Daniel Rueckert

Chen Chen, Zeju Li, Cheng Ouyang et al.

Convolutional neural networks (CNNs) have achieved remarkable segmentation accuracy on benchmark datasets where training and test sets are from the same domain, yet their performance can degrade significantly on unseen domains, which hinders the deployment of CNNs in many clinical scenarios. Most existing works improve model out-of-domain (OOD) robustness by collecting multi-domain datasets for training, which is expensive and may not always be feasible due to privacy and logistical issues. In this work, we focus on improving model robustness using a single-domain dataset only. We propose a novel data augmentation framework called MaxStyle, which maximizes the effectiveness of style augmentation for model OOD performance. It attaches an auxiliary style-augmented image decoder to a segmentation network for robust feature learning and data augmentation. Importantly, MaxStyle augments data with improved image style diversity and hardness, by expanding the style space with noise and searching for the worst-case style composition of latent features via adversarial training. With extensive experiments on multiple public cardiac and prostate MR datasets, we demonstrate that MaxStyle leads to significantly improved out-of-distribution robustness against unseen corruptions as well as common distribution shifts across multiple, different, unseen sites and unknown image sequences under both low- and high-training data settings. The code can be found at https://github.com/cherise215/MaxStyle.

Julian McGinnis, Suprosanna Shit, Hongwei Bran Li et al.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

Karim Lekadir, Aasa Feragen, Abdul Joseph Fofanah et al. · eth-zurich

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.

Felix Meissen, Johannes Paetzold, Georgios Kaissis et al.

Unsupervised Anomaly Detection has become a popular method to detect pathologies in medical images as it does not require supervision or labels for training. Most commonly, the anomaly detection model generates a "normal" version of an input image, and the pixel-wise $l^p$-difference of the two is used to localize anomalies. However, large residuals often occur due to imperfect reconstruction of the complex anatomical structures present in most medical images. This method also fails to detect anomalies that are not characterized by large intensity differences to the surrounding tissue. We propose to tackle this problem using a feature-mapping function that transforms the input intensity images into a space with multiple channels where anomalies can be detected along different discriminative feature maps extracted from the original image. We then train an Autoencoder model in this space using structural similarity loss that does not only consider differences in intensity but also in contrast and structure. Our method significantly increases performance on two medical data sets for brain MRI. Code and experiments are available at https://github.com/FeliMe/feature-autoencoder

Jiazhen Pan, Wenqi Huang, Daniel Rueckert et al.

In cardiac CINE, motion-compensated MR reconstruction (MCMR) is an effective approach to address highly undersampled acquisitions by incorporating motion information between frames. In this work, we propose a novel perspective for addressing the MCMR problem and a more integrated and efficient solution to the MCMR field. Contrary to state-of-the-art (SOTA) MCMR methods which break the original problem into two sub-optimization problems, i.e. motion estimation and reconstruction, we formulate this problem as a single entity with one single optimization. Our approach is unique in that the motion estimation is directly driven by the ultimate goal, reconstruction, but not by the canonical motion-warping loss (similarity measurement between motion-warped images and target images). We align the objectives of motion estimation and reconstruction, eliminating the drawbacks of artifacts-affected motion estimation and therefore error-propagated reconstruction. Further, we can deliver high-quality reconstruction and realistic motion without applying any regularization/smoothness loss terms, circumventing the non-trivial weighting factor tuning. We evaluate our method on two datasets: 1) an in-house acquired 2D CINE dataset for the retrospective study and 2) the public OCMR cardiac dataset for the prospective study. The conducted experiments indicate that the proposed MCMR framework can deliver artifact-free motion estimation and high-quality MR images even for imaging accelerations up to 20x, outperforming SOTA non-MCMR and MCMR methods in both qualitative and quantitative evaluation across all experiments. The code is available at https://github.com/JZPeterPan/MCMR-Recon-Driven-Motion.

Özgün Turgut, Philip Müller, Paul Hager et al.

Cardiovascular diseases (CVD) can be diagnosed using various diagnostic modalities. The electrocardiogram (ECG) is a cost-effective and widely available diagnostic aid that provides functional information of the heart. However, its ability to classify and spatially localise CVD is limited. In contrast, cardiac magnetic resonance (CMR) imaging provides detailed structural information of the heart and thus enables evidence-based diagnosis of CVD, but long scan times and high costs limit its use in clinical routine. In this work, we present a deep learning strategy for cost-effective and comprehensive cardiac screening solely from ECG. Our approach combines multimodal contrastive learning with masked data modelling to transfer domain-specific information from CMR imaging to ECG representations. In extensive experiments using data from 40,044 UK Biobank subjects, we demonstrate the utility and generalisability of our method for subject-specific risk prediction of CVD and the prediction of cardiac phenotypes using only ECG data. Specifically, our novel multimodal pre-training paradigm improves performance by up to 12.19 % for risk prediction and 27.59 % for phenotype prediction. In a qualitative analysis, we demonstrate that our learned ECG representations incorporate information from CMR image regions of interest. Our entire pipeline is publicly available at https://github.com/oetu/MMCL-ECG-CMR.

Tim Tanida, Philip Müller, Georgios Kaissis et al.

The automatic generation of radiology reports has the potential to assist radiologists in the time-consuming task of report writing. Existing methods generate the full report from image-level features, failing to explicitly focus on anatomical regions in the image. We propose a simple yet effective region-guided report generation model that detects anatomical regions and then describes individual, salient regions to form the final report. While previous methods generate reports without the possibility of human intervention and with limited explainability, our method opens up novel clinical use cases through additional interactive capabilities and introduces a high degree of transparency and explainability. Comprehensive experiments demonstrate our method's effectiveness in report generation, outperforming previous state-of-the-art models, and highlight its interactive capabilities. The code and checkpoints are available at https://github.com/ttanida/rgrg .

Simon Dahan, Logan Z. J. Williams, Daniel Rueckert et al.

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.

Chinmay Prabhakar, Hongwei Bran Li, Johannes C. Paetzold et al.

Multiple Sclerosis (MS) is a severe neurological disease characterized by inflammatory lesions in the central nervous system. Hence, predicting inflammatory disease activity is crucial for disease assessment and treatment. However, MS lesions can occur throughout the brain and vary in shape, size and total count among patients. The high variance in lesion load and locations makes it challenging for machine learning methods to learn a globally effective representation of whole-brain MRI scans to assess and predict disease. Technically it is non-trivial to incorporate essential biomarkers such as lesion load or spatial proximity. Our work represents the first attempt to utilize graph neural networks (GNN) to aggregate these biomarkers for a novel global representation. We propose a two-stage MS inflammatory disease activity prediction approach. First, a 3D segmentation network detects lesions, and a self-supervised algorithm extracts their image features. Second, the detected lesions are used to build a patient graph. The lesions act as nodes in the graph and are initialized with image features extracted in the first stage. Finally, the lesions are connected based on their spatial proximity and the inflammatory disease activity prediction is formulated as a graph classification task. Furthermore, we propose a self-pruning strategy to auto-select the most critical lesions for prediction. Our proposed method outperforms the existing baseline by a large margin (AUCs of 0.67 vs. 0.61 and 0.66 vs. 0.60 for one-year and two-year inflammatory disease activity, respectively). Finally, our proposed method enjoys inherent explainability by assigning an importance score to each lesion for the overall prediction. Code is available at https://github.com/chinmay5/ms_ida.git

Tobias Bernecker, Annette Peters, Christopher L. Schlett et al. · eth-zurich

Given the high incidence and effective treatment options for liver diseases, they are of great socioeconomic importance. One of the most common methods for analyzing CT and MRI images for diagnosis and follow-up treatment is liver segmentation. Recent advances in deep learning have demonstrated encouraging results for automatic liver segmentation. Despite this, their success depends primarily on the availability of an annotated database, which is often not available because of privacy concerns. Federated Learning has been recently proposed as a solution to alleviate these challenges by training a shared global model on distributed clients without access to their local databases. Nevertheless, Federated Learning does not perform well when it is trained on a high degree of heterogeneity of image data due to multi-modal imaging, such as CT and MRI, and multiple scanner types. To this end, we propose Fednorm and its extension \fednormp, two Federated Learning algorithms that use a modality-based normalization technique. Specifically, Fednorm normalizes the features on a client-level, while Fednorm+ employs the modality information of single slices in the feature normalization. Our methods were validated using 428 patients from six publicly available databases and compared to state-of-the-art Federated Learning algorithms and baseline models in heterogeneous settings (multi-institutional, multi-modal data). The experimental results demonstrate that our methods show an overall acceptable performance, achieve Dice per patient scores up to 0.961, consistently outperform locally trained models, and are on par or slightly better than centralized models.

Simon Dahan, Logan Z. J. Williams, Abdulah Fawaz et al.

The extension of convolutional neural networks (CNNs) to non-Euclidean geometries has led to multiple frameworks for studying manifolds. Many of those methods have shown design limitations resulting in poor modelling of long-range associations, as the generalisation of convolutions to irregular surfaces is non-trivial. Recent state-of-the-art performance of Vision Transformers (ViTs) demonstrates that a general-purpose architecture, which implements self-attention, could replace the local feature learning operations of CNNs. Motivated by the success of attention-modelling in computer vision, we extend ViTs to surfaces by reformulating the task of surface learning as a sequence-to-sequence problem and propose a patching mechanism for surface meshes. We validate the performance of the proposed Surface Vision Transformer (SiT) on two brain age prediction tasks in the developing Human Connectome Project (dHCP) dataset and investigate the impact of pre-training on model performance. Experiments show that the SiT outperforms many surface CNNs, while indicating some evidence of general transformation invariance. Code available at https://github.com/metrics-lab/surface-vision-transformers

Dmitrii Usynin, Helena Klause, Johannes C. Paetzold et al.

In federated learning for medical image analysis, the safety of the learning protocol is paramount. Such settings can often be compromised by adversaries that target either the private data used by the federation or the integrity of the model itself. This requires the medical imaging community to develop mechanisms to train collaborative models that are private and robust against adversarial data. In response to these challenges, we propose a practical open-source framework to study the effectiveness of combining differential privacy, model compression and adversarial training to improve the robustness of models against adversarial samples under train- and inference-time attacks. Using our framework, we achieve competitive model performance, a significant reduction in model's size and an improved empirical adversarial robustness without a severe performance degradation, critical in medical image analysis.

Mengyun Qiao, Berke Doga Basaran, Huaqi Qiu et al.

Cardiovascular disease, the leading cause of death globally, is an age-related disease. Understanding the morphological and functional changes of the heart during ageing is a key scientific question, the answer to which will help us define important risk factors of cardiovascular disease and monitor disease progression. In this work, we propose a novel conditional generative model to describe the changes of 3D anatomy of the heart during ageing. The proposed model is flexible and allows integration of multiple clinical factors (e.g. age, gender) into the generating process. We train the model on a large-scale cross-sectional dataset of cardiac anatomies and evaluate on both cross-sectional and longitudinal datasets. The model demonstrates excellent performance in predicting the longitudinal evolution of the ageing heart and modelling its data distribution. The codes are available at https://github.com/MengyunQ/AgeHeart.

Simon Dahan, Logan Z. J. Williams, Yourong Guo et al.

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 .

Simon Dahan, Hao Xu, Logan Z. J. Williams et al.

Recent state-of-the-art performances of Vision Transformers (ViT) in computer vision tasks demonstrate that a general-purpose architecture, which implements long-range self-attention, could replace the local feature learning operations of convolutional neural networks. In this paper, we extend ViTs to surfaces by reformulating the task of surface learning as a sequence-to-sequence learning problem, by proposing patching mechanisms for general surface meshes. Sequences of patches are then processed by a transformer encoder and used for classification or regression. We validate our method on a range of different biomedical surface domains and tasks: brain age prediction in the developing Human Connectome Project (dHCP), fluid intelligence prediction in the Human Connectome Project (HCP), and coronary artery calcium score classification using surfaces from the Scottish Computed Tomography of the Heart (SCOT-HEART) dataset, and investigate the impact of pretraining and data augmentation on model performance. Results suggest that Surface Vision Transformers (SiT) demonstrate consistent improvement over geometric deep learning methods for brain age and fluid intelligence prediction and achieve comparable performance on calcium score classification to standard metrics used in clinical practice. Furthermore, analysis of transformer attention maps offers clear and individualised predictions of the features driving each task. Code is available on Github: https://github.com/metrics-lab/surface-vision-transformers

Ioannis Lagogiannis, Felix Meissen, Georgios Kaissis et al.

Deep unsupervised approaches are gathering increased attention for applications such as pathology detection and segmentation in medical images since they promise to alleviate the need for large labeled datasets and are more generalizable than their supervised counterparts in detecting any kind of rare pathology. As the Unsupervised Anomaly Detection (UAD) literature continuously grows and new paradigms emerge, it is vital to continuously evaluate and benchmark new methods in a common framework, in order to reassess the state-of-the-art (SOTA) and identify promising research directions. To this end, we evaluate a diverse selection of cutting-edge UAD methods on multiple medical datasets, comparing them against the established SOTA in UAD for brain MRI. Our experiments demonstrate that newly developed feature-modeling methods from the industrial and medical literature achieve increased performance compared to previous work and set the new SOTA in a variety of modalities and datasets. Additionally, we show that such methods are capable of benefiting from recently developed self-supervised pre-training algorithms, further increasing their performance. Finally, we perform a series of experiments in order to gain further insights into some unique characteristics of selected models and datasets. Our code can be found under https://github.com/iolag/UPD_study/.

Kerstin Hammernik, Thomas Küstner, Burhaneddin Yaman et al.

Physics-driven deep learning methods have emerged as a powerful tool for computational magnetic resonance imaging (MRI) problems, pushing reconstruction performance to new limits. This article provides an overview of the recent developments in incorporating physics information into learning-based MRI reconstruction. We consider inverse problems with both linear and non-linear forward models for computational MRI, and review the classical approaches for solving these. We then focus on physics-driven deep learning approaches, covering physics-driven loss functions, plug-and-play methods, generative models, and unrolled networks. We highlight domain-specific challenges such as real- and complex-valued building blocks of neural networks, and translational applications in MRI with linear and non-linear forward models. Finally, we discuss common issues and open challenges, and draw connections to the importance of physics-driven learning when combined with other downstream tasks in the medical imaging pipeline.

Matan Atad, David Schinz, Hendrik Moeller et al.

Counterfactual explanations (CEs) aim to enhance the interpretability of machine learning models by illustrating how alterations in input features would affect the resulting predictions. Common CE approaches require an additional model and are typically constrained to binary counterfactuals. In contrast, we propose a novel method that operates directly on the latent space of a generative model, specifically a Diffusion Autoencoder (DAE). This approach offers inherent interpretability by enabling the generation of CEs and the continuous visualization of the model's internal representation across decision boundaries. Our method leverages the DAE's ability to encode images into a semantically rich latent space in an unsupervised manner, eliminating the need for labeled data or separate feature extraction models. We show that these latent representations are helpful for medical condition classification and the ordinal regression of severity pathologies, such as vertebral compression fractures (VCF) and diabetic retinopathy (DR). Beyond binary CEs, our method supports the visualization of ordinal CEs using a linear model, providing deeper insights into the model's decision-making process and enhancing interpretability. Experiments across various medical imaging datasets demonstrate the method's advantages in interpretability and versatility. The linear manifold of the DAE's latent space allows for meaningful interpolation and manipulation, making it a powerful tool for exploring medical image properties. Our code is available at https://doi.org/10.5281/zenodo.13859266.

Paul Hager, Martin J. Menten, Daniel Rueckert

Medical datasets and especially biobanks, often contain extensive tabular data with rich clinical information in addition to images. In practice, clinicians typically have less data, both in terms of diversity and scale, but still wish to deploy deep learning solutions. Combined with increasing medical dataset sizes and expensive annotation costs, the necessity for unsupervised methods that can pretrain multimodally and predict unimodally has risen. To address these needs, we propose the first self-supervised contrastive learning framework that takes advantage of images and tabular data to train unimodal encoders. Our solution combines SimCLR and SCARF, two leading contrastive learning strategies, and is simple and effective. In our experiments, we demonstrate the strength of our framework by predicting risks of myocardial infarction and coronary artery disease (CAD) using cardiac MR images and 120 clinical features from 40,000 UK Biobank subjects. Furthermore, we show the generalizability of our approach to natural images using the DVM car advertisement dataset. We take advantage of the high interpretability of tabular data and through attribution and ablation experiments find that morphometric tabular features, describing size and shape, have outsized importance during the contrastive learning process and improve the quality of the learned embeddings. Finally, we introduce a novel form of supervised contrastive learning, label as a feature (LaaF), by appending the ground truth label as a tabular feature during multimodal pretraining, outperforming all supervised contrastive baselines.

Bailiang Jian, Jiazhen Pan, Morteza Ghahremani et al.

Our findings indicate that adopting "advanced" computational elements fails to significantly improve registration accuracy. Instead, well-established registration-specific designs offer fair improvements, enhancing results by a marginal 1.5\% over the baseline. Our findings emphasize the importance of rigorous, unbiased evaluation and contribution disentanglement of all low- and high-level registration components, rather than simply following the computer vision trends with "more advanced" computational blocks. We advocate for simpler yet effective solutions and novel evaluation metrics that go beyond conventional registration accuracy, warranting further research across diverse organs and modalities. The code is available at \url{https://github.com/BailiangJ/rethink-reg}.

Hendrik Möller, Hanna Schoen, Robert Graf et al.

The human spine commonly consists of seven cervical, twelve thoracic, and five lumbar vertebrae. However, enumeration anomalies may result in individuals having eleven or thirteen thoracic vertebrae and four or six lumbar vertebrae. Although the identification of enumeration anomalies has potential clinical implications for chronic back pain and operation planning, the thoracolumbar junction is often poorly assessed and rarely described in clinical reports. Additionally, even though multiple deep-learning-based vertebra labeling algorithms exist, there is a lack of methods to automatically label enumeration anomalies. Our work closes that gap by introducing "Vertebra Identification with Anomaly Handling" (VERIDAH), a novel vertebra labeling algorithm based on multiple classification heads combined with a weighted vertebra sequence prediction algorithm. We show that our approach surpasses existing models on T2w TSE sagittal (98.30% vs. 94.24% of subjects with all vertebrae correctly labeled, p < 0.001) and CT imaging (99.18% vs. 77.26% of subjects with all vertebrae correctly labeled, p < 0.001) and works in arbitrary field-of-view images. VERIDAH correctly labeled the presence 2 Möller et al. of thoracic enumeration anomalies in 87.80% and 96.30% of T2w and CT images, respectively, and lumbar enumeration anomalies in 94.48% and 97.22% for T2w and CT, respectively. Our code and models are available at: https://github.com/Hendrik-code/spineps.

Wenqi Huang, Hongwei Li, Jiazhen Pan et al.

In this work, we propose a novel image reconstruction framework that directly learns a neural implicit representation in k-space for ECG-triggered non-Cartesian Cardiac Magnetic Resonance Imaging (CMR). While existing methods bin acquired data from neighboring time points to reconstruct one phase of the cardiac motion, our framework allows for a continuous, binning-free, and subject-specific k-space representation.We assign a unique coordinate that consists of time, coil index, and frequency domain location to each sampled k-space point. We then learn the subject-specific mapping from these unique coordinates to k-space intensities using a multi-layer perceptron with frequency domain regularization. During inference, we obtain a complete k-space for Cartesian coordinates and an arbitrary temporal resolution. A simple inverse Fourier transform recovers the image, eliminating the need for density compensation and costly non-uniform Fourier transforms for non-Cartesian data. This novel imaging framework was tested on 42 radially sampled datasets from 6 subjects. The proposed method outperforms other techniques qualitatively and quantitatively using data from four and one heartbeat(s) and 30 cardiac phases. Our results for one heartbeat reconstruction of 50 cardiac phases show improved artifact removal and spatio-temporal resolution, leveraging the potential for real-time CMR.

Aswathi Varma, Suprosanna Shit, Chinmay Prabhakar et al.

Vision Transformers (ViTs) have emerged as the state-of-the-art architecture in representation learning, leveraging self-attention mechanisms to excel in various tasks. ViTs split images into fixed-size patches, constraining them to a predefined size and necessitating pre-processing steps like resizing, padding, or cropping. This poses challenges in medical imaging, particularly with irregularly shaped structures like tumors. A fixed bounding box crop size produces input images with highly variable foreground-to-background ratios. Resizing medical images can degrade information and introduce artefacts, impacting diagnosis. Hence, tailoring variable-sized crops to regions of interest can enhance feature representation capabilities. Moreover, large images are computationally expensive, and smaller sizes risk information loss, presenting a computation-accuracy tradeoff. We propose VariViT, an improved ViT model crafted to handle variable image sizes while maintaining a consistent patch size. VariViT employs a novel positional embedding resizing scheme for a variable number of patches. We also implement a new batching strategy within VariViT to reduce computational complexity, resulting in faster training and inference times. In our evaluations on two 3D brain MRI datasets, VariViT surpasses vanilla ViTs and ResNet in glioma genotype prediction and brain tumor classification. It achieves F1-scores of 75.5% and 76.3%, respectively, learning more discriminative features. Our proposed batching strategy reduces computation time by up to 30% compared to conventional architectures. These findings underscore the efficacy of VariViT in image representation learning. Our code can be found here: https://github.com/Aswathi-Varma/varivit

Alina F. Dima, Veronika A. Zimmer, Martin J. Menten et al.

Automated segmentation of the blood vessels in 3D volumes is an essential step for the quantitative diagnosis and treatment of many vascular diseases. 3D vessel segmentation is being actively investigated in existing works, mostly in deep learning approaches. However, training 3D deep networks requires large amounts of manual 3D annotations from experts, which are laborious to obtain. This is especially the case for 3D vessel segmentation, as vessels are sparse yet spread out over many slices and disconnected when visualized in 2D slices. In this work, we propose a novel method to segment the 3D peripancreatic arteries solely from one annotated 2D projection per training image with depth supervision. We perform extensive experiments on the segmentation of peripancreatic arteries on 3D contrast-enhanced CT images and demonstrate how well we capture the rich depth information from 2D projections. We demonstrate that by annotating a single, randomly chosen projection for each training sample, we obtain comparable performance to annotating multiple 2D projections, thereby reducing the annotation effort. Furthermore, by mapping the 2D labels to the 3D space using depth information and incorporating this into training, we almost close the performance gap between 3D supervision and 2D supervision. Our code is available at: https://github.com/alinafdima/3Dseg-mip-depth.

Linus Kreitner, Johannes C. Paetzold, Nikolaus Rauch et al.

Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the visible blood vessels is a common first step when extracting quantitative biomarkers from these images. Classical segmentation algorithms based on thresholding are strongly affected by image artifacts and limited signal-to-noise ratio. The use of modern, deep learning-based segmentation methods has been inhibited by a lack of large datasets with detailed annotations of the blood vessels. To address this issue, recent work has employed transfer learning, where a segmentation network is trained on synthetic OCTA images and is then applied to real data. However, the previously proposed simulations fail to faithfully model the retinal vasculature and do not provide effective domain adaptation. Because of this, current methods are unable to fully segment the retinal vasculature, in particular the smallest capillaries. In this work, we present a lightweight simulation of the retinal vascular network based on space colonization for faster and more realistic OCTA synthesis. We then introduce three contrast adaptation pipelines to decrease the domain gap between real and artificial images. We demonstrate the superior segmentation performance of our approach in extensive quantitative and qualitative experiments on three public datasets that compare our method to traditional computer vision algorithms and supervised training using human annotations. Finally, we make our entire pipeline publicly available, including the source code, pretrained models, and a large dataset of synthetic OCTA images.

Helena Klause, Alexander Ziller, Daniel Rueckert et al.

The training of neural networks with Differentially Private Stochastic Gradient Descent offers formal Differential Privacy guarantees but introduces accuracy trade-offs. In this work, we propose to alleviate these trade-offs in residual networks with Group Normalisation through a simple architectural modification termed ScaleNorm by which an additional normalisation layer is introduced after the residual block's addition operation. Our method allows us to further improve on the recently reported state-of-the art on CIFAR-10, achieving a top-1 accuracy of 82.5% (ε=8.0) when trained from scratch.

Tobias Rueckert, Daniel Rueckert, Christoph Palm

In the field of computer- and robot-assisted minimally invasive surgery, enormous progress has been made in recent years based on the recognition of surgical instruments in endoscopic images and videos. In particular, the determination of the position and type of instruments is of great interest. Current work involves both spatial and temporal information, with the idea that predicting the movement of surgical tools over time may improve the quality of the final segmentations. The provision of publicly available datasets has recently encouraged the development of new methods, mainly based on deep learning. In this review, we identify and characterize datasets used for method development and evaluation and quantify their frequency of use in the literature. We further present an overview of the current state of research regarding the segmentation and tracking of minimally invasive surgical instruments in endoscopic images and videos. The paper focuses on methods that work purely visually, without markers of any kind attached to the instruments, considering both single-frame semantic and instance segmentation approaches, as well as those that incorporate temporal information. The publications analyzed were identified through the platforms Google Scholar, Web of Science, and PubMed. The search terms used were "instrument segmentation", "instrument tracking", "surgical tool segmentation", and "surgical tool tracking", resulting in a total of 741 articles published between 01/2015 and 07/2023, of which 123 were included using systematic selection criteria. A discussion of the reviewed literature is provided, highlighting existing shortcomings and emphasizing the available potential for future developments.

Veronika A. Zimmer, Alberto Gomez, Emily Skelton et al.

Automatic segmentation of the placenta in fetal ultrasound (US) is challenging due to the (i) high diversity of placenta appearance, (ii) the restricted quality in US resulting in highly variable reference annotations, and (iii) the limited field-of-view of US prohibiting whole placenta assessment at late gestation. In this work, we address these three challenges with a multi-task learning approach that combines the classification of placental location (e.g., anterior, posterior) and semantic placenta segmentation in a single convolutional neural network. Through the classification task the model can learn from larger and more diverse datasets while improving the accuracy of the segmentation task in particular in limited training set conditions. With this approach we investigate the variability in annotations from multiple raters and show that our automatic segmentations (Dice of 0.86 for anterior and 0.83 for posterior placentas) achieve human-level performance as compared to intra- and inter-observer variability. Lastly, our approach can deliver whole placenta segmentation using a multi-view US acquisition pipeline consisting of three stages: multi-probe image acquisition, image fusion and image segmentation. This results in high quality segmentation of larger structures such as the placenta in US with reduced image artifacts which are beyond the field-of-view of single probes.

Qingjie Meng, Chen Qin, Wenjia Bai et al.

Recovering the 3D motion of the heart from cine cardiac magnetic resonance (CMR) imaging enables the assessment of regional myocardial function and is important for understanding and analyzing cardiovascular disease. However, 3D cardiac motion estimation is challenging because the acquired cine CMR images are usually 2D slices which limit the accurate estimation of through-plane motion. To address this problem, we propose a novel multi-view motion estimation network (MulViMotion), which integrates 2D cine CMR images acquired in short-axis and long-axis planes to learn a consistent 3D motion field of the heart. In the proposed method, a hybrid 2D/3D network is built to generate dense 3D motion fields by learning fused representations from multi-view images. To ensure that the motion estimation is consistent in 3D, a shape regularization module is introduced during training, where shape information from multi-view images is exploited to provide weak supervision to 3D motion estimation. We extensively evaluate the proposed method on 2D cine CMR images from 580 subjects of the UK Biobank study for 3D motion tracking of the left ventricular myocardium. Experimental results show that the proposed method quantitatively and qualitatively outperforms competing methods.

Chen Qin, Shuo Wang, Chen Chen et al.

Myocardial motion and deformation are rich descriptors that characterize cardiac function. Image registration, as the most commonly used technique for myocardial motion tracking, is an ill-posed inverse problem which often requires prior assumptions on the solution space. In contrast to most existing approaches which impose explicit generic regularization such as smoothness, in this work we propose a novel method that can implicitly learn an application-specific biomechanics-informed prior and embed it into a neural network-parameterized transformation model. Particularly, the proposed method leverages a variational autoencoder-based generative model to learn a manifold for biomechanically plausible deformations. The motion tracking then can be performed via traversing the learnt manifold to search for the optimal transformations while considering the sequence information. The proposed method is validated on three public cardiac cine MRI datasets with comprehensive evaluations. The results demonstrate that the proposed method can outperform other approaches, yielding higher motion tracking accuracy with reasonable volume preservation and better generalizability to varying data distributions. It also enables better estimates of myocardial strains, which indicates the potential of the method in characterizing spatiotemporal signatures for understanding cardiovascular diseases.

Cosmin I Bercea, Benedikt Wiestler, Daniel Rueckert et al.

Early and accurate disease detection is crucial for patient management and successful treatment outcomes. However, the automatic identification of anomalies in medical images can be challenging. Conventional methods rely on large labeled datasets which are difficult to obtain. To overcome these limitations, we introduce a novel unsupervised approach, called PHANES (Pseudo Healthy generative networks for ANomaly Segmentation). Our method has the capability of reversing anomalies, i.e., preserving healthy tissue and replacing anomalous regions with pseudo-healthy (PH) reconstructions. Unlike recent diffusion models, our method does not rely on a learned noise distribution nor does it introduce random alterations to the entire image. Instead, we use latent generative networks to create masks around possible anomalies, which are refined using inpainting generative networks. We demonstrate the effectiveness of PHANES in detecting stroke lesions in T1w brain MRI datasets and show significant improvements over state-of-the-art (SOTA) methods. We believe that our proposed framework will open new avenues for interpretable, fast, and accurate anomaly segmentation with the potential to support various clinical-oriented downstream tasks.

Dmitrii Usynin, Daniel Rueckert, Georgios Kaissis

Collaborative machine learning settings like federated learning can be susceptible to adversarial interference and attacks. One class of such attacks is termed model inversion attacks, characterised by the adversary reverse-engineering the model to extract representations and thus disclose the training data. Prior implementations of this attack typically only rely on the captured data (i.e. the shared gradients) and do not exploit the data the adversary themselves control as part of the training consortium. In this work, we propose a novel model inversion framework that builds on the foundations of gradient-based model inversion attacks, but additionally relies on matching the features and the style of the reconstructed image to data that is controlled by an adversary. Our technique outperforms existing gradient-based approaches both qualitatively and quantitatively, while still maintaining the same honest-but-curious threat model, allowing the adversary to obtain enhanced reconstructions while remaining concealed.

Athanasios Vlontzos, Daniel Rueckert, Bernhard Kainz

Medical image analysis is a vibrant research area that offers doctors and medical practitioners invaluable insight and the ability to accurately diagnose and monitor disease. Machine learning provides an additional boost for this area. However, machine learning for medical image analysis is particularly vulnerable to natural biases like domain shifts that affect algorithmic performance and robustness. In this paper we analyze machine learning for medical image analysis within the framework of Technology Readiness Levels and review how causal analysis methods can fill a gap when creating robust and adaptable medical image analysis algorithms. We review methods using causality in medical imaging AI/ML and find that causal analysis has the potential to mitigate critical problems for clinical translation but that uptake and clinical downstream research has been limited so far.

Martin J. Menten, Johannes C. Paetzold, Alina Dima et al.

Optical coherence tomography angiography (OCTA) can non-invasively image the eye's circulatory system. In order to reliably characterize the retinal vasculature, there is a need to automatically extract quantitative metrics from these images. The calculation of such biomarkers requires a precise semantic segmentation of the blood vessels. However, deep-learning-based methods for segmentation mostly rely on supervised training with voxel-level annotations, which are costly to obtain. In this work, we present a pipeline to synthesize large amounts of realistic OCTA images with intrinsically matching ground truth labels; thereby obviating the need for manual annotation of training data. Our proposed method is based on two novel components: 1) a physiology-based simulation that models the various retinal vascular plexuses and 2) a suite of physics-based image augmentations that emulate the OCTA image acquisition process including typical artifacts. In extensive benchmarking experiments, we demonstrate the utility of our synthetic data by successfully training retinal vessel segmentation algorithms. Encouraged by our method's competitive quantitative and superior qualitative performance, we believe that it constitutes a versatile tool to advance the quantitative analysis of OCTA images.

Tamara T. Mueller, Dmitrii Usynin, Johannes C. Paetzold et al.

In this work, we study the applications of differential privacy (DP) in the context of graph-structured data. We discuss the formulations of DP applicable to the publication of graphs and their associated statistics as well as machine learning on graph-based data, including graph neural networks (GNNs). The formulation of DP in the context of graph-structured data is difficult, as individual data points are interconnected (often non-linearly or sparsely). This connectivity complicates the computation of individual privacy loss in differentially private learning. The problem is exacerbated by an absence of a single, well-established formulation of DP in graph settings. This issue extends to the domain of GNNs, rendering private machine learning on graph-structured data a challenging task. A lack of prior systematisation work motivated us to study graph-based learning from a privacy perspective. In this work, we systematise different formulations of DP on graphs, discuss challenges and promising applications, including the GNN domain. We compare and separate works into graph analysis tasks and graph learning tasks with GNNs. Finally, we conclude our work with a discussion of open questions and potential directions for further research in this area.

Felix Meissen, Philip Müller, Georgios Kaissis et al.

Detection of pathologies is a fundamental task in medical imaging and the evaluation of algorithms that can perform this task automatically is crucial. However, current object detection metrics for natural images do not reflect the specific clinical requirements in pathology detection sufficiently. To tackle this problem, we propose Robust Detection Outcome (RoDeO); a novel metric for evaluating algorithms for pathology detection in medical images, especially in chest X-rays. RoDeO evaluates different errors directly and individually, and reflects clinical needs better than current metrics. Extensive evaluation on the ChestX-ray8 dataset shows the superiority of our metrics compared to existing ones. We released the code at https://github.com/FeliMe/RoDeO and published RoDeO as pip package (rodeometric).

Adam Marcus, Paul Bentley, Daniel Rueckert

The cornerstone of stroke care is expedient management that varies depending on the time since stroke onset. Consequently, clinical decision making is centered on accurate knowledge of timing and often requires a radiologist to interpret Computed Tomography (CT) of the brain to confirm the occurrence and age of an event. These tasks are particularly challenging due to the subtle expression of acute ischemic lesions and the dynamic nature of their appearance. Automation efforts have not yet applied deep learning to estimate lesion age and treated these two tasks independently, so, have overlooked their inherent complementary relationship. To leverage this, we propose a novel end-to-end multi-task transformer-based network optimized for concurrent segmentation and age estimation of cerebral ischemic lesions. By utilizing gated positional self-attention and CT-specific data augmentation, the proposed method can capture long-range spatial dependencies while maintaining its ability to be trained from scratch under low-data regimes commonly found in medical imaging. Furthermore, to better combine multiple predictions, we incorporate uncertainty by utilizing quantile loss to facilitate estimating a probability density function of lesion age. The effectiveness of our model is then extensively evaluated on a clinical dataset consisting of 776 CT images from two medical centers. Experimental results demonstrate that our method obtains promising performance, with an area under the curve (AUC) of 0.933 for classifying lesion ages <=4.5 hours compared to 0.858 using a conventional approach, and outperforms task-specific state-of-the-art algorithms.

Jiazhen Pan, Daniel Rueckert, Thomas Küstner et al.

Motion-compensated MR reconstruction (MCMR) is a powerful concept with considerable potential, consisting of two coupled sub-problems: Motion estimation, assuming a known image, and image reconstruction, assuming known motion. In this work, we propose a learning-based self-supervised framework for MCMR, to efficiently deal with non-rigid motion corruption in cardiac MR imaging. Contrary to conventional MCMR methods in which the motion is estimated prior to reconstruction and remains unchanged during the iterative optimization process, we introduce a dynamic motion estimation process and embed it into the unrolled optimization. We establish a cardiac motion estimation network that leverages temporal information via a group-wise registration approach, and carry out a joint optimization between the motion estimation and reconstruction. Experiments on 40 acquired 2D cardiac MR CINE datasets demonstrate that the proposed unrolled MCMR framework can reconstruct high quality MR images at high acceleration rates where other state-of-the-art methods fail. We also show that the joint optimization mechanism is mutually beneficial for both sub-tasks, i.e., motion estimation and image reconstruction, especially when the MR image is highly undersampled.

Robbie Holland, Oliver Leingang, Hrvoje Bogunović et al.

Deep learning has potential to automate screening, monitoring and grading of disease in medical images. Pretraining with contrastive learning enables models to extract robust and generalisable features from natural image datasets, facilitating label-efficient downstream image analysis. However, the direct application of conventional contrastive methods to medical datasets introduces two domain-specific issues. Firstly, several image transformations which have been shown to be crucial for effective contrastive learning do not translate from the natural image to the medical image domain. Secondly, the assumption made by conventional methods, that any two images are dissimilar, is systematically misleading in medical datasets depicting the same anatomy and disease. This is exacerbated in longitudinal image datasets that repeatedly image the same patient cohort to monitor their disease progression over time. In this paper we tackle these issues by extending conventional contrastive frameworks with a novel metadata-enhanced strategy. Our approach employs widely available patient metadata to approximate the true set of inter-image contrastive relationships. To this end we employ records for patient identity, eye position (i.e. left or right) and time series information. In experiments using two large longitudinal datasets containing 170,427 retinal OCT images of 7,912 patients with age-related macular degeneration (AMD), we evaluate the utility of using metadata to incorporate the temporal dynamics of disease progression into pretraining. Our metadata-enhanced approach outperforms both standard contrastive methods and a retinal image foundation model in five out of six image-level downstream tasks related to AMD. Due to its modularity, our method can be quickly and cost-effectively tested to establish the potential benefits of including available metadata in contrastive pretraining.

Mengyun Qiao, Shuo Wang, Huaqi Qiu et al.

Two key questions in cardiac image analysis are to assess the anatomy and motion of the heart from images; and to understand how they are associated with non-imaging clinical factors such as gender, age and diseases. While the first question can often be addressed by image segmentation and motion tracking algorithms, our capability to model and to answer the second question is still limited. In this work, we propose a novel conditional generative model to describe the 4D spatio-temporal anatomy of the heart and its interaction with non-imaging clinical factors. The clinical factors are integrated as the conditions of the generative modelling, which allows us to investigate how these factors influence the cardiac anatomy. We evaluate the model performance in mainly two tasks, anatomical sequence completion and sequence generation. The model achieves a high performance in anatomical sequence completion, comparable to or outperforming other state-of-the-art generative models. In terms of sequence generation, given clinical conditions, the model can generate realistic synthetic 4D sequential anatomies that share similar distributions with the real data.

Florian Kofler, Johannes Wahle, Ivan Ezhov et al.

Machine learning models are typically evaluated by computing similarity with reference annotations and trained by maximizing similarity with such. Especially in the biomedical domain, annotations are subjective and suffer from low inter- and intra-rater reliability. Since annotations only reflect one interpretation of the real world, this can lead to sub-optimal predictions even though the model achieves high similarity scores. Here, the theoretical concept of PGT is introduced. PGT marks the point beyond which an increase in similarity with the \emph{reference annotation} stops translating to better RWMP. Additionally, a quantitative technique to approximate PGT by computing inter- and intra-rater reliability is proposed. Finally, four categories of PGT-aware strategies to evaluate and improve model performance are reviewed.

Ario Sadafi, Oleksandra Adonkina, Ashkan Khakzar et al.

Explainability is a key requirement for computer-aided diagnosis systems in clinical decision-making. Multiple instance learning with attention pooling provides instance-level explainability, however for many clinical applications a deeper, pixel-level explanation is desirable, but missing so far. In this work, we investigate the use of four attribution methods to explain a multiple instance learning models: GradCAM, Layer-Wise Relevance Propagation (LRP), Information Bottleneck Attribution (IBA), and InputIBA. With this collection of methods, we can derive pixel-level explanations on for the task of diagnosing blood cancer from patients' blood smears. We study two datasets of acute myeloid leukemia with over 100 000 single cell images and observe how each attribution method performs on the multiple instance learning architecture focusing on different properties of the white blood single cells. Additionally, we compare attribution maps with the annotations of a medical expert to see how the model's decision-making differs from the human standard. Our study addresses the challenge of implementing pixel-level explainability in multiple instance learning models and provides insights for clinicians to better understand and trust decisions from computer-aided diagnosis systems.

Liu Li, Qiang Ma, Matthew Sinclair et al.

Fetal Magnetic Resonance Imaging (MRI) is used in prenatal diagnosis and to assess early brain development. Accurate segmentation of the different brain tissues is a vital step in several brain analysis tasks, such as cortical surface reconstruction and tissue thickness measurements. Fetal MRI scans, however, are prone to motion artifacts that can affect the correctness of both manual and automatic segmentation techniques. In this paper, we propose a novel network structure that can simultaneously generate conditional atlases and predict brain tissue segmentation, called CAS-Net. The conditional atlases provide anatomical priors that can constrain the segmentation connectivity, despite the heterogeneity of intensity values caused by motion or partial volume effects. The proposed method is trained and evaluated on 253 subjects from the developing Human Connectome Project (dHCP). The results demonstrate that the proposed method can generate conditional age-specific atlas with sharp boundary and shape variance. It also segment multi-category brain tissues for fetal MRI with a high overall Dice similarity coefficient (DSC) of $85.2\%$ for the selected 9 tissue labels.

Robert Graf, Joachim Schmitt, Sarah Schlaeger et al.

Background: Automated segmentation of spinal MR images plays a vital role both scientifically and clinically. However, accurately delineating posterior spine structures presents challenges. Methods: This retrospective study, approved by the ethical committee, involved translating T1w and T2w MR image series into CT images in a total of n=263 pairs of CT/MR series. Landmark-based registration was performed to align image pairs. We compared 2D paired (Pix2Pix, denoising diffusion implicit models (DDIM) image mode, DDIM noise mode) and unpaired (contrastive unpaired translation, SynDiff) image-to-image translation using "peak signal to noise ratio" (PSNR) as quality measure. A publicly available segmentation network segmented the synthesized CT datasets, and Dice scores were evaluated on in-house test sets and the "MRSpineSeg Challenge" volumes. The 2D findings were extended to 3D Pix2Pix and DDIM. Results: 2D paired methods and SynDiff exhibited similar translation performance and Dice scores on paired data. DDIM image mode achieved the highest image quality. SynDiff, Pix2Pix, and DDIM image mode demonstrated similar Dice scores (0.77). For craniocaudal axis rotations, at least two landmarks per vertebra were required for registration. The 3D translation outperformed the 2D approach, resulting in improved Dice scores (0.80) and anatomically accurate segmentations in a higher resolution than the original MR image. Conclusion: Two landmarks per vertebra registration enabled paired image-to-image translation from MR to CT and outperformed all unpaired approaches. The 3D techniques provided anatomically correct segmentations, avoiding underprediction of small structures like the spinous process.

Jiazhen Pan, Suprosanna Shit, Özgün Turgut et al.

In dynamic Magnetic Resonance Imaging (MRI), k-space is typically undersampled due to limited scan time, resulting in aliasing artifacts in the image domain. Hence, dynamic MR reconstruction requires not only modeling spatial frequency components in the x and y directions of k-space but also considering temporal redundancy. Most previous works rely on image-domain regularizers (priors) to conduct MR reconstruction. In contrast, we focus on interpolating the undersampled k-space before obtaining images with Fourier transform. In this work, we connect masked image modeling with k-space interpolation and propose a novel Transformer-based k-space Global Interpolation Network, termed k-GIN. Our k-GIN learns global dependencies among low- and high-frequency components of 2D+t k-space and uses it to interpolate unsampled data. Further, we propose a novel k-space Iterative Refinement Module (k-IRM) to enhance the high-frequency components learning. We evaluate our approach on 92 in-house 2D+t cardiac MR subjects and compare it to MR reconstruction methods with image-domain regularizers. Experiments show that our proposed k-space interpolation method quantitatively and qualitatively outperforms baseline methods. Importantly, the proposed approach achieves substantially higher robustness and generalizability in cases of highly-undersampled MR data. For video presentation, poster, GIF results and code please check our project page: https://jzpeterpan.github.io/k-gin.github.io/.

Qingjie Meng, Wenjia Bai, Tianrui Liu et al.

3D motion estimation from cine cardiac magnetic resonance (CMR) images is important for the assessment of cardiac function and diagnosis of cardiovascular diseases. Most of the previous methods focus on estimating pixel-/voxel-wise motion fields in the full image space, which ignore the fact that motion estimation is mainly relevant and useful within the object of interest, e.g., the heart. In this work, we model the heart as a 3D geometric mesh and propose a novel deep learning-based method that can estimate 3D motion of the heart mesh from 2D short- and long-axis CMR images. By developing a differentiable mesh-to-image rasterizer, the method is able to leverage the anatomical shape information from 2D multi-view CMR images for 3D motion estimation. The differentiability of the rasterizer enables us to train the method end-to-end. One advantage of the proposed method is that by tracking the motion of each vertex, it is able to keep the vertex correspondence of 3D meshes between time frames, which is important for quantitative assessment of the cardiac function on the mesh. We evaluate the proposed method on CMR images acquired from the UK Biobank study. Experimental results show that the proposed method quantitatively and qualitatively outperforms both conventional and learning-based cardiac motion tracking methods.

Bastian Wittmann, Johannes C. Paetzold, Chinmay Prabhakar et al.

Link prediction algorithms aim to infer the existence of connections (or links) between nodes in network-structured data and are typically applied to refine the connectivity among nodes. In this work, we focus on link prediction for flow-driven spatial networks, which are embedded in a Euclidean space and relate to physical exchange and transportation processes (e.g., blood flow in vessels or traffic flow in road networks). To this end, we propose the Graph Attentive Vectors (GAV) link prediction framework. GAV models simplified dynamics of physical flow in spatial networks via an attentive, neighborhood-aware message-passing paradigm, updating vector embeddings in a constrained manner. We evaluate GAV on eight flow-driven spatial networks given by whole-brain vessel graphs and road networks. GAV demonstrates superior performances across all datasets and metrics and outperformed the state-of-the-art on the ogbl-vessel benchmark at the time of submission by 12% (98.38 vs. 87.98 AUC). All code is publicly available on GitHub.

Philip Müller, Georgios Kaissis, Daniel Rueckert

Image-text contrastive learning has proven effective for pretraining medical image models. When targeting localized downstream tasks like semantic segmentation or object detection, additional local contrastive losses that align image regions with sentences have shown promising results. We study how local contrastive losses are related to global (per-sample) contrastive losses and which effects they have on localized medical downstream tasks. Based on a theoretical comparison, we propose to remove some components of local losses and replace others by a novel distribution prior which enforces uniformity of representations within each sample. We empirically study this approach on chest X-ray tasks and find it to be very effective, outperforming methods without local losses on 12 of 18 tasks.

Mehmet Yigit Avci, Emily Chan, Veronika Zimmer et al.

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.

Cosmin I. Bercea, Daniel Rueckert, Julia A. Schnabel

Even though auto-encoders (AEs) have the desirable property of learning compact representations without labels and have been widely applied to out-of-distribution (OoD) detection, they are generally still poorly understood and are used incorrectly in detecting outliers where the normal and abnormal distributions are strongly overlapping. In general, the learned manifold is assumed to contain key information that is only important for describing samples within the training distribution, and that the reconstruction of outliers leads to high residual errors. However, recent work suggests that AEs are likely to be even better at reconstructing some types of OoD samples. In this work, we challenge this assumption and investigate what auto-encoders actually learn when they are posed to solve two different tasks. First, we propose two metrics based on the Fréchet inception distance (FID) and confidence scores of a trained classifier to assess whether AEs can learn the training distribution and reliably recognize samples from other domains. Second, we investigate whether AEs are able to synthesize normal images from samples with abnormal regions, on a more challenging lung pathology detection task. We have found that state-of-the-art (SOTA) AEs are either unable to constrain the latent manifold and allow reconstruction of abnormal patterns, or they are failing to accurately restore the inputs from their latent distribution, resulting in blurred or misaligned reconstructions. We propose novel deformable auto-encoders (MorphAEus) to learn perceptually aware global image priors and locally adapt their morphometry based on estimated dense deformation fields. We demonstrate superior performance over unsupervised methods in detecting OoD and pathology.