soltany, Reza Azad, Ehsan Khodapanah, Aghdam Julien Cohen-Adad, Dorit Merhof*


[18th Jul., 2022] [WACV, 2023] \

[[PDF]](https://arxiv.org/abs/2207.08518) [[GitHub](https://github.com/amirhossein-kz/HiFormer)]

**Self Pre-training with Masked Autoencoders for Medical Image Analysis**


*Lei Zhou, Huidong Liu, Joseph Bae, Junjun He, Dimitris Samaras, Prateek Prasanna*


[10th Mar., 2022] [arXiv, 2022] \

[[PDF](https://arxiv.org/abs/2203.05573)] 

**Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images**


*Ali Hatamizadeh, Vishwesh Nath, Yucheng Tang, Dong Yang, Holger Roth, Daguang Xu*  


[4th Jan., 2022] [MICCAI Workshop] \

[[PDF](https://arxiv.org/abs/2201.01266)] [[GitHub](https://github.com/Project-MONAI/research-contributions/tree/main/SwinUNETR)]

**Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer**


*Xiangde Luo, Minhao Hu, Tao Song, Guotai Wang, Shaoting Zhang*


[9th Dec., 2021] [MIDL, 2022] \

[[PDF](https://arxiv.org/abs/2112.04894)] [[Github](https://github.com/HiLab-git/SSL4MIS)]

**T-AutoML: Automated Machine Learning for Lesion Segmentation using Transformers in 3D Medical Imaging**


*Dong Yang, Andriy Myronenko, Xiaosong Wang, Ziyue Xu, Holger R. Roth, Daguang Xu*


[15th Nov., 2021] [ICCV, 2021] \

[[PDF](https://arxiv.org/abs/2111.07535)]

**MISSFormer: An Effective Medical Image Segmentation Transformer**


*Xiaohong Huang, Zhifang Deng, Dandan Li, Xueguang Yuan*


[15th Sep., 2021] [TMI Journal, 2022] \

[[PDF]](https://arxiv.org/abs/2109.07162) [[GitHub](https://github.com/ZhifangDeng/MISSFormer)]

**nnFormer: Interleaved Transformer for Volumetric Segmentation**


*Hong-Yu Zhou, Jiansen Guo, Yinghao Zhang, Lequan Yu, Liansheng Wang, Yizhou Yu*


[7th Sep., 2021] [arXiv, 2021] \

[[PDF]](https://arxiv.org/abs/2109.03201) [[GitHub](https://github.com/282857341/nnFormer)]

**Medical Image Segmentation Using Squeeze-and-Expansion Transformers**


*Shaohua Li, Xiuchao Sui, Xiangde Luo, Xinxing Xu, Yong Liu, Rick Goh*


[20th May, 2021] [IJCAI, 2021] \

[[PDF](https://arxiv.org/abs/2105.09511)] [[GitHub](https://github.com/askerlee/segtran)]

**Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation**


*Hu Cao, Yueyue Wang, Joy Chen, Dongsheng Jiang, Xiaopeng Zhang, Qi Tian, Manning Wang*  


[12th May, 2021] [arXiv, 2021] \

[[PDF](https://arxiv.org/abs/2105.05537)] [[GitHub](https://github.com/HuCaoFighting/Swin-Unet)]

**UNETR: Transformers for 3D Medical Image Segmentation**


*Ali Hatamizadeh, Yucheng Tang, Vishwesh Nath, Dong Yang, Andriy Myronenko, Bennett Landman, Holger Roth, Daguang Xu*


[18th Mar., 2021] [WACV, 2022] \

[[PDF](https://arxiv.org/abs/2103.10504)] [[GitHub](https://github.com/Project-MONAI/research-contributions/tree/main/UNETR/BTCV)]

 

**TransBTS: Multimodal Brain Tumor Segmentation Using Transformer**


*Jiangyun Li, Wenxuan Wang, Chen Chen, Tianxiang Zhang, Sen Zha, Hong Yu, Jing Wang*


[7th Mar, 2021] [MICCAI, 2021] \

[[PDF](https://arxiv.org/abs/2103.04430)] [[GitHub](https://github.com/Wenxuan-1119/TransBTS)]

**CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation**  


*Yutong Xie, Jianpeng Zhang, Chunhua Shen, Yong Xia* 


[4th Mar., 2021] [MICCAI, 2021] \

[[PDF](https://arxiv.org/abs/2103.03024)] [[GitHub](https://github.com/YtongXie/CoTr)]

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


*Jeya Maria Jose Valanarasu, Poojan Oza, Ilker Hacihaliloglu, Vishal M. Patel*


[21th Feb., 2021] [MICCAI, 2021] \

[[PDF](https://arxiv.org/abs/2102.10662)] [[GitHub](https://github.com/jeya-maria-jose/Medical-Transformer)]

 

**TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation**


*Yundong Zhang, Huiye Liu, Qiang Hu*


[16th Feb., 2021] [arXiv, 2021] \

[[PDF](https://arxiv.org/abs/2102.08005)] [[GitHub](https://github.com/Rayicer/TransFuse)]

**TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation** 


*Jieneng Chen, Yongyi Lu, Qihang Yu, Xiangde Luo, Ehsan Adeli, Yan Wang, Le Lu, Alan L. Yuille, Yuyin Zhou*


[8th Feb., 2021] [arXiv, 2021] \

[[PDF](https://arxiv.org/abs/2102.04306)] [[GitHub](https://github.com/Beckschen/TransUNet)]

---

### Image Reconstruction

**Transformer-based Dual-domain Network for Few-view Dedicated Cardiac SPECT Image Reconstructions** 


*Huidong Xie, Bo Zhou, Xiongchao Chen, Xueqi Guo, Stephanie Thorn, Yi-Hwa Liu, Ge Wang, Albert Sinusas, Chi Liu*


[18th July., 2023] [MICCAI, 2023] \

[[PDF](https://arxiv.org/abs/2307.09624)] 

**TransCT: Dual-path Transformer for Low Dose Computed Tomography** 


*Zhicheng Zhang, Lequan Yu, Xiaokun Liang, Wei Zhao, Lei Xing*


[28th Feb., 2021] [MICCAI, 2021] \

[[PDF](https://arxiv.org/abs/2103.00634)] [[GitHub](https://github.com/zzc623/TransCT)]

**TED-net: Convolution-free T2T Vision Transformer-based Encoder-decoder Dilation network for Low-dose CT Denoising** 


*Dayang Wang, Zhan Wu, Hengyong Yu*


[8th Jun., 2021] [MICCAI Workshop, 2021]\

[[PDF](https://arxiv.org/abs/2106.04650)] [[GitHub](https://github.com/wdayang/CTformer)]

**Eformer: Edge Enhancement based Transformer for Medical Image Denoising** 


*Achleshwar Luthra, Harsh Sulakhe, Tanish Mittal, Abhishek Iyer, Santosh Yadav*


[16th Sep., 2021] [arXiv, 2021]\

[[PDF](https://arxiv.org/abs/2109.08044)]

**3D Transformer-GAN for High-Quality PET Reconstruction** 


*Yanmei Luo, Yan Wang, Chen Zu, Bo Zhan, Xi Wu, Jiliu Zhou, Dinggang Shen, Luping Zhou*


[21st Sep., 2021] [MICCAI, 2021]\

[[PDF](https://link.springer.com/chapter/10.1007/978-3-030-87231-1_27)]

**Spatial Adaptive and Transformer Fusion Network (STFNet) for Low-count PET Blind Denoising with MRI** 


*Lipei Zhang, Zizheng Xiao, Chao Zhou, Jianmin Yuan, Qiang He, Yongfeng Yang, Xin Liu, Dong Liang, Hairong Zheng, Wei Fan, Xu Zhang, Zhanli Hu*


[19th Nov., 2021] [Medical Physics, 2021]\

[[PDF](https://aapm.onlinelibrary.wiley.com/doi/abs/10.1002/mp.15368)]

**CTformer: Convolution-free Token2Token Dilated Vision Transformer for Low-dose CT Denoising** 


*Dayang Wang, Fenglei Fan, Zhan Wu, Rui Liu, Fei Wang, Hengyong Yu*


[28th Feb., 2022] [arXiv, 2022]\

[[PDF](https://arxiv.org/abs/2202.13517)] [[GitHub](https://github.com/wdayang/CTformer)]

**Low-Dose CT Denoising via Sinogram Inner-Structure Transformer** 


*Liutao Yang, Zhongnian Li, Rongjun Ge, Junyong Zhao, Haipeng Si, Daoqiang Zhang*


[7th Apr., 2022] [IEEE Transactions on Medical Imaging, 2022]\

[[PDF](https://arxiv.org/abs/2204.03163)]

**DuDoTrans: Dual-Domain Transformer Provides More Attention for Sinogram Restoration in Sparse-View CT Reconstruction** 


*Ce Wang, Kun Shang, Haimiao Zhang, Qian Li, Yuan Hui, S. Kevin Zhou*


[21th Nov., 2021] [arXiv, 2021]\

[[PDF](https://arxiv.org/abs/2111.10790)] [[GitHub](https://github.com/DuDoTrans/CODE)]

**Fourier Image Transformer** 


*Tim-Oliver Buchholz, Florian Jug*


[6th Apr., 2021] [CVPR, 2022]\

[[PDF](https://openaccess.thecvf.com/content/CVPR2022W/CVMI/html/Buchholz_Fourier_Image_Transformer_CVPRW_2022_paper.html)] [[GitHub](https://github.com/juglab/FourierImageTransformer)]

**Dual-domain sparse-view CT reconstruction with Transformers** 


*Changrong Shi, Yongshun Xiao, Zhiqiang Chen*


[22nd Mar., 2022] [ELSEVIER Physica Medica, 2022]\

[[PDF](https://www.sciencedirect.com/science/article/abs/pii/S1120179722020154)]

**Adaptively Re-weighting Multi-Loss Untrained Transformer for Sparse-View Cone-Beam CT Reconstruction** 


*Minghui Wu, Yangdi Xu, Yingying Xu, Guangwei Wu, Qingqing Chen, Hongxiang Lin*


[23th Mar., 2022] [arXiv, 2022]\

[[PDF](https://arxiv.org/abs/2203.12476)]

**Vision Transformers Enable Fast and Robust Accelerated MRI** 


*Chun-Mei Feng, Yunlu Yan, Huazhu Fu, Li Chen, Yong Xu*


[10th Dec., 2021] [MIDL, 2022]\

[[PDF](https://proceedings.mlr.press/v172/lin22a.html)] [[GitHub](https://github.com/MLI-lab/transformers_for_imaging)]

**Task Transformer Network for Joint MRI Reconstruction and Super-Resolution** 


*Chun-Mei Feng, Yunlu Yan, Huazhu Fu, Li Chen, Yong Xu*


[12th Jun., 2021] [MICCAI, 2021]\

[[PDF](https://arxiv.org/abs/2106.06742)] [[GitHub](https://github.com/chunmeifeng/T2Net)]

**MR Image Super Resolution By Combining Feature Disentanglement CNNs and Vision Transformers** 


*Chun-Mei Feng, Yunlu Yan, Huazhu Fu, Li Chen, Yong Xu*


[9th Dec., 2021] [MIDL, 2022]\

[[PDF](https://proceedings.mlr.press/v172/mahapatra22a.html)]

**Cross-Modality High-Frequency Transformer for MR Image Super-Resolution** 


*Chaowei Fang, Dingwen Zhang, Liang Wang, Yulun Zhang, Lechao Cheng, Junwei Han*


[29th Mar., 2022] [ACM MM, 2022]\

[[PDF](https://arxiv.org/abs/2203.15314)]

---

### Image Synthesizing

**One Model to Synthesize Them All: Multi-contrast Multi-scale Transformer for Missing Data Imputation** 


*Jiang Liu, Srivathsa Pasumarthi, Ben Duffy, Enhao Gong, Greg Zaharchuk, Keshav Datta*


[28th Apr., 2022] [arXiv, 2021]\

[[PDF](https://arxiv.org/abs/2204.13738)] 

**CyTran: Cycle-Consistent Transformers for Non-Contrast to Contrast CT Translation** 


*Nicolae-Catalin Ristea, Andreea-Iuliana Miron, Olivian Savencu, Mariana-Iuliana Georgescu, Nicolae Verga, Fahad Shahbaz Khan, Radu Tudor Ionescu*


[12th Oct., 2021] [arXiv, 2021] \

[[PDF](https://arxiv.org/abs/2110.06400)] [[GitHub](https://github.com/ristea/cycle-transformer)]

**ResViT: Residual vision transformers for multi-modal medical image synthesis** 


*Onat Dalmaz, Mahmut Yurt, Tolga Çukur*


[30th Jun., 2021] [TMI Journal, 2021] \

[[PDF](https://arxiv.org/abs/2106.16031)] [[GitHub](https://github.com/icon-lab/ResViT)]

**PTNet: A High-Resolution Infant MRI Synthesizer Based on Transformer** 


*Xuzhe Zhang, Xinzi He, Jia Guo, Nabil Ettehadi, Natalie Aw, David Semanek, Jonathan Posner, Andrew Laine, Yun Wang*


[28th May., 2021] [arXiv, 2021] \

[[PDF](https://arxiv.org/abs/2105.13993)] [[GitHub](https://github.com/XuzheZ/PTNet3D)]

**VTGAN: Semi-supervised Retinal Image Synthesis and Disease Prediction using Vision Transformers** 


*Sharif Amit Kamran, Khondker Fariha Hossain, Alireza Tavakkoli, Stewart Lee Zuckerbrod, Salah A. Baker*


[14th Apr., 2021] [ICCV Workshop, 2021] \

[[PDF](https://arxiv.org/abs/2104.06757)] [[GitHub](https://github.com/SharifAmit/VTGAN)]

---

### Object Detection

**Focused Decoding Enables 3D Anatomical Detection by Transformers**


*Bastian Wittmann, Fernando Navarro, Suprosanna Shit, Bjoern Menze*


[21st Jul., 2022] [arXiv, 2022] \

[[PDF](https://arxiv.org/abs/2207.10774)] [[GitHub](https://github.com/bwittmann/transoar)]

**CellCentroidFormer: Combining Self-attention and Convolution for Cell Detection**


*Royden Wagner, Karl Rohr*


[1st Jun., 2022] [MIUA, 2022] \

[[PDF](https://arxiv.org/abs/2206.00338)] [[Github](https://github.com/roydenwa/cell-centroid-former)]

 

**CT-CAD: Context-Aware Transformers for End-to-End Chest Abnormality Detection on X-Rays**


*Qiran Kong, Yirui Wu, Chi Yuan, Yongli Wang*


[9th Dec., 2021] [BIBM, 2021] \

[[PDF](https://ieeexplore.ieee.org/document/9669743)] 

**RDFNet: A Fast Caries Detection Method Incorporating Transformer Mechanism**


*Hao Jiang, Peiliang Zhang, Chao Che, Bo Jin*


[10th Nov., 2021] [Computational and Mathematical Methods in Medicine Journal, 2021] \

[[PDF](https://www.hindawi.com/journals/cmmm/2021/9773917/)] 

**Spine-Transformers: Vertebra Detection and Localization in Arbitrary Field-of-View Spine CT with Transformers**


*Rong Tao, Guoyan Zheng*


[21st Sep., 2021] [MICCAI, 2021] \

[[PDF](https://link.springer.com/chapter/10.1007/978-3-030-87199-4_9)]

**Transformer Network for Significant Stenosis Detection in CCTA of Coronary Arteries**


*Xinghua Ma, Gongning Luo, Wei Wang, Kuanquan Wang*


[7th Jul., 2021] [MICCAI, 2021] \

[[PDF](https://arxiv.org/abs/2107.03035)] [[Github](https://github.com/XinghuaMa/TR-Net)]

**COTR: Convolution in Transformer Network for End to End Polyp Detection**


*Zhiqiang Shen, Chaonan Lin, Shaohua Zheng*


[23rd May, 2021] [ICCC, 2021] \

[[PDF](https://arxiv.org/abs/2105.10925)]

---

### Image Registration

**SVoRT: Iterative Transformer for Slice-to-Volume Registration in Fetal Brain MRI.** 


*Junshen Xu, Daniel Moyer, P. Ellen Grant, Polina Golland, Juan Eugenio Iglesias, Elfar Adalsteinsson.*


[22th Jun., 2022] [MICCAI, 2022] \

[[PDF](https://arxiv.org/abs/2206.10802?context=eess)] [[GitHub](https://github.com/daviddmc/svort)]

**XMorpher: Full Transformer for Deformable Medical Image Registration via Cross Attention**


*Jiacheng Shi, Yuting He, Youyong Kong, Jean-Louis Coatrieux, Huazhong Shu, Guanyu Yang, Shuo Li*


[15th Jun., 2022] [MICCAI, 2022] \

[[PDF](https://arxiv.org/abs/2206.07349)] [[GitHub](https://github.com/solemoon/xmorpher)]

**TransMorph: Transformer for unsupervised medical image registration** 


*Junyu Chen, Eric C. Frey, Yufan He, William P. Segars, Ye Li, Yong Du*


[19th Nov., 2021] [MedIA Journal]\

[[PDF](https://arxiv.org/abs/2111.10480)] [[GitHub](https://github.com/junyuchen245/TransMorph_Transformer_for_Medical_Image_Registration)]

**Learning dual transformer network for diffeomorphic registration** 


*Yungeng Zhang, Yuru Pei & Hongbin Zha*


[21th Sep., 2021] [MICCAI, 2021] \

[[PDF](https://link.springer.com/chapter/10.1007/978-3-030-87202-1_13)]

**ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration** 


*Junyu Chen, Yufan He, Eric C. Frey, Ye Li, Yong Du*


[13th Apr., 2021] [MIDL, 2021] \

[[PDF](https://arxiv.org/abs/2104.06468)] [[GitHub](https://github.com/junyuchen245/ViT-V-Net_for_3D_Image_Registration_Pytorch)]

**Affine Medical Image Registration with Coarse-to-Fine Vision Transformer** 


*Tony C. W. Mok, Albert C. S. Chung*


[29th Mar., 2022] [CVPR, 2022] \

[[PDF](https://arxiv.org/abs/2203.15216)] [[GitHub](https://github.com/cwmok/C2FViT)]

---

### Report Generation

**Cross-modal Memory Networks for Radiology Report Generation** 


*Zhihong Chen, Yaling Shen, Yan Song, Xiang Wan*


[28th Apr., 2022] [ACL-IJCNLP, 2021] \

[[PDF](https://arxiv.org/abs/2204.13258)] [[GitHub](https://github.com/zhjohnchan/R2GenCMN)]

**AlignTransformer: Hierarchical Alignment of Visual Regions and Disease Tags for Medical Report Generation** 


*Di You, Fenglin Liu, Shen Ge, Xiaoxia Xie, Jing Zhang, Xian Wu*


[18th Mar., 2022] [MICCAI, 2021] \

[[PDF](https://arxiv.org/abs/2203.10095)] 

**Automated Generation of Accurate \& Fluent Medical X-ray Reports** 


*Hoang T.N. Nguyen, Dong Nie, Taivanbat Badamdorj, Yujie Liu, Yingying Zhu, Jason Truong, Li Cheng*


[27th Aug., 2021] [EMNLP, 2021] \

[[PDF](https://arxiv.org/abs/2108.12126)] [[GitHub](https://github.com/ginobilinie/xray_report_generation)]

**Medical-vlbert: Medical visual language bert for covid-19 ct report generation with alternate learning** 


*Guangyi Liu, Yinghong Liao, Fuyu Wang, Bin Zhang, Lu Zhang, Xiaodan Liang, Xiang Wan, Shaolin Li, Zhen Li, Shuixing Zhang, Shuguang Cui*


[11th Aug., 2021] [IEEE Transactions on Neural Networks and Learning Systems, 2021] \

[[PDF](https://arxiv.org/abs/2108.05067)] 

**Surgical Instruction Generation with Transformers**


*Jinglu Zhang, Yinyu Nie, Jian Chang, Jian Jun Zhang*


[14th Jul., 2021] [MICCAI, 2021] \

[[PDF](https://arxiv.org/abs/2107.06964)] 

**Trust It or Not: Confidence-Guided Automatic Radiology Report Generation** 


*Yixin Wang, Zihao Lin, Zhe Xu, Haoyu Dong, Jiang Tian, Jie Luo, Zhongchao Shi, Yang Zhang, Jianping Fan, Zhiqiang He*


[21st Jun., 2021] [arXiv , 2021] \

[[PDF](https://arxiv.org/abs/2106.10887)]

**Exploring and Distilling Posterior and Prior Knowledge for Radiology Report Generation** 


*Fenglin Liu, Xian Wu, Shen Ge, Wei Fan, Yuexian Zou*


[13th Jun., 2021] [CVPR, 2021] \

[[PDF](https://arxiv.org/abs/2106.06963)]

**Progressive Transformer-Based Generation of Radiology Reports** 


*Farhad Nooralahzadeh, Nicolas Perez Gonzalez, Thomas Frauenfelder, Koji Fujimoto, Michael Krauthammer*


[19th Feb., 2021] [EMNLP , 2021] \

[[PDF](https://arxiv.org/abs/2102.09777)] [[GitHub](https://github.com/uzh-dqbm-cmi/argon)]

**Learning to Generate Clinically Coherent Chest X-Ray Reports** 


*Justin Lovelace, Bobak Mortazavi*


[1st Nov., 2020] [EMNLP, 2020] \

[[PDF](https://aclanthology.org/2020.findings-emnlp.110/)] [[GitHub](https://github.com/justinlovelace/coherent-xray-report-generation)]

**Generating Radiology Reports via Memory-driven Transformer**


*Zhihong Chen, Yan Song, Tsung-Hui Chang, Xiang Wan*


[30th Oct., 2020] [EMNLP, 2020] \

[[PDF](https://arxiv.org/abs/2010.16056)] [[GitHub](https://github.com/cuhksz-nlp/R2Gen)]

**Reinforced Transformer for Medical Image Captioning** 


*Yuxuan Xiong, Bo Du, Pingkun Yan*


[10th Oct., 2019][MICCAI Workshop, 2019] \

[[PDF](https://doi.org/10.1007/978-3-030-32692-0_77)]

**Knowledge-driven Encode, Retrieve, Paraphrase for Medical Image Report Generation** 


*Christy Y. Li, Xiaodan Liang, Zhiting Hu, Eric P. Xing*


[25th Mar., 2019] [AAAI, 2019] \

[[PDF](https://arxiv.org/abs/1903.10122)]