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Item type:Publication, Access status: with files , A review of deep learning-based unsupervised anomaly detection in brain MRI(Elsevier, 2026-07-01); ; ; ; The manual assessment of brain Magnetic Resonance Imaging (MRI) scans can be labor-intensive and time-consuming for radiologists. Deep Learning methods have demonstrated the potential to aid this process. However, their effectiveness relies on the availability of large, annotated data sets. Unsupervised Anomaly Detection (UAD) presents a promising alternative, offering the potential to identify and localize anomalies without per-pixel annotations. Instead, a normative distribution is learned using healthy data, enabling the identification of abnormalities as deviations. This allows UAD methods to detect abnormalities that were unseen during training. This appealing feature has led to numerous studies proposing innovations and novel approaches. In this work, we provide a review of the literature and systematically collect and compare the proposed approaches. We observe that UAD has made significant advancements in brain MRI analysis. However, individual approaches are often evaluated in different contexts, i.e., changes in acquisition parameters, pre- and post-processing, and anomaly scoring. This variability makes it challenging to assess which models perform best, underscoring the need for comprehensive comparative studies concerning the specific context of MRI scans. Our collection, featuring public data sets, research studies, and open implementations, is available at our GitHub repository https://github.com/FinnBehrendt/Unsupervised-Anomaly-Detection-in-Brain-MRI .Publicationtype: Review Article14 26 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Guided reconstruction with conditioned diffusion models for unsupervised anomaly detection in brain MRIs(2025-01-22); ; ; ; The application of supervised models to clinical screening tasks is challenging due to the need for annotated data for each considered pathology. Unsupervised Anomaly Detection (UAD) is an alternative approach that aims to identify any anomaly as an outlier from a healthy training distribution. A prevalent strategy for UAD in brain MRI involves using generative models to learn the reconstruction of healthy brain anatomy for a given input image. As these models should fail to reconstruct unhealthy structures, the reconstruction errors indicate anomalies. However, a significant challenge is to balance the accurate reconstruction of healthy anatomy and the undesired replication of abnormal structures. While diffusion models have shown promising results with detailed and accurate reconstructions, they face challenges in preserving intensity characteristics, resulting in false positives. We propose conditioning the denoising process of diffusion models with additional information derived from a latent representation of the input image. We demonstrate that this conditioning allows for accurate and local adaptation to the general input intensity distribution while avoiding the replication of unhealthy structures. We compare the novel approach to different state-of-the-art methods and for different data sets. Our results show substantial improvements in the segmentation performance, with the Dice score improved by 11.9%, 20.0%, and 44.6%, for the BraTS, ATLAS and MSLUB data sets, respectively, while maintaining competitive performance on the WMH data set. Furthermore, our results indicate effective domain adaptation across different MRI acquisitions and simulated contrasts, an important attribute for general anomaly detection methods. The code for our work is available at https://github.com/FinnBehrendt/Conditioned-Diffusion-Models-UAD.Publicationtype: Journal Article39 40 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Combining Reconstruction-based Unsupervised Anomaly Detection with Supervised Segmentation for Brain MRIsIn contrast to supervised deep learning approaches, unsupervised anomaly detection (UAD) methods can be trained with healthy data only and do not require pixel-level annotations, enabling the identification of unseen pathologies. While this is promising for clinical screening tasks, reconstruction-based UAD methods fall short in segmentation accuracy compared to supervised models. Therefore, self-supervised UAD approaches have been proposed to improve segmentation accuracy. Typically, synthetic anomalies are used to train a segmentation network in a supervised fashion. However, this approach does not effectively generalize to real pathologies. We propose a framework combining reconstruction-based and self-supervised UAD methods to improve both segmentation performance for known anomalies and generalization to unknown pathologies. The framework includes an unsupervised diffusion model trained on healthy data to produce pseudo-healthy reconstructions and a supervised Unet trained to delineate anomalies from deviations between input- reconstruction pairs. Besides the effective use of synthetic training data, this framework allows for weakly-supervised training with small annotated data sets, generalizing to unseen pathologies. Our results show that with our approach, utilizing annotated data sets during training can substantially improve the segmentation performance for in-domain data while maintaining the generalizability of reconstruction-based approaches to pathologies unseen during trainingPublicationtype: Conference Paper30 26 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Diffusion models with ensembled structure-based anomaly scoring for unsupervised anomaly detectionSupervised deep learning techniques show promise in medical image analysis. However, they require comprehensive annotated data sets, which poses challenges, particularly for rare diseases. Consequently, unsupervised anomaly detection (UAD) emerges as a viable alternative for pathology segmentation, as only healthy data is required for training. However, recent UAD anomaly scoring functions often focus on intensity only and neglect structural differences, which impedes the segmentation performance. This work investigates the potential of Structural Similarity (SSIM) to bridge this gap. SSIM captures both intensity and structural disparities and can be advantageous over the classical l1 error. However, we show that there is more than one optimal kernel size for the SSIM calculation for different pathologies. Therefore, we investigate an adaptive ensembling strategy for various kernel sizes to offer a more pathology-agnostic scoring mechanism. We demonstrate that this ensembling strategy can enhance the performance of DMs and mitigate the sensitivity to different kernel sizes across varying pathologies, highlighting its promise for brain MRI anomaly detection.Publicationtype: Conference Paper10 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Quantitative evaluation of activation maps for weakly-supervised lung nodule segmentation(SPIE, 2024-01); ; ; ; The manual assessment of chest radiographs by radiologists is a time-consuming and error-prone process that relies on the availability of trained professionals. Deep learning methods have the potential to alleviate the workload of radiologists in pathology detection and diagnosis. However, one major drawback of deep learning methods is their lack of explainable decision-making, which is crucial in computer-aided diagnosis. To address this issue, activation maps of the underlying convolutional neural networks (CNN) are frequently used to indicate the regions of focus for the network during predictions. However, often, an evaluation of these activation maps concerning the actual predicted pathology is missing. In this study, we quantitatively evaluate the usage of activation maps for segmenting pulmonary nodules in chest radiographs. We compare transformer-based, CNN-based, and hybrid architectures using different visualization methods. Our results show that although high performance can be achieved in the classification task across all models, the activation masks show little correlation with the actual position of the nodules.Publicationtype: Conference Paper12 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Leveraging the Mahalanobis Distance to Enhance Unsupervised Brain MRI Anomaly Detection(Springer, 2024); ; ; ; Unsupervised Anomaly Detection (UAD) methods rely on healthy data distributions to identify anomalies as outliers. In brain MRI, a common approach is reconstruction-based UAD, where generative models reconstruct healthy brain MRIs, and anomalies are detected as deviations between input and reconstruction. However, this method is sensitive to imperfect reconstructions, leading to false positives that impede the segmentation. To address this limitation, we construct multiple reconstructions with probabilistic diffusion models. We then analyze the resulting distribution of these reconstructions using the Mahalanobis distance to identify anomalies as outliers. By leveraging information about normal variations and covariance of individual pixels within this distribution, we effectively refine anomaly scoring, leading to improved segmentation. Our experimental results demonstrate substantial performance improvements across various data sets. Specifically, compared to relying solely on single reconstructions, our approach achieves relative improvements of 15.9%, 35.4%, 48.0%, and 4.7% in terms of AUPRC for the BRATS21, ATLAS, MSLUB and WMH data sets, respectively.Publicationtype: Conference Paper30 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , A systematic approach to deep learning-based nodule detection in chest radiographsLung cancer is a serious disease responsible for millions of deaths every year. Early stages of lung cancer can be manifested in pulmonary lung nodules. To assist radiologists in reducing the number of overseen nodules and to increase the detection accuracy in general, automatic detection algorithms have been proposed. Particularly, deep learning methods are promising. However, obtaining clinically relevant results remains challenging. While a variety of approaches have been proposed for general purpose object detection, these are typically evaluated on benchmark data sets. Achieving competitive performance for specific real-world problems like lung nodule detection typically requires careful analysis of the problem at hand and the selection and tuning of suitable deep learning models. We present a systematic comparison of state-of-the-art object detection algorithms for the task of lung nodule detection. In this regard, we address the critical aspect of class imbalance and and demonstrate a data augmentation approach as well as transfer learning to boost performance. We illustrate how this analysis and a combination of multiple architectures results in state-of-the-art performance for lung nodule detection, which is demonstrated by the proposed model winning the detection track of the Node21 competition. The code for our approach is available at https://github.com/FinnBehrendt/node21-submit.Publicationtype: Journal ArticleScopus© Citations 2 25 57 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Nodule detection in chest radiographs with unsupervised pre-trained detection transformers(IEEE, 2023-09-01); ; ; ; The detection of pulmonary nodules in chest x-rays is important for early observation and monitoring of lung cancer which is a major reason for death worldwide. However, detecting nodules from x-rays is challenging as nodules are easily overseen by radiologists. Convolutional neural networks (CNN) show promising results in supporting the clinical practice by automatic lung nodule detection and localization. Recently, attention-based Vision Transformers have been successfully applied in computer vision tasks. For object detection, end-to-end solutions have been proposed that reduce the amount of encoded prior knowledge and manual postprocessing. This is desirable particularly for medical applications where data domains often vary.In this work, we evaluate the application of Detection Transformers for nodule detection in chest x-rays and compare them against four CNN-based baseline object detection algorithms. To overcome the data inefficiency of Vision Transformers, we investigate the use of self-supervision from large-scale data sources. Our results demonstrate the high performance of transformer-based object detectors, by consistently outperforming CNN-based baselines on the Node21 data set. Furthermore, we demonstrate that self-supervision improves the detection performance without the costly requirement of collecting annotated data.Publicationtype: Conference Paper23 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Patched diffusion models for unsupervised anomaly detection in brain MRIThe use of supervised deep learning techniques to detect pathologies in brain MRI scans can be challenging due to the diversity of brain anatomy and the need for annotated data sets. An alternative approach is to use unsupervised anomaly detection, which only requires sample-level labels of healthy brains to create a reference representation. This reference representation can then be compared to unhealthy brain anatomy in a pixel-wise manner to identify abnormalities. To accomplish this, generative models are needed to create anatomically consistent MRI scans of healthy brains. While recent diffusion models have shown promise in this task, accurately generating the complex structure of the human brain remains a challenge. In this paper, we propose a method that reformulates the generation task of diffusion models as a patch-based estimation of healthy brain anatomy, using spatial context to guide and improve reconstruction. We evaluate our approach on data of tumors and multiple sclerosis lesions and demonstrate a relative improvement of 25.1% compared to existing baselinesPublicationtype: Conference Paper34 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Patched Diffusion Models for Unsupervised Anomaly Detection in Brain MRIThe use of supervised deep learning techniques to detect pathologies in brain MRI scans can be challenging due to the diversity of brain anatomy and the need for annotated data sets. An alternative approach is to use unsupervised anomaly detection, which only requires sample-level labels of healthy brains to create a reference representation. This reference representation can then be compared to unhealthy brain anatomy in a pixel-wise manner to identify abnormalities. To accomplish this, generative models are needed to create anatomically consistent MRI scans of healthy brains. While recent diffusion models have shown promise in this task, accurately generating the complex structure of the human brain remains a challenge. In this paper, we propose a method that reformulates the generation task of diffusion models as a patch-based estimation of healthy brain anatomy, using spatial context to guide and improve reconstruction. We evaluate our approach on data of tumors and multiple sclerosis lesions and demonstrate a relative improvement of 25.1% compared to existing baselines.Publicationtype: Conference Paper21