The role of noise in denoising models for anomaly detection in medical images
Canon Medical Research Europe（佳能医疗欧洲研究中心）；University of Glasgow（格拉斯哥大学）；University of Edinburgh（爱丁堡大学）；The Alan Turing Institute（艾伦·图灵研究所）
Antanas Kascenas, Pedro Sanchez, Patrick Schrempf, Chaoyang Wang, William Clackett, Shadia S. Mikhael, Jeremy P. Voisey, Keith Goatman, Alexander Weir, Nicolas … 展开作者
Antanas Kascenas, Pedro Sanchez, Patrick Schrempf, Chaoyang Wang, William Clackett, Shadia S. Mikhael, Jeremy P. Voisey, Keith Goatman, Alexander Weir, Nicolas Pugeault, Sotirios A. Tsaftaris, Alison Q. O'Neil
备注：
Submitted to Medical Image Analysis special issue for MIDL 2022
Pathological brain lesions exhibit diverse appearance in brain images, in terms of intensity, texture, shape, size, and location. Comprehensive sets of data and annotations are difficult to acquire. Therefore, unsupervised anomaly detection approaches have been proposed using only normal data for training, with the aim of detecting outlier anomalous voxels at test time. Denoising methods, for instance classical denoising autoencoders (DAEs) and more recently emerging diffusion models, are a promising approach, however naive application of pixelwise noise leads to poor anomaly detection performance. We show that optimization of the spatial resolution and magnitude of the noise improves the performance of different model training regimes, with similar noise parameter adjustments giving good performance for both DAEs and diffusion models. Visual inspection of the reconstructions suggests that the training noise influences the trade-off between the extent of the detail that is reconstructed and the extent of erasure of anomalies, both of which contribute to better anomaly detection performance. We validate our findings on two real-world datasets (tumor detection in brain MRI and hemorrhage/ischemia/tumor detection in brain CT), showing good detection on diverse anomaly appearances. Overall, we find that a DAE trained with coarse noise is a fast and simple method that gives state-of-the-art accuracy. Diffusion models applied to anomaly detection are as yet in their infancy and provide a promising avenue for further research.
Peking University（北京大学）；Academy for Advanced Interdisciplinary Studies（前沿交叉学科研究院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
We propose a novel and unified method, measurement-conditioned denoising diffusion probabilistic model (MC-DDPM), for under-sampled medical image reconstruction based on DDPM. Different from previous works, MC-DDPM is defined in measurement domain (e.g. k-space in MRI reconstruction) and conditioned on under-sampling mask. We apply this method to accelerate MRI reconstruction and the experimental results show excellent performance, outperforming full supervision baseline and the state-of-the-art score-based reconstruction method. Due to its generative nature, MC-DDPM can also quantify the unce…
Image denoising is of great importance for medical imaging system, since it can improve image quality for disease diagnosis and downstream image analyses. In a variety of applications, dynamic imaging techniques are utilized to capture the time-varying features of the subject, where multiple images are acquired for the same subject at different time points. Although signal-to-noise ratio of each time frame is usually limited by the short acquisition time, the correlation among different time frames can be exploited to improve denoising results with shared information across time frames. With t…
Image denoising is an important pre-processing step in medical image analysis. Different algorithms have been proposed in past three decades with varying denoising performances. More recently, having outperformed all conventional methods, deep learning based models have shown a great promise. These methods are however limited for requirement of large training sample size and high computational costs. In this paper we show that using small sample size, denoising autoencoders constructed using convolutional layers can be used for efficient denoising of medical images. Heterogeneous images can be…
University of Electronic Science and Technology of China（电子科技大学）；Sichuan University（四川大学）
Deep learning has achieved notable performance in the denoising task of low-quality medical images and the detection task of lesions, respectively. However, existing low-quality medical image denoising approaches are disconnected from the detection task of lesions. Intuitively, the quality of denoised images will influence the lesion detection accuracy that in turn can be used to affect the denoising performance. To this end, we propose a play-and-plug medical image denoising framework, namely Lesion-Inspired Denoising Network (LIDnet), to collaboratively improve both denoising performance and…
Southern University of Science and Technology（南方科技大学）；University of British Columbia（不列颠哥伦比亚大学）
Due to the high cost of manually annotating medical images, especially for large-scale datasets, anomaly detection has been explored through training models with only normal data. Lacking prior knowledge of true anomalies is the main reason for the limited application of previous anomaly detection methods, especially in the medical image analysis realm. In this work, we propose a one-shot anomaly detection framework, namely LesionPaste, that utilizes true anomalies from a single annotated sample and synthesizes artificial anomalous samples for anomaly detection. First, a lesion bank is constru…
We cast the problem of image denoising as a domain translation problem between high and low noise domains. By modifying the cycleGAN model, we are able to learn a mapping between these domains on unpaired retinal optical coherence tomography images. In quantitative measurements and a qualitative evaluation by ophthalmologists, we show how this approach outperforms other established methods. The results indicate that the network differentiates subtle changes in the level of noise in the image. Further investigation of the model's feature maps reveals that it has learned to distinguish retinal l…
UiT The Arctic University of Norway（特罗姆瑟大学（挪威北极圈大学））
Recent work has shown that label-efficient few-shot learning through self-supervision can achieve promising medical image segmentation results. However, few-shot segmentation models typically rely on prototype representations of the semantic classes, resulting in a loss of local information that can degrade performance. This is particularly problematic for the typically large and highly heterogeneous background class in medical image segmentation problems. Previous works have attempted to address this issue by learning additional prototypes for each class, but since the prototypes are based on…
National Tsing Hua University（国立清华大学）；Florida International University（佛罗里达国际大学）；Lehigh University（理海大学）；Guangdong Provincial People’s Hospital（广东省人民医院）；Guangdong Academy of Medical Science（广东省医学科学院）；University of Notre Dame（圣母大学）
Deep learning had already demonstrated its power in medical images, including denoising, classification, segmentation, etc. All these applications are proposed to automatically analyze medical images beforehand, which brings more information to radiologists during clinical assessment for accuracy improvement. Recently, many medical denoising methods had shown their significant artifact reduction result and noise removal both quantitatively and qualitatively. However, those existing methods are developed around human-vision, i.e., they are designed to minimize the noise effect that can be perce…
Emory University（埃默里大学）；Indiana University-Purdue University Indianapolis（印第安纳大学-普渡大学印第安纳波利斯分校）；Arizona State University（亚利桑那州立大学）
Detecting out-of-distribution (OOD) samples in medical imaging plays an important role for downstream medical diagnosis. However, existing OOD detectors are demonstrated on natural images composed of inter-classes and have difficulty generalizing to medical images. The key issue is the granularity of OOD data in the medical domain, where intra-class OOD samples are predominant. We focus on the generalizability of OOD detection for medical images and propose a self-supervised Cascade Variational autoencoder-based Anomaly Detector (CVAD). We use a variational autoencoders' cascade architecture, …
MediCLIP: Adapting CLIP for Few-shot Medical Image Anomaly Detection
College of Information and Engineering, Capital Normal University（首都师范大学信息工程学院）；Peking University Third Hospital（北京大学第三医院）；School of Artificial Intelligence, Beijing University of Posts and Telecommunications（北京邮电大学人工智能学院）
Center for Advanced Medical Computing and Analysis, Massachusetts General Hospital and Harvard Medical School（麻省总医院与哈佛医学院高级医学计算与分析中心）；Gordon Center for Medical Imaging, Massachusetts General Hospital and Harvard Medical School（麻省总医院与哈佛医学院戈登医学成像中心）
Deep neural networks have been proved efficient for medical image denoising. Current training methods require both noisy and clean images. However, clean images cannot be acquired for many practical medical applications due to naturally noisy signal, such as dynamic imaging, spectral computed tomography, arterial spin labeling magnetic resonance imaging, etc. In this paper we proposed a training method which learned denoising neural networks from noisy training samples only. Training data in the acquisition domain was split to two subsets and the network was trained to map one noisy set to the…
Synomaly Noise and Multi-Stage Diffusion: A Novel Approach for Unsupervised Anomaly Detection in Medical Images
Computer Aided Medical Procedures, Technical University of Munich, Munich, Germany（技术大学慕尼黑计算机辅助医疗程序）；Munich Center of Machine Learning, Munich, Germany（慕尼黑机器学习中心）；Department for Vascular and Endovascular Surgery, rechts der Isar University Hospital, Technical University of Munich, Munich, Germany（技术大学慕尼黑血管和内血管外科部门）
University Hospital Aachen（亚琛大学医院）；RWTH Aachen University（亚琛工业大学）；Ocumeda AG（奥库梅达股份公司）；University Hospital Heidelberg（海德堡大学医院）；University Hospital Würzburg（维尔茨堡大学医院）；University of Mainz（美因茨大学）；RWTH Aachen（亚琛工业大学）
Recent advances in computer vision have shown promising results in image generation. Diffusion probabilistic models in particular have generated realistic images from textual input, as demonstrated by DALL-E 2, Imagen and Stable Diffusion. However, their use in medicine, where image data typically comprises three-dimensional volumes, has not been systematically evaluated. Synthetic images may play a crucial role in privacy preserving artificial intelligence and can also be used to augment small datasets. Here we show that diffusion probabilistic models can synthesize high quality medical imagi…
RelativeFlow: Taming Medical Image Denoising Learning with Noisy Reference
School of Computer Science and Engineering, Southeast University, China（东南大学计算机科学与工程学院，中国）；Department of Biomedical Engineering, Case Western Reserve University, USA（凯斯西储大学生物医学工程系，美国）；School of Instrument Science and Engineering, Southeast University, China（东南大学仪器科学与工程学院，中国）；Department of Optical Sciences, University of Arizona, USA（亚利桑那大学光学科学系，美国）
SD-MAD: Sign-Driven Few-shot Multi-Anomaly Detection in Medical Images
Shanghai Academy of AI for Science University of Queensland（上海人工智能科学研究院 华南理工大学）；Fudan University Shanghai Academy of AI for Science（复旦大学 上海人工智能科学研究院）；University of Queensland（昆士兰大学）
Indian Institute of Information Technology Vadodara（瓦多达拉印度信息技术学院）
Medical image acquisition is often intervented by unwanted noise that corrupts the information content. This paper introduces an unsupervised medical image denoising technique that learns noise characteristics from the available images and constructs denoised images. It comprises of two blocks of data processing, viz., patch-based dictionaries that indirectly learn the noise and residual learning (RL) that directly learns the noise. The model is generalized to account for both 2D and 3D images considering different medical imaging instruments. The images are considered one-by-one from the stac…
University of Georgia（佐治亚大学）；Zhongnan Hospital of Wuhan University（武汉大学中南医院）；Shanghai Jiao Tong University（上海交通大学）
In this paper we consider the problem of unsupervised anomaly segmentation in medical images, which has attracted increasing attention in recent years due to the expensive pixel-level annotations from experts and the existence of a large amount of unannotated normal and abnormal image scans. We introduce a segmentation network that utilizes adversarial learning to partition an image into two cuts, with one of them falling into a reference distribution provided by the user. This Adversarial-based Selective Cutting network (ASC-Net) bridges the two domains of cluster-based deep segmentation and …
The University of Tokyo Hospital（东京大学医院）；The University of Tokyo（东京大学）；RIKEN（理化学研究所）
Oversight in medical images is a crucial problem, and timely reporting of medical images is desired. Therefore, an all-purpose anomaly detection method that can detect virtually all types of lesions/diseases in a given image is strongly desired. However, few commercially available and versatile anomaly detection methods for medical images have been provided so far. Recently, anomaly detection methods built upon deep learning methods have been rapidly growing in popularity, and these methods seem to provide reasonable solutions to the problem. However, the workload to label the images necessary…
Distributed Deep Learning for Medical Image Denoising with Data Obfuscation
Computer Engineering Department, King Fahd University of Petroleum and Minerals（国王法赫德石油与矿物大学计算机工程系）；King Fahd University of Petroleum and Minerals（国王法赫德石油与矿物大学）；SDAIA-KFUPM Joint Research Center for Artificial Intelligence（SDAIA-KFUPM人工智能联合研究中心）
Towards Universal Unsupervised Anomaly Detection in Medical Imaging
Technical University of Munich（慕尼黑工业大学）；Helmholtz AI and Helmholtz Center Munich（亥姆霍兹人工智能与亥姆霍兹慕尼黑中心）；Klinikum Rechts der Isar（伊萨尔河右岸医院）；Imperial College London（伦敦帝国理工学院）
Philips Research（飞利浦研究院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）；Goethe University Frankfurt（法兰克福歌德大学）
Anomaly detection is the problem of recognizing abnormal inputs based on the seen examples of normal data. Despite recent advances of deep learning in recognizing image anomalies, these methods still prove incapable of handling complex medical images, such as barely visible abnormalities in chest X-rays and metastases in lymph nodes. To address this problem, we introduce a new powerful method of image anomaly detection. It relies on the classical autoencoder approach with a re-designed training pipeline to handle high-resolution, complex images and a robust way of computing an image abnormalit…
Unsupervised Anomaly Detection in Medical Images with a Memory-augmented Multi-level Cross-attentional Masked Autoencoder
Harvard University（哈佛大学）；Singapore Management University（新加坡管理大学）；Australian Institute for Machine Learning（澳大利亚机器学习研究所）；University of Adelaide（阿德莱德大学）；South Australian Health and Medical Research Institute（南澳大利亚健康与医学研究所）；University of Surrey（萨里大学）
City, University of London（伦敦大学城市学院）；Imperial College（帝国理工学院）
We propose a novel unsupervised out-of-distribution detection method for medical images based on implicit fields image representations. In our approach, an auto-decoder feed-forward neural network learns the distribution of healthy images in the form of a mapping between spatial coordinates and probabilities over a proxy for tissue types. At inference time, the learnt distribution is used to retrieve, from a given test image, a restoration, i.e. an image maximally consistent with the input one but belonging to the healthy distribution. Anomalies are localized using the voxel-wise probability p…
Emory University（埃默里大学）；Indiana University-Purdue University Indianapolis（印第安纳大学-普渡大学印第安纳波利斯分校）；Mayo Clinic（梅奥诊所）；Arizona State University（亚利桑那州立大学）
To curate a high-quality dataset, identifying data variance between the internal and external sources is a fundamental and crucial step. However, methods to detect shift or variance in data have not been significantly researched. Challenges to this are the lack of effective approaches to learn dense representation of a dataset and difficulties of sharing private data across medical institutions. To overcome the problems, we propose a unified pipeline called MedShift to detect the top-level shift samples and thus facilitate the medical curation. Given an internal dataset A as the base source, w…
We propose a novel deep learning model for classifying medical images in the setting where there is a large amount of unlabelled medical data available, but labelled data is in limited supply. We consider the specific case of classifying skin lesions as either malignant or benign. In this setting, the proposed approach -- the semi-supervised, denoising adversarial autoencoder -- is able to utilise vast amounts of unlabelled data to learn a representation for skin lesions, and small amounts of labelled data to assign class labels based on the learned representation. We analyse the contributions…
The Hong Kong University of Science and Technology（香港科技大学）；Huazhong University of Science and Technology（华中科技大学）
Medical anomaly detection is a crucial yet challenging task aimed at recognizing abnormal images to assist in diagnosis. Due to the high-cost annotations of abnormal images, most methods utilize only known normal images during training and identify samples deviating from the normal profile as anomalies in the testing phase. Many readily available unlabeled images containing anomalies are thus ignored in the training phase, restricting the performance. To solve this problem, we introduce one-class semi-supervised learning (OC-SSL) to utilize known normal and unlabeled images for training, and p…
Obtaining ground truth data in medical imaging has difficulties due to the fact that it requires a lot of annotating time from the experts in the field. Also, when trained with supervised learning, it detects only the cases included in the labels. In real practice, we want to also open to other possibilities than the named cases while examining the medical images. As a solution, the need for anomaly detection that can detect and localize abnormalities by learning the normal characteristics using only normal images is emerging. With medical image data, we can design either 2D or 3D networks of …
Self-Consistent Recursive Diffusion Bridge for Medical Image Translation
Bilkent University（毕尔肯大学）；National Magnetic Resonance Research Center (UMRAM)（国家磁共振研究中心）；Stanford University（斯坦福大学）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Korea Advanced Institute of Science and Technology（韩国科学技术院）；Samsung Electronics（三星电子）
Anomaly detection in medical imaging is to distinguish the relevant biomarkers of diseases from those of normal tissues. Deep supervised learning methods have shown potentials in various detection tasks, but its performances would be limited in medical imaging fields where collecting annotated anomaly data is limited and labor-intensive. Therefore, unsupervised anomaly detection can be an effective tool for clinical practices, which uses only unlabeled normal images as training data. In this paper, we developed an unsupervised learning framework for pixel-wise anomaly detection in multi-contra…
Counterfactual MRI Data Augmentation using Conditional Denoising Diffusion Generative Models
Instituto Superior Técnico（高等技术学院）；Universidade de Lisboa（里斯本大学）；Digital Surgery LAB（数字外科实验室）；Champalimaud Foundation（尚帕利莫基金会）；Faculdade de Medicina, Universidade de Lisboa（里斯本大学医学院）；Instituto de Telecomunicações（电信研究所）
ShanghaiTech University（上海科技大学）；Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences（中国科学院上海微系统与信息技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Shanghai Jiao Tong University（上海交通大学）；Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR)（新加坡科技研究局高性能计算研究所）；Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR)（新加坡科技研究局资讯通信研究院）；Southern University of Science and Technology（南方科技大学）；Cixi Institute of Biomedical Engineering, Chinese Academy of Sciences（中国科学院慈溪生物医学工程研究所）
Anomaly detection in medical images refers to the identification of abnormal images with only normal images in the training set. Most existing methods solve this problem with a self-reconstruction framework, which tends to learn an identity mapping and reduces the sensitivity to anomalies. To mitigate this problem, in this paper, we propose a novel Proxy-bridged Image Reconstruction Network (ProxyAno) for anomaly detection in medical images. Specifically, we use an intermediate proxy to bridge the input image and the reconstructed image. We study different proxy types, and we find that the sup…
MTL-MAD: Multi-Task Learners are Effective Medical Anomaly Detectors
Rayscape；University of Bucharest（布加勒斯特大学）；Polytechnic University of Timişoara（蒂米什瓦拉工业大学）；Colţea Clinical Hospital（科尔切亚医院）；Carol Davila University of Medicine and Pharmacy（卡罗尔·迪瓦ila医学院和药理学大学）
Information Technology University（信息技术大学）；University of Toronto（多伦多大学）
Among the plethora of techniques devised to curb the prevalence of noise in medical images, deep learning based approaches have shown the most promise. However, one critical limitation of these deep learning based denoisers is the requirement of high-quality noiseless ground truth images that are difficult to obtain in many medical imaging applications such as X-rays. To circumvent this issue, we leverage recently proposed approach of [7] that incorporates Stein's Unbiased Risk Estimator (SURE) to train a deep convolutional neural network without requiring denoised ground truth X-ray data. Our…
Osaka University Graduate School of Medicine（大阪大学医学研究生院）
Large numbers of labeled medical images are essential for the accurate detection of anomalies, but manual annotation is labor-intensive and time-consuming. Self-supervised learning (SSL) is a training method to learn data-specific features without manual annotation. Several SSL-based models have been employed in medical image anomaly detection. These SSL methods effectively learn representations in several field-specific images, such as natural and industrial product images. However, owing to the requirement of medical expertise, typical SSL-based models are inefficient in medical image anomal…
VinBigData JSC（VinBigData股份公司）；VinUniversity（VinUniversity（温纳大学））；VinUni-Illinois Smart Health Center（VinUni-伊利诺伊智慧健康中心）
Building an accurate computer-aided diagnosis system based on data-driven approaches requires a large amount of high-quality labeled data. In medical imaging analysis, multiple expert annotators often produce subjective estimates about "ground truth labels" during the annotation process, depending on their expertise and experience. As a result, the labeled data may contain a variety of human biases with a high rate of disagreement among annotators, which significantly affect the performance of supervised machine learning algorithms. To tackle this challenge, we propose a simple yet effective a…
