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Add to EdgeBenedikt Wiestler
The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)
Apr 29, 2024
Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge, focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors.
Multi-Image Visual Question Answering for Unsupervised Anomaly Detection
Apr 11, 2024Unsupervised anomaly detection enables the identification of potential pathological areas by juxtaposing original images with their pseudo-healthy reconstructions generated by models trained exclusively on normal images. However, the clinical interpretation of resultant anomaly maps presents a challenge due to a lack of detailed, understandable explanations. Recent advancements in language models have shown the capability of mimicking human-like understanding and providing detailed descriptions. This raises an interesting question: \textit{How can language models be employed to make the anomaly maps more explainable?} To the best of our knowledge, we are the first to leverage a language model for unsupervised anomaly detection, for which we construct a dataset with different questions and answers. Additionally, we present a novel multi-image visual question answering framework tailored for anomaly detection, incorporating diverse feature fusion strategies to enhance visual knowledge extraction. Our experiments reveal that the framework, augmented by our new Knowledge Q-Former module, adeptly answers questions on the anomaly detection dataset. Besides, integrating anomaly maps as inputs distinctly aids in improving the detection of unseen pathologies.
A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge
Apr 03, 2024
Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.
Denoising Diffusion Models for 3D Healthy Brain Tissue Inpainting
Mar 21, 2024
Monitoring diseases that affect the brain's structural integrity requires automated analysis of magnetic resonance (MR) images, e.g., for the evaluation of volumetric changes. However, many of the evaluation tools are optimized for analyzing healthy tissue. To enable the evaluation of scans containing pathological tissue, it is therefore required to restore healthy tissue in the pathological areas. In this work, we explore and extend denoising diffusion models for consistent inpainting of healthy 3D brain tissue. We modify state-of-the-art 2D, pseudo-3D, and 3D methods working in the image space, as well as 3D latent and 3D wavelet diffusion models, and train them to synthesize healthy brain tissue. Our evaluation shows that the pseudo-3D model performs best regarding the structural-similarity index, peak signal-to-noise ratio, and mean squared error. To emphasize the clinical relevance, we fine-tune this model on data containing synthetic MS lesions and evaluate it on a downstream brain tissue segmentation task, whereby it outperforms the established FMRIB Software Library (FSL) lesion-filling method.
Diffusion Models with Implicit Guidance for Medical Anomaly Detection
Mar 13, 2024
Diffusion models have advanced unsupervised anomaly detection by improving the transformation of pathological images into pseudo-healthy equivalents. Nonetheless, standard approaches may compromise critical information during pathology removal, leading to restorations that do not align with unaffected regions in the original scans. Such discrepancies can inadvertently increase false positive rates and reduce specificity, complicating radiological evaluations. This paper introduces Temporal Harmonization for Optimal Restoration (THOR), which refines the de-noising process by integrating implicit guidance through temporal anomaly maps. THOR aims to preserve the integrity of healthy tissue in areas unaffected by pathology. Comparative evaluations show that THOR surpasses existing diffusion-based methods in detecting and segmenting anomalies in brain MRIs and wrist X-rays. Code: https://github.com/ci-ber/THOR_DDPM.
A Learnable Prior Improves Inverse Tumor Growth Modeling
Mar 07, 2024
Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients. However, the inverse problem-solving aspect of these models presents a substantial challenge, either due to the high computational requirements of model-based approaches or the limited robustness of deep learning (DL) methods. We propose a novel framework that leverages the unique strengths of both approaches in a synergistic manner. Our method incorporates a DL ensemble for initial parameter estimation, facilitating efficient downstream evolutionary sampling initialized with this DL-based prior. We showcase the effectiveness of integrating a rapid deep-learning algorithm with a high-precision evolution strategy in estimating brain tumor cell concentrations from magnetic resonance images. The DL-Prior plays a pivotal role, significantly constraining the effective sampling-parameter space. This reduction results in a fivefold convergence acceleration and a Dice-score of 95%
Towards Universal Unsupervised Anomaly Detection in Medical Imaging
Jan 19, 2024The increasing complexity of medical imaging data underscores the need for advanced anomaly detection methods to automatically identify diverse pathologies. Current methods face challenges in capturing the broad spectrum of anomalies, often limiting their use to specific lesion types in brain scans. To address this challenge, we introduce a novel unsupervised approach, termed \textit{Reversed Auto-Encoders (RA)}, designed to create realistic pseudo-healthy reconstructions that enable the detection of a wider range of pathologies. We evaluate the proposed method across various imaging modalities, including magnetic resonance imaging (MRI) of the brain, pediatric wrist X-ray, and chest X-ray, and demonstrate superior performance in detecting anomalies compared to existing state-of-the-art methods. Our unsupervised anomaly detection approach may enhance diagnostic accuracy in medical imaging by identifying a broader range of unknown pathologies. Our code is publicly available at: \url{https://github.com/ci-ber/RA}.
Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps
Dec 05, 2023This paper introduces panoptica, a versatile and performance-optimized package designed for computing instance-wise segmentation quality metrics from 2D and 3D segmentation maps. panoptica addresses the limitations of existing metrics and provides a modular framework that complements the original intersection over union-based panoptic quality with other metrics, such as the distance metric Average Symmetric Surface Distance. The package is open-source, implemented in Python, and accompanied by comprehensive documentation and tutorials. panoptica employs a three-step metrics computation process to cover diverse use cases. The efficacy of panoptica is demonstrated on various real-world biomedical datasets, where an instance-wise evaluation is instrumental for an accurate representation of the underlying clinical task. Overall, we envision panoptica as a valuable tool facilitating in-depth evaluation of segmentation methods.
Personalized Predictions of Glioblastoma Infiltration: Mathematical Models, Physics-Informed Neural Networks and Multimodal Scans
Nov 28, 2023Predicting the infiltration of Glioblastoma (GBM) from medical MRI scans is crucial for understanding tumor growth dynamics and designing personalized radiotherapy treatment plans.Mathematical models of GBM growth can complement the data in the prediction of spatial distributions of tumor cells. However, this requires estimating patient-specific parameters of the model from clinical data, which is a challenging inverse problem due to limited temporal data and the limited time between imaging and diagnosis. This work proposes a method that uses Physics-Informed Neural Networks (PINNs) to estimate patient-specific parameters of a reaction-diffusion PDE model of GBM growth from a single 3D structural MRI snapshot. PINNs embed both the data and the PDE into a loss function, thus integrating theory and data. Key innovations include the identification and estimation of characteristic non-dimensional parameters, a pre-training step that utilizes the non-dimensional parameters and a fine-tuning step to determine the patient specific parameters. Additionally, the diffuse domain method is employed to handle the complex brain geometry within the PINN framework. Our method is validated both on synthetic and patient datasets, and shows promise for real-time parametric inference in the clinical setting for personalized GBM treatment.
(Predictable) Performance Bias in Unsupervised Anomaly Detection
Sep 25, 2023
Background: With the ever-increasing amount of medical imaging data, the demand for algorithms to assist clinicians has amplified. Unsupervised anomaly detection (UAD) models promise to aid in the crucial first step of disease detection. While previous studies have thoroughly explored fairness in supervised models in healthcare, for UAD, this has so far been unexplored. Methods: In this study, we evaluated how dataset composition regarding subgroups manifests in disparate performance of UAD models along multiple protected variables on three large-scale publicly available chest X-ray datasets. Our experiments were validated using two state-of-the-art UAD models for medical images. Finally, we introduced a novel subgroup-AUROC (sAUROC) metric, which aids in quantifying fairness in machine learning. Findings: Our experiments revealed empirical "fairness laws" (similar to "scaling laws" for Transformers) for training-dataset composition: Linear relationships between anomaly detection performance within a subpopulation and its representation in the training data. Our study further revealed performance disparities, even in the case of balanced training data, and compound effects that exacerbate the drop in performance for subjects associated with multiple adversely affected groups. Interpretation: Our study quantified the disparate performance of UAD models against certain demographic subgroups. Importantly, we showed that this unfairness cannot be mitigated by balanced representation alone. Instead, the representation of some subgroups seems harder to learn by UAD models than that of others. The empirical fairness laws discovered in our study make disparate performance in UAD models easier to estimate and aid in determining the most desirable dataset composition.