Diffusion Models in Medical Imaging
🔥🔥This is a collection of awesome articles about diffusion models in the medical imaging🔥🔥
📢 Our survey paper published on arXiv: Diffusion Models for Medical Image Analysis: A Comprehensive Survey ❤️
Citation
@article{kazerouni2022diffusion,
title={Diffusion Models for Medical Image Analysis: A Comprehensive Survey},
author={Kazerouni, Amirhossein and Aghdam, Ehsan Khodapanah and Heidari, Moein and Azad, Reza and Fayyaz, Mohsen and Hacihaliloglu, Ilker and Merhof, Dorit},
journal={arXiv preprint arXiv:2211.07804},
year={2022}
}
Contents
Survey Papers in Vision
Efficient Diffusion Models for Vision: A Survey
Anwaar Ulhaq, Naveed Akhtar, Ganna Pogrebna
[7th Oct., 2022] [arXiv, 2022]
[Paper]
Diffusion Models in Vision: A Survey
Florinel-Alin Croitoru, Vlad Hondru, Radu Tudor Ionescu, Mubarak Shah
[10th Sep., 2022] [arXiv, 2022]
[Paper] [Github]
A Survey on Generative Diffusion Model
Hanqun Cao, Cheng Tan, Zhangyang Gao, Guangyong Chen, Pheng-Ann Heng, Stan Z. Li
[6th Sep., 2022] [arXiv, 2022]
[Paper] [Github]
Diffusion Models: A Comprehensive Survey of Methods and Applications
Ling Yang, Zhilong Zhang, Yang Song, Shenda Hong, Runsheng Xu, Yue Zhao, Yingxia Shao, Wentao Zhang, Bin Cui, Ming-Hsuan Yang
[2nd Sep., 2022] [arXiv, 2022]
[Paper] [Github]
Papers
Anomaly Detection
What is Healthy? Generative Counterfactual Diffusion for Lesion Localization
Pedro Sanchez, Antanas Kascenas, Xiao Liu, Alison Q. O'Neil, Sotirios A. Tsaftaris
[25th Jul., 2022] [MICCAI Workshop, 2022]
[Paper] [Github]
AnoDDPM: Anomaly Detection with Denoising Diffusion Probabilistic Models using Simplex Noise
Julian Wyatt, Adam Leach, Sebastian M. Schmon, Chris G. Willcocks
[1st Jun., 2022] [CVPR Workshop, 2022]
[Paper] [Github]
The Swiss Army Knife for Image-to-Image Translation: Multi-Task Diffusion Models
Julia Wolleb, Robin Sandkühler, Florentin Bieder, Philippe C. Cattin
[6th Apr., 2022] [arXiv, 2022]
[Paper]
Diffusion Models for Medical Anomaly Detection
Julia Wolleb, Florentin Bieder, Robin Sandkühler, Philippe C. Cattin
[8th Mar., 2022] [MICCAI, 2022]
[Paper] [Github]
Denoising
Low-Dose CT Using Denoising Diffusion Probabilistic Model for 20× Speedup
Wenjun Xia, Qing Lyu, Ge Wang
[29th Sep., 2022] [arXiv, 2022]
[Paper]
Unsupervised Denoising of Retinal OCT with Diffusion Probabilistic Model
Dewei Hu, Yuankai K. Tao, Ipek Oguz
[27th Jan., 2022] [arXiv, 2022]
[Paper] [Github]
PET image denoising based on denoising diffusion probabilistic models
Kuang Gong, Keith A. Johnson, Georges El Fakhri, Quanzheng Li, Tinsu Pan
[13th Sep., 2022] [arXiv, 2022]
[Paper]
Segmentation
Improved HER2 Tumor Segmentation with Subtype Balancing using Deep Generative Networks
Mathias Öttl, Jana Mönius, Matthias Rübner, Carol I. Geppert, Jingna Qiu, Frauke Wilm, Arndt Hartmann, Matthias W. Beckmann, Peter A. Fasching, Andreas Maier, Ramona Erber, Katharina Breininger
[11th Nov., 2022] [arXiv, 2022]
[Paper]
MedSegDiff: Medical Image Segmentation with Diffusion Probabilistic Model
Junde Wu, Huihui Fang, Yu Zhang, Yehui Yang, Yanwu Xu
[1st Nov., 2022] [arXiv, 2022]
[Paper]
Accelerating Diffusion Models via Pre-segmentation Diffusion Sampling for Medical Image Segmentation
Xutao Guo, Yanwu Yang, Chenfei Ye, Shang Lu, Yang Xiang, Ting Ma
[27th Oct., 2022] [arXiv, 2022]
[Paper]
Diffusion Adversarial Representation Learning for Self-supervised Vessel Segmentation
Boah Kim, Yujin Oh, Jong Chul Ye
[19th Sep., 2022] [arXiv, 2022]
[Paper]
Can segmentation models be trained with fully synthetically generated data?
Virginia Fernandez, Walter Hugo Lopez Pinaya, Pedro Borges, Petru-Daniel Tudosiu, Mark S Graham, Tom Vercauteren, M Jorge Cardoso
[17th Sep., 2022] [MICCAI Workshop , 2022]
[Paper]
Diffusion Models for Implicit Image Segmentation Ensembles
Julia Wolleb, Robin Sandkühler, Florentin Bieder, Philippe Valmaggia, Philippe C. Cattin
[6th Dec., 2021] [MIDL, 2021]
[Paper][Github]
Image-to-Image Translation
Brain PET Synthesis from MRI Using Joint Probability Distribution of Diffusion Model at Ultrahigh Fields
Xie Taofeng, Cao Chentao, Cui Zhuoxu, Li Fanshi, Wei Zidong, Zhu Yanjie, Li Ye, Liang Dong, Jin Qiyu, Chen Guoqing, Wang Haifeng
[16th Nov., 2022] [arXiv, 2022]
[Paper]
Conversion Between CT and MRI Images Using Diffusion and Score-Matching Models
Qing Lyu, Ge Wang
[24th Sep., 2022] [arXiv, 2022]
[Paper]
Unsupervised Medical Image Translation with Adversarial Diffusion Models
Muzaffer Özbey, Salman UH Dar, Hasan A Bedel, Onat Dalmaz, Şaban Özturk, Alper Güngör, Tolga Çukur
[17th Jul., 2022] [arXiv, 2022]
[Paper]
A Novel Unified Conditional Score-based Generative Framework for Multi-modal Medical Image Completion
Xiangxi Meng, Yuning Gu, Yongsheng Pan, Nizhuan Wang, Peng Xue, Mengkang Lu, Xuming He, Yiqiang Zhan, Dinggang Shen
[7th Jul., 2022] [arXiv, 2022]
[Paper]
DiffuseMorph: Unsupervised Deformable Image Registration Along Continuous Trajectory Using Diffusion Models
Boah Kim, Inhwa Han, Jong Chul Ye
[9th Dec., 2021] [ECCV, 2022]
[Paper]
Reconstruction
Self-Score: Self-Supervised Learning on Score-Based Models for MRI Reconstruction
Zhuo-Xu Cui, Chentao Cao, Shaonan Liu, Qingyong Zhu, Jing Cheng, Haifeng Wang, Yanjie Zhu, Dong Liang
[2nd Sep., 2022] [IEEE TMI, 2022]
[Paper]
One-shot Generative Prior in Hankel-k-space for Parallel Imaging Reconstruction
Chentao Cao, Zhuo-Xu Cui, Shaonan Liu, Dong Liang, Yanjie Zhu
[15th Aug., 2022] [arXiv, 2022]
[Paper] [Github]
High-Frequency Space Diffusion Models for Accelerated MRI
Chentao Cao, Zhuo-Xu Cui, Shaonan Liu, Dong Liang, Yanjie Zhu
[10th Aug., 2022] [arXiv, 2022]
[Paper]
Adaptive Diffusion Priors for Accelerated MRI Reconstruction
Salman UH Dar, Şaban Öztürk, Yilmaz Korkmaz, Gokberk Elmas, Muzaffer Özbey, Alper Güngör, Tolga Çukur
[12th Jul., 2022] [arXiv, 2022]
[Paper]
Improving Diffusion Models for Inverse Problems using Manifold Constraints
Hyungjin Chung, Byeongsu Sim, Dohoon Ryu, Jong Chul Ye
[2nd Jun., 2022] [arXiv, 2022]
[Paper]
WKGM: Weight-K-space Generative Model for Parallel Imaging Reconstruction
Hyungjin Chung, Byeongsu Sim, Dohoon Ryu, Jong Chul Ye
[8th May, 2022] [arXiv, 2022]
[Paper] [Github]
Towards performant and reliable undersampled MR reconstruction via diffusion model sampling
Cheng Peng, Pengfei Guo, S. Kevin Zhou, Vishal Patel, Rama Chellappa
[8th Mar., 2022] [MICCAI, 2022]
[Paper] [Github]
Measurement-conditioned Denoising Diffusion Probabilistic Model for Under-sampled Medical Image Reconstruction
Yutong Xie, Quanzheng Li
[5th Mar., 2022] [MICCAI, 2022]
[Paper] [Github]
MRI Reconstruction via Data Driven Markov Chain with Joint Uncertainty Estimation
Guanxiong Luo, Martin Heide, Martin Uecker
[3rd Feb., 2022] [arXiv, 2022]
[Paper] [Github]
Come-Closer-Diffuse-Faster: Accelerating Conditional Diffusion Models for Inverse Problems through Stochastic Contraction
Hyungjin Chung, Byeongsu Sim, Jong Chul Ye
[9th Dec., 2021] [CVPR, 2021]
[Paper]
Solving Inverse Problems in Medical Imaging with Score-Based Generative Models
Yang Song, Liyue Shen, Lei Xing, Stefano Ermon
[15th Nov., 2021] [NeurIPS Workshop, 2021]
[Paper] [Github]
Score-based diffusion models for accelerated MRI
Hyungjin Chung, Jong chul Ye
[8th Oct., 2021] [MIA, 2021]
[Paper] [Github]
Robust Compressed Sensing MRI with Deep Generative Priors
Ajil Jalal, Marius Arvinte, Giannis Daras, Eric Price, Alexandros G. Dimakis, Jonathan I. Tamir
[3rd Aug., 2021] [NeurIPS, 2021]
[Paper] [Github]
Image Generation
Seeing Beyond the Brain: Conditional Diffusion Model with Sparse Masked Modeling for Vision Decoding
Zijiao Chen, Jiaxin Qing, Tiange Xiang, Wan Lin Yue, Juan Helen Zhou
[13th Nov., 2022] [arXiv, 2022]
[Paper]
An unobtrusive quality supervision approach for medical image annotation
Sonja Kunzmann, Mathias Öttl, Prathmesh Madhu, Felix Denzinger, Andreas Maier
[11th Nov., 2022] [arXiv, 2022]
[Paper]
Medical Diffusion -- Denoising Diffusion Probabilistic Models for 3D Medical Image Generation
Firas Khader, Gustav Mueller-Franzes, Soroosh Tayebi Arasteh, Tianyu Han, Christoph Haarburger, Maximilian Schulze-Hagen, Philipp Schad, Sandy Engelhardt, Bettina Baessler, Sebastian Foersch, Johannes Stegmaier, Christiane Kuhl, Sven Nebelung, Jakob Nikolas Kather, Daniel Truhn
[7th Nov., 2022] [arXiv, 2022]
[Paper]
Generation of Anonymous Chest Radiographs Using Latent Diffusion Models for Training Thoracic Abnormality Classification Systems
Kai Packhäuser, Lukas Folle, Florian Thamm, Andreas Maier
[2nd Nov., 2022] [arXiv, 2022]
[Paper]
Spot the fake lungs: Generating Synthetic Medical Images using Neural Diffusion Models
Hazrat Ali, Shafaq Murad, Zubair Shah
[2nd Nov., 2022] [arXiv, 2022]
[Paper]
A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images
Puria Azadi Moghadam, Sanne Van Dalen, Karina C. Martin, Jochen Lennerz, Stephen Yip, Hossein Farahani, Ali Bashashati
[27th Sep., 2022] [arXiv, 2022]
[Paper]
Brain Imaging Generation with Latent Diffusion Models
Walter H. L. Pinaya, Petru-Daniel Tudosiu, Jessica Dafflon, Pedro F da Costa, Virginia Fernandez, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso
[15th Sep., 2022] [MICCAI Workshop, 2022]
[Paper]
A Diffusion Model Predicts 3D Shapes from 2D Microscopy Images
Dominik J. E. Waibel, Ernst Röell, Bastian Rieck, Raja Giryes, Carsten Marr
[30th Aug., 2022] [arXiv, 2022]
[Paper] [Github]
Diffusion Deformable Model for 4D Temporal Medical Image Generation
Boah Kim, Jong Chul Ye
[27th Jan., 2022] [arXiv, 2022]
[Paper] [Github]
Three-Dimensional Medical Image Synthesis with Denoising Diffusion Probabilistic Models
Zolnamar Dorjsembe, Sodtavilan Odonchimed, Furen Xiao
[22nd Apr., 2022] [MIDL, 2022]
[Paper] [Github]
Biology and Molecular Generation
Protein Sequence and Structure Co-Design with Equivariant Translation
Chence Shi, Chuanrui Wang, Jiarui Lu, Bozitao Zhong, Jian Tang
[17th Oct., 2022] [arXiv, 2022]
[Paper]
Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design
Ilia Igashov, Hannes Stärk, Clément Vignac, Victor Garcia Satorras, Pascal Frossard, Max Welling, Michael Bronstein, Bruno Correia
[11th Oct., 2022] [arXiv, 2022]
[Paper] [Github]
Dynamic-Backbone Protein-Ligand Structure Prediction with Multiscale Generative Diffusion Models
Zhuoran Qiao, Weili Nie, Arash Vahdat, Thomas F. Miller III, Anima Anandkumar
[30th Sep., 2022] [arXiv, 2022]
[Paper]
Equivariant Energy-Guided SDE for Inverse Molecular Design
Fan Bao, Min Zhao, Zhongkai Hao, Peiyao Li, Chongxuan Li, Jun Zhu
[30th Sep., 2022] [arXiv, 2022]
[Paper]
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
[30th Sep., 2022] [arXiv, 2022]
[Paper]
MDM: Molecular Diffusion Model for 3D Molecule Generation
Lei Huang, Hengtong Zhang, Tingyang Xu, Ka-Chun Wong
[13th Sep., 2022] [arXiv, 2022]
[Paper]
Diffusion-based Molecule Generation with Informative Prior Bridges
Lemeng Wu, Chengyue Gong, Xingchao Liu, Mao Ye, Qiang Liu
[2nd Sep., 2022] [NeurIPS, 2022]
[Paper]
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models
Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma
[11th Jul., 2022] [BioRXiv, 2022]
[Paper]
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem
Brian L. Trippe, Jason Yim, Doug Tischer, Tamara Broderick, David Baker, Regina Barzilay, Tommi Jaakkola
[8th Jun., 2022] [CoRR, 2022]
[Paper]
Torsional Diffusion for Molecular Conformer Generation
Bowen Jing, Gabriele Corso, Regina Barzilay, Tommi S. Jaakkola
[1st Jun., 2022] [ICLR Workshop, 2022]
[Paper] [Github]
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
Namrata Anand, Tudor Achim
[26th May, 2022] [arXiv, 2022]
[Paper] [Github] [Project]
A Score-based Geometric Model for Molecular Dynamics Simulations
Fang Wu, Qiang Zhang, Xurui Jin, Yinghui Jiang, Stan Z. Li
[19th Apr., 2022] [CoRR, 2022]
CoRR 2022. [Paper]
Equivariant Diffusion for Molecule Generation in 3D
Emiel Hoogeboom, Victor Garcia Satorras, Clément Vignac, Max Welling
[31st Mar., 2022] [ICML, 2022]
[Paper] [Github]
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation
Minkai Xu, Lantao Yu, Yang Song, Chence Shi, Stefano Ermon, Jian Tang
[6th Mar., 2022] [ICLR, 2022]
[Paper] [Github]
Crystal Diffusion Variational Autoencoder for Periodic Material Generation
Tian Xie, Xiang Fu, Octavian-Eugen Ganea, Regina Barzilay, Tommi Jaakkola
[12th Oct., 2021] [NeurIPS, 2021]
[Paper] [Github]
Predicting Molecular Conformation via Dynamic Graph Score Matching
Shitong Luo, Chence Shi, Minkai Xu, Jian Tang
[22th May, 2021] [NeurIPS, 2021]
[Paper]
Inpainting
Multitask Brain Tumor Inpainting with Diffusion Models: A Methodological Report
Pouria Rouzrokh, Bardia Khosravi, Shahriar Faghani, Mana Moassefi, Sanaz Vahdati, Bradley J. Erickson
[21st Oct., 2022] [arXiv, 2022]
[Paper] [Github] [Online Tool]
Adversarial Attacks
Fight Fire With Fire: Reversing Skin Adversarial Examples by Multiscale Diffusive and Denoising Aggregation Mechanism
Yongwei Wang, Yuan Li, Zhiqi Shen
[22nd Aug., 2022] [arXiv, 2022]
[Paper]
Text-to-Image
Adapting Pretrained Vision-Language Foundational Models to Medical Imaging Domains
Pierre Chambon, Christian Bluethgen, Curtis P. Langlotz, Akshay Chaudhari
[9th Oct., 2022] [arXiv, 2022]
[Paper]
Time Series
Restoration of Time-Series Medical Data with Diffusion Model
Jiwoon Lee, Cheolsoo Park
[6th Oct., 2022] [arXiv, 2022]
[Paper]
Multi-task
Anatomically constrained CT image translation for heterogeneous blood vessel segmentation
Giammarco La Barbera, Haithem Boussaid, Francesco Maso, Sabine Sarnacki, Laurence Rouet, Pietro Gori, Isabelle Bloch
[4th Oct., 2022] [BMVC, 2022]
[Paper]
Fast Unsupervised Brain Anomaly Detection and Segmentation with Diffusion Models
Walter H. L. Pinaya, Mark S. Graham, Robert Gray, Pedro F Da Costa, Petru-Daniel Tudosiu, Paul Wright, Yee H. Mah, Andrew D. MacKinnon, James T. Teo, Rolf Jager, David Werring, Geraint Rees, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardos
[7th Jun., 2022] [MICCAI, 2022]
[Paper]
MR Image Denoising and Super-Resolution Using Regularized Reverse Diffusion
Hyungjin Chung, Eun Sun Lee, Jong Chul Ye
[23rd Mar., 2022] [arXiv, 2022]
[Paper]