arXiv subjects

Daniel Rueckert

Publications and source records attributed to Daniel Rueckert.

At least 181 records · Page 10Linked to original sources

arXiv2024

Machine Unlearning for Medical Imaging

Machine unlearning is the process of removing the impact of a particular set of training samples from a pretrained model. It aims to fulfill the "right to be forgotten", which grants the individuals such as patients the right to reconsider their contribution in models including medical imaging models. In this study, we evaluate the effectiveness (performance) and computational efficiency of different unlearning algorithms in medical imaging domain. Our evaluations demonstrate that the considered unlearning algorithms perform well on the retain set (samples whose influence on the model is allowed to be retained) and forget set (samples whose contribution to the model should be eliminated), and show no bias against male or female samples. They, however, adversely impact the generalization of the model, especially for larger forget set sizes. Moreover, they might be biased against easy or hard samples, and need additional computational overhead for hyper-parameter tuning. In conclusion, machine unlearning seems promising for medical imaging, but the existing unlearning algorithms still needs further improvements to become more practical for medical applications.

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arXiv2024

FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI.

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arXiv2024

Unsupervised Analysis of Alzheimer's Disease Signatures using 3D Deformable Autoencoders

With the increasing incidence of neurodegenerative diseases such as Alzheimer's Disease (AD), there is a need for further research that enhances detection and monitoring of the diseases. We present MORPHADE (Morphological Autoencoders for Alzheimer's Disease Detection), a novel unsupervised learning approach which uses deformations to allow the analysis of 3D T1-weighted brain images. To the best of our knowledge, this is the first use of deformations with deep unsupervised learning to not only detect, but also localize and assess the severity of structural changes in the brain due to AD. We obtain markedly higher anomaly scores in clinically important areas of the brain in subjects with AD compared to healthy controls, showcasing that our method is able to effectively locate AD-related atrophy. We additionally observe a visual correlation between the severity of atrophy highlighted in our anomaly maps and medial temporal lobe atrophy scores evaluated by a clinical expert. Finally, our method achieves an AUROC of 0.80 in detecting AD, out-performing several supervised and unsupervised baselines. We believe our framework shows promise as a tool towards improved understanding, monitoring and detection of AD. To support further research and application, we have made our code publicly available at github.com/ci-ber/MORPHADE.

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arXiv2024

Attention Incorporated Network for Sharing Low-rank, Image and K-space Information during MR Image Reconstruction to Achieve Single Breath-hold Cardiac Cine Imaging

Cardiac Cine Magnetic Resonance Imaging (MRI) provides an accurate assessment of heart morphology and function in clinical practice. However, MRI requires long acquisition times, with recent deep learning-based methods showing great promise to accelerate imaging and enhance reconstruction quality. Existing networks exhibit some common limitations that constrain further acceleration possibilities, including single-domain learning, reliance on a single regularization term, and equal feature contribution. To address these limitations, we propose to embed information from multiple domains, including low-rank, image, and k-space, in a novel deep learning network for MRI reconstruction, which we denote as A-LIKNet. A-LIKNet adopts a parallel-branch structure, enabling independent learning in the k-space and image domain. Coupled information sharing layers realize the information exchange between domains. Furthermore, we introduce attention mechanisms into the network to assign greater weights to more critical coils or important temporal frames. Training and testing were conducted on an in-house dataset, including 91 cardiovascular patients and 38 healthy subjects scanned with 2D cardiac Cine using retrospective undersampling. Additionally, we evaluated A-LIKNet on the real-time 8x prospectively undersampled data from the OCMR dataset. The results demonstrate that our proposed A-LIKNet outperforms existing methods and provides high-quality reconstructions. The network can effectively reconstruct highly retrospectively undersampled dynamic MR images up to 24x accelerations, indicating its potential for single breath-hold imaging.

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arXiv2024

Framing image registration as a landmark detection problem for label-noise-aware task representation (HitR)

Accurate image registration is pivotal in biomedical image analysis, where selecting suitable registration algorithms demands careful consideration. While numerous algorithms are available, the evaluation metrics to assess their performance have remained relatively static. This study addresses this challenge by introducing a novel evaluation metric termed Landmark Hit Rate (HitR), which focuses on the clinical relevance of image registration accuracy. Unlike traditional metrics such as Target Registration Error, which emphasize subresolution differences, HitR considers whether registration algorithms successfully position landmarks within defined confidence zones. This paradigm shift acknowledges the inherent annotation noise in medical images, allowing for more meaningful assessments. To equip HitR with label-noise-awareness, we propose defining these confidence zones based on an Inter-rater Variance analysis. Consequently, hit rate curves are computed for varying landmark zone sizes, enabling performance measurement for a task-specific level of accuracy. Our approach offers a more realistic and meaningful assessment of image registration algorithms, reflecting their suitability for clinical and biomedical applications.

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arXiv2024

DCSM 2.0: Deep Conditional Shape Models for Data Efficient Segmentation

Segmentation is often the first step in many medical image analyses workflows. Deep learning approaches, while giving state-of-the-art accuracies, are data intensive and do not scale well to low data regimes. We introduce Deep Conditional Shape Models 2.0, which uses an edge detector, along with an implicit shape function conditioned on edge maps, to leverage cross-modality shape information. The shape function is trained exclusively on a source domain (contrasted CT) and applied to the target domain of interest (3D echocardiography). We demonstrate data efficiency in the target domain by varying the amounts of training data used in the edge detection stage. We observe that DCSM 2.0 outperforms the baseline at all data levels in terms of Hausdorff distances, and while using 50% or less of the training data in terms of average mesh distance, and at 10% or less of the data with the dice coefficient. The method scales well to low data regimes, with gains of up to 5% in dice coefficient, 2.58 mm in average surface distance and 21.02 mm in Hausdorff distance when using just 2% (22 volumes) of the training data.

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arXiv2024

Weakly Supervised Learning of Cortical Surface Reconstruction from Segmentations

Existing learning-based cortical surface reconstruction approaches heavily rely on the supervision of pseudo ground truth (pGT) cortical surfaces for training. Such pGT surfaces are generated by traditional neuroimage processing pipelines, which are time consuming and difficult to generalize well to low-resolution brain MRI, e.g., from fetuses and neonates. In this work, we present CoSeg, a learning-based cortical surface reconstruction framework weakly supervised by brain segmentations without the need for pGT surfaces. CoSeg introduces temporal attention networks to learn time-varying velocity fields from brain MRI for diffeomorphic surface deformations, which fit an initial surface to target cortical surfaces within only 0.11 seconds for each brain hemisphere. A weakly supervised loss is designed to reconstruct pial surfaces by inflating the white surface along the normal direction towards the boundary of the cortical gray matter segmentation. This alleviates partial volume effects and encourages the pial surface to deform into deep and challenging cortical sulci. We evaluate CoSeg on 1,113 adult brain MRI at 1mm and 2mm resolution. CoSeg achieves superior geometric and morphological accuracy compared to existing learning-based approaches. We also verify that CoSeg can extract high-quality cortical surfaces from fetal brain MRI on which traditional pipelines fail to produce acceptable results.

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arXiv2024

The Multiscale Surface Vision Transformer

Surface meshes are a favoured domain for representing structural and functional information on the human cortex, but their complex topology and geometry pose significant challenges for deep learning analysis. While Transformers have excelled as domain-agnostic architectures for sequence-to-sequence learning, the quadratic cost of the self-attention operation remains an obstacle for many dense prediction tasks. Inspired by some of the latest advances in hierarchical modelling with vision transformers, we introduce the Multiscale Surface Vision Transformer (MS-SiT) as a backbone architecture for surface deep learning. The self-attention mechanism is applied within local-mesh-windows to allow for high-resolution sampling of the underlying data, while a shifted-window strategy improves the sharing of information between windows. Neighbouring patches are successively merged, allowing the MS-SiT to learn hierarchical representations suitable for any prediction task. Results demonstrate that the MS-SiT outperforms existing surface deep learning methods for neonatal phenotyping prediction tasks using the Developing Human Connectome Project (dHCP) dataset. Furthermore, building the MS-SiT backbone into a U-shaped architecture for surface segmentation demonstrates competitive results on cortical parcellation using the UK Biobank (UKB) and manually-annotated MindBoggle datasets. Code and trained models are publicly available at https://github.com/metrics-lab/surface-vision-transformers.

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arXiv2024

Spatio-Temporal Encoding of Brain Dynamics with Surface Masked Autoencoders

The development of robust and generalisable models for encoding the spatio-temporal dynamics of human brain activity is crucial for advancing neuroscientific discoveries. However, significant individual variation in the organisation of the human cerebral cortex makes it difficult to identify population-level trends in these signals. Recently, Surface Vision Transformers (SiTs) have emerged as a promising approach for modelling cortical signals, yet they face some limitations in low-data scenarios due to the lack of inductive biases in their architecture. To address these challenges, this paper proposes the surface Masked AutoEncoder (sMAE) and video surface Masked AutoEncoder (vsMAE) - for multivariate and spatio-temporal pre-training of cortical signals over regular icosahedral grids. These models are trained to reconstruct cortical feature maps from masked versions of the input by learning strong latent representations of cortical structure and function. Such representations translate into better modelling of individual phenotypes and enhanced performance in downstream tasks. The proposed approach was evaluated on cortical phenotype regression using data from the young adult Human Connectome Project (HCP) and developing HCP (dHCP). Results show that (v)sMAE pre-trained models improve phenotyping prediction performance on multiple tasks by $\ge 26\%$, and offer faster convergence relative to models trained from scratch. Finally, we show that pre-training vision transformers on large datasets, such as the UK Biobank (UKB), supports transfer learning to low-data regimes. Our code and pre-trained models are publicly available at https://github.com/metrics-lab/surface-masked-autoencoders .

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arXiv2024

Whole Heart 3D+T Representation Learning Through Sparse 2D Cardiac MR Images

Cardiac Magnetic Resonance (CMR) imaging serves as the gold-standard for evaluating cardiac morphology and function. Typically, a multi-view CMR stack, covering short-axis (SA) and 2/3/4-chamber long-axis (LA) views, is acquired for a thorough cardiac assessment. However, efficiently streamlining the complex, high-dimensional 3D+T CMR data and distilling compact, coherent representation remains a challenge. In this work, we introduce a whole-heart self-supervised learning framework that utilizes masked imaging modeling to automatically uncover the correlations between spatial and temporal patches throughout the cardiac stacks. This process facilitates the generation of meaningful and well-clustered heart representations without relying on the traditionally required, and often costly, labeled data. The learned heart representation can be directly used for various downstream tasks. Furthermore, our method demonstrates remarkable robustness, ensuring consistent representations even when certain CMR planes are missing/flawed. We train our model on 14,000 unlabeled CMR data from UK BioBank and evaluate it on 1,000 annotated data. The proposed method demonstrates superior performance to baselines in tasks that demand comprehensive 3D+T cardiac information, e.g. cardiac phenotype (ejection fraction and ventricle volume) prediction and multi-plane/multi-frame CMR segmentation, highlighting its effectiveness in extracting comprehensive cardiac features that are both anatomically and pathologically relevant.

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arXiv2024

Learning Visual Prompts for Guiding the Attention of Vision Transformers

Visual prompting infuses visual information into the input image to adapt models toward specific predictions and tasks. Recently, manually crafted markers such as red circles are shown to guide the model to attend to a target region on the image. However, these markers only work on models trained with data containing those markers. Moreover, finding these prompts requires guesswork or prior knowledge of the domain on which the model is trained. This work circumvents manual design constraints by proposing to learn the visual prompts for guiding the attention of vision transformers. The learned visual prompt, added to any input image would redirect the attention of the pre-trained vision transformer to its spatial location on the image. Specifically, the prompt is learned in a self-supervised manner without requiring annotations and without fine-tuning the vision transformer. Our experiments demonstrate the effectiveness of the proposed optimization-based visual prompting strategy across various pre-trained vision encoders.

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arXiv2024

Direct Cardiac Segmentation from Undersampled K-space Using Transformers

The prevailing deep learning-based methods of predicting cardiac segmentation involve reconstructed magnetic resonance (MR) images. The heavy dependency of segmentation approaches on image quality significantly limits the acceleration rate in fast MR reconstruction. Moreover, the practice of treating reconstruction and segmentation as separate sequential processes leads to artifact generation and information loss in the intermediate stage. These issues pose a great risk to achieving high-quality outcomes. To leverage the redundant k-space information overlooked in this dual-step pipeline, we introduce a novel approach to directly deriving segmentations from sparse k-space samples using a transformer (DiSK). DiSK operates by globally extracting latent features from 2D+time k-space data with attention blocks and subsequently predicting the segmentation label of query points. We evaluate our model under various acceleration factors (ranging from 4 to 64) and compare against two image-based segmentation baselines. Our model consistently outperforms the baselines in Dice and Hausdorff distances across foreground classes for all presented sampling rates.

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arXiv2024

3DTINC: Time-Equivariant Non-Contrastive Learning for Predicting Disease Progression from Longitudinal OCTs

Self-supervised learning (SSL) has emerged as a powerful technique for improving the efficiency and effectiveness of deep learning models. Contrastive methods are a prominent family of SSL that extract similar representations of two augmented views of an image while pushing away others in the representation space as negatives. However, the state-of-the-art contrastive methods require large batch sizes and augmentations designed for natural images that are impractical for 3D medical images. To address these limitations, we propose a new longitudinal SSL method, 3DTINC, based on non-contrastive learning. It is designed to learn perturbation-invariant features for 3D optical coherence tomography (OCT) volumes, using augmentations specifically designed for OCT. We introduce a new non-contrastive similarity loss term that learns temporal information implicitly from intra-patient scans acquired at different times. Our experiments show that this temporal information is crucial for predicting progression of retinal diseases, such as age-related macular degeneration (AMD). After pretraining with 3DTINC, we evaluated the learned representations and the prognostic models on two large-scale longitudinal datasets of retinal OCTs where we predict the conversion to wet-AMD within a six months interval. Our results demonstrate that each component of our contributions is crucial for learning meaningful representations useful in predicting disease progression from longitudinal volumetric scans.

cs.CV↗

arXiv2024

Detecting and clustering swallow events in esophageal long-term high-resolution manometry

High-resolution manometry (HRM) is the gold standard in diagnosing esophageal motility disorders. As HRM is typically conducted under short-term laboratory settings, intermittently occurring disorders are likely to be missed. Therefore, long-term (up to 24h) HRM (LTHRM) is used to gain detailed insights into the swallowing behavior. However, analyzing the extensive data from LTHRM is challenging and time consuming as medical experts have to analyze the data manually, which is slow and prone to errors. To address this challenge, we propose a Deep Learning based swallowing detection method to accurately identify swallowing events and secondary non-deglutitive-induced esophageal motility disorders in LTHRM data. We then proceed with clustering the identified swallows into distinct classes, which are analyzed by highly experienced clinicians to validate the different swallowing patterns. We evaluate our computational pipeline on a total of 25 LTHRMs, which were meticulously annotated by medical experts. By detecting more than 94% of all relevant swallow events and providing all relevant clusters for a more reliable diagnostic process among experienced clinicians, we are able to demonstrate the effectiveness as well as positive clinical impact of our approach to make LTHRM feasible in clinical care.

cs.CV↗

arXiv2024

Attention-aware non-rigid image registration for accelerated MR imaging

Accurate motion estimation at high acceleration factors enables rapid motion-compensated reconstruction in Magnetic Resonance Imaging (MRI) without compromising the diagnostic image quality. In this work, we introduce an attention-aware deep learning-based framework that can perform non-rigid pairwise registration for fully sampled and accelerated MRI. We extract local visual representations to build similarity maps between the registered image pairs at multiple resolution levels and additionally leverage long-range contextual information using a transformer-based module to alleviate ambiguities in the presence of artifacts caused by undersampling. We combine local and global dependencies to perform simultaneous coarse and fine motion estimation. The proposed method was evaluated on in-house acquired fully sampled and accelerated data of 101 patients and 62 healthy subjects undergoing cardiac and thoracic MRI. The impact of motion estimation accuracy on the downstream task of motion-compensated reconstruction was analyzed. We demonstrate that our model derives reliable and consistent motion fields across different sampling trajectories (Cartesian and radial) and acceleration factors of up to 16x for cardiac motion and 30x for respiratory motion and achieves superior image quality in motion-compensated reconstruction qualitatively and quantitatively compared to conventional and recent deep learning-based approaches. The code is publicly available at https://github.com/lab-midas/GMARAFT.

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arXiv2024

SPINEPS -- Automatic Whole Spine Segmentation of T2-weighted MR images using a Two-Phase Approach to Multi-class Semantic and Instance Segmentation

Purpose. To present SPINEPS, an open-source deep learning approach for semantic and instance segmentation of 14 spinal structures (ten vertebra substructures, intervertebral discs, spinal cord, spinal canal, and sacrum) in whole body T2w MRI. Methods. During this HIPPA-compliant, retrospective study, we utilized the public SPIDER dataset (218 subjects, 63% female) and a subset of the German National Cohort (1423 subjects, mean age 53, 49% female) for training and evaluation. We combined CT and T2w segmentations to train models that segment 14 spinal structures in T2w sagittal scans both semantically and instance-wise. Performance evaluation metrics included Dice similarity coefficient, average symmetrical surface distance, panoptic quality, segmentation quality, and recognition quality. Statistical significance was assessed using the Wilcoxon signed-rank test. An in-house dataset was used to qualitatively evaluate out-of-distribution samples. Results. On the public dataset, our approach outperformed the baseline (instance-wise vertebra dice score 0.929 vs. 0.907, p-value<0.001). Training on auto-generated annotations and evaluating on manually corrected test data from the GNC yielded global dice scores of 0.900 for vertebrae, 0.960 for intervertebral discs, and 0.947 for the spinal canal. Incorporating the SPIDER dataset during training increased these scores to 0.920, 0.967, 0.958, respectively. Conclusions. The proposed segmentation approach offers robust segmentation of 14 spinal structures in T2w sagittal images, including the spinal cord, spinal canal, intervertebral discs, endplate, sacrum, and vertebrae. The approach yields both a semantic and instance mask as output, thus being easy to utilize. This marks the first publicly available algorithm for whole spine segmentation in sagittal T2w MR imaging.

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arXiv2024

Incentivising the federation: gradient-based metrics for data selection and valuation in private decentralised training

Obtaining high-quality data for collaborative training of machine learning models can be a challenging task due to A) regulatory concerns and B) a lack of data owner incentives to participate. The first issue can be addressed through the combination of distributed machine learning techniques (e.g. federated learning) and privacy enhancing technologies (PET), such as the differentially private (DP) model training. The second challenge can be addressed by rewarding the participants for giving access to data which is beneficial to the training model, which is of particular importance in federated settings, where the data is unevenly distributed. However, DP noise can adversely affect the underrepresented and the atypical (yet often informative) data samples, making it difficult to assess their usefulness. In this work, we investigate how to leverage gradient information to permit the participants of private training settings to select the data most beneficial for the jointly trained model. We assess two such methods, namely variance of gradients (VoG) and the privacy loss-input susceptibility score (PLIS). We show that these techniques can provide the federated clients with tools for principled data selection even in stricter privacy settings.

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arXiv2024

Intensity-based 3D motion correction for cardiac MR images

Cardiac magnetic resonance (CMR) image acquisition requires subjects to hold their breath while 2D cine images are acquired. This process assumes that the heart remains in the same position across all slices. However, differences in breathhold positions or patient motion introduce 3D slice misalignments. In this work, we propose an algorithm that simultaneously aligns all SA and LA slices by maximizing the pair-wise intensity agreement between their intersections. Unlike previous works, our approach is formulated as a subject-specific optimization problem and requires no prior knowledge of the underlying anatomy. We quantitatively demonstrate that the proposed method is robust against a large range of rotations and translations by synthetically misaligning 10 motion-free datasets and aligning them back using the proposed method.

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