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Researcher profile

Daniel Rueckert

Daniel Rueckert contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer Visioneess.IVMachine LearningCryptography and SecurityArtificial IntelligenceQuantitative MethodsNeurons and CognitionComputation and LanguageMultiagent Systemsphysics.med-ph

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Published work

51 published item(s)

preprint2026arXiv

Does DINOv3 Set a New Medical Vision Standard? Benchmarking 2D and 3D Classification, Segmentation, and Registration

The advent of large-scale vision foundation models, pre-trained on diverse natural images, has marked a paradigm shift in computer vision. However, how the frontier vision foundation models' efficacies transfer to specialised domains such as medical imaging remains an open question. This report investigates whether DINOv3, a state-of-the-art self-supervised vision transformer (ViT) pre-trained on natural images, can directly serve as a powerful, unified encoder for medical vision tasks without domain-specific fine-tuning. To answer this, we benchmark DINOv3 across common medical vision tasks, including 2D and 3D classification, segmentation, and registration on a wide range of medical imaging modalities. We systematically analyse its scalability by varying model sizes and input image resolutions. Our findings reveal that DINOv3 shows impressive performance and establishes a formidable new baseline. Remarkably, it can even outperform medical-specific foundation models like BiomedCLIP and CT-Net on several tasks, despite being trained solely on natural images. However, we identify clear limitations: The model's features degrade in scenarios requiring deep domain specialisation, such as in whole-slide images (WSIs), electron microscopy (EM), and positron emission tomography (PET). Furthermore, we observe that DINOv3 does not consistently follow the scaling law in the medical domain. Its performance does not reliably increase with larger models or finer feature resolutions, showing diverse scaling behaviours across tasks. Overall, our work establishes DINOv3 as a strong baseline, whose powerful visual features can serve as a robust prior for multiple medical tasks. This opens promising future directions, such as leveraging its features to enforce multiview consistency in 3D reconstruction.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Multimodal Graph-based Classification of Esophageal Motility Disorders

Diagnosing esophageal motility disorders pose significant challenges due to the complexity of high-resolution impedance manometry (HRIM) data and variability in clinical interpretation. This work explores the feasibility of a multimodal Machine Learning (ML)-based classification approach that combines HRIM recordings with patient-specific information and incorporates a graph-based modeling of esophageal physiology. We analyze HRIM recordings with corresponding patient information from 104 patients with esophageal motility disorders. Patient data includes demographic, clinical, and symptom information extracted from structured questionnaires and free-text notes using keyword detection and large language model-based processing. HRIM data is represented as spatio-temporal graphs, where nodes correspond to pressure values along the esophagus and edges encode spatial adjacency and impedance dynamics. A graph neural network (GNN) is applied to learn physiologically meaningful representations, which are fused with patient embeddings for multi-category, multi-class classification of swallow events. The impact of patient features and graph-based modeling is evaluated by ablation studies and comparison to vision-based classifier baselines. The proposed multimodal approach indicates improvements over models that rely solely on HRIM-derived features across all classification categories. Additionally, the graph-based modeling provides gains compared to vision-based baselines. Our experiments systematically assess the complementary contribution of multiple modalities, as well as demonstrate the feasibility of our proposed graph-based approach. Our initial findings demonstrate that integrating patient-level data with graph-based representations of HRIM signals appears to be a promising direction for more accurate classification of esophageal motility disorders.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

One Sequence to Segment Them All: Efficient Data Augmentation for CT and MRI Cross-Domain 3D Spine Segmentation

Deep learning-based medical image segmentation is increasingly used to support clinical diagnosis and develop new treatment strategies. However, model performance remains limited by the scarcity of high-quality annotated data and insufficient generalization across imaging protocols. This limitation is particularly evident in MRI and CT, where models are typically trained on a single acquisition sequence and exhibit reduced robustness when applied to unseen sequences or contrasts. Although data augmentation is widely used to improve general robustness on medical images, its impact on cross-modality generalization has not been quantitatively explored. In this work, we study a targeted set of data augmentation techniques designed to improve cross-modality transfer. We train three spine segmentation models, each on a single-modality/sequence dataset, and evaluate them across seven out-of-distribution datasets (spanning CT and MRI), reflecting a realistic single-sequence training and multi-sequence/contrast/modality deployment scenario. Our results demonstrate substantial performance gains on unseen domains (average Dice gain of 155 %) while preserving in-domain accuracy (average Dice decrease of 0.008 %), including effective transfer between CT and MRI. To mitigate the computational cost typically associated with strong data augmentation, we implement GPU-optimized augmentations that maintain, and even improve, training efficiency by approximately 10 %. We release our approach as an open-source toolbox, enabling seamless integration into commonly used frameworks such as nnUNet and MONAI. These augmentations significantly enhance robustness to heterogeneous clinical imaging scenarios without compromising training speed.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

RealICU: Do LLM Agents Understand Long-Context ICU Data? A Benchmark Beyond Behavior Imitation

Intensive care units (ICU) generate long, dense and evolving streams of clinical information, where physicians must repeatedly reassess patient states under time pressure, underscoring a clear need for reliable AI decision support. Existing ICU benchmarks typically treat historical clinician actions as ground truth. However, these actions are made under incomplete information and limited temporal context of the underlying patient state, and may therefore be suboptimal, making it difficult to assess the true reasoning capabilities of AI systems. We introduce RealICU, a hindsight-annotated benchmark for evaluating large language models (LLMs) under realistic ICU conditions, where labels are created after senior physicians review the full patient trajectory. We formulate four physician-motivated tasks: assess Patient Status, Acute Problems, Recommended Actions, and Red Flag actions that risk unsafe outcomes. We partition each trajectory with 30-min windows and release two datasets: RealICU-Gold with 930-window annotations from 94 MIMIC-IV patients, and RealICU-Scale with 11,862 windows extended by Oracle, a physician-validated LLM hindsight labeler. Existing LLMs including memory-augmented ones performed poorly on RealICU, exposing two failure modes: a recall-safety tradeoff for clinical recommendations, and an anchoring bias to early interpretations of the patient. We further introduce ICU-Evo to study structured-memory agents that improves long-horizon reasoning but does not fully eliminate safety failures. Together, RealICU provides a clinically grounded testbed for measuring and improving AI sequential decision-support in high-stakes care. Project page: https://chengzhi-leo.github.io/RealICU-Bench/

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

What Cohort INRs Encode and Where to Freeze Them

Reusing the early layers of cohort-trained INRs as initialization for new signals has been shown to accelerate and improve signal fitting, yet it remains unclear which layers of the shared encoder learn transferable representations and what those representations encode. We address both questions for two standard backbones, SIREN and Fourier-feature MLPs (FFMLP). First, sweeping the freeze depth across the shared encoder at test time, we find that the optimum coincides with the layer of highest weight stable rank. Moreover, freezing at this depth matches or improves on the standard fine-tuning recipe across all our experiments. Second, identifying which layer transfers does not characterize what that layer encodes. To address this we adopt sparse autoencoders (SAEs), the dominant tool in mechanistic interpretability, and present the first SAE decomposition of INR activations into sparse dictionary atoms. Interestingly, SIREN and FFMLP achieve comparable cohort-fitting quality, but learn qualitatively different dictionaries. Cohort SIREN's atoms are localized, tiling the coordinate plane such that each atom fires in a confined region independent of cohort content. Cohort FFMLP's atoms are image-spanning, tracing the contours of memorized cohort signals. Single-atom ablations confirm causal use of these dictionaries: a single FFMLP atom out of 4096 can drop PSNR by up to 10.6 dB across the image, while SIREN ablations remain confined to where the atom fires. Together, these results give the first mechanistic account of what transfers in cohort-trained INRs and turn their activations into inspectable dictionary atoms. These tools open a path towards characterizing what INRs encode and towards architectures designed for generalization rather than memorization.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

On Discprecncies between Perturbation Evaluations of Graph Neural Network Attributions

Neural networks are increasingly finding their way into the realm of graphs and modeling relationships between features. Concurrently graph neural network explanation approaches are being invented to uncover relationships between the nodes of the graphs. However, there is a disparity between the existing attribution methods, and it is unclear which attribution to trust. Therefore research has introduced evaluation experiments that assess them from different perspectives. In this work, we assess attribution methods from a perspective not previously explored in the graph domain: retraining. The core idea is to retrain the network on important (or not important) relationships as identified by the attributions and evaluate how networks can generalize based on these relationships. We reformulate the retraining framework to sidestep issues lurking in the previous formulation and propose guidelines for correct analysis. We run our analysis on four state-of-the-art GNN attribution methods and five synthetic and real-world graph classification datasets. The analysis reveals that attributions perform variably depending on the dataset and the network. Most importantly, we observe that the famous GNNExplainer performs similarly to an arbitrary designation of edge importance. The study concludes that the retraining evaluation cannot be used as a generalized benchmark and recommends it as a toolset to evaluate attributions on a specifically addressed network, dataset, and sparsity.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

Single-subject Multi-contrast MRI Super-resolution via Implicit Neural Representations

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/

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

An automatic differentiation system for the age of differential privacy

We introduce Tritium, an automatic differentiation-based sensitivity analysis framework for differentially private (DP) machine learning (ML). Optimal noise calibration in this setting requires efficient Jacobian matrix computations and tight bounds on the L2-sensitivity. Our framework achieves these objectives by relying on a functional analysis-based method for sensitivity tracking, which we briefly outline. This approach interoperates naturally and seamlessly with static graph-based automatic differentiation, which enables order-of-magnitude improvements in compilation times compared to previous work. Moreover, we demonstrate that optimising the sensitivity of the entire computational graph at once yields substantially tighter estimates of the true sensitivity compared to interval bound propagation techniques. Our work naturally befits recent developments in DP such as individual privacy accounting, aiming to offer improved privacy-utility trade-offs, and represents a step towards the integration of accessible machine learning tooling with advanced privacy accounting systems.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

AutoSeg -- Steering the Inductive Biases for Automatic Pathology Segmentation

In medical imaging, un-, semi-, or self-supervised pathology detection is often approached with anomaly- or out-of-distribution detection methods, whose inductive biases are not intentionally directed towards detecting pathologies, and are therefore sub-optimal for this task. To tackle this problem, we propose AutoSeg, an engine that can generate diverse artificial anomalies that resemble the properties of real-world pathologies. Our method can accurately segment unseen artificial anomalies and outperforms existing methods for pathology detection on a challenging real-world dataset of Chest X-ray images. We experimentally evaluate our method on the Medical Out-of-Distribution Analysis Challenge 2021.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Beyond Gradients: Exploiting Adversarial Priors in Model Inversion Attacks

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Can collaborative learning be private, robust and scalable?

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

CAS-Net: Conditional Atlas Generation and Brain Segmentation for Fetal MRI

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

CortexODE: Learning Cortical Surface Reconstruction by Neural ODEs

We present CortexODE, a deep learning framework for cortical surface reconstruction. CortexODE leverages neural ordinary differential equations (ODEs) to deform an input surface into a target shape by learning a diffeomorphic flow. The trajectories of the points on the surface are modeled as ODEs, where the derivatives of their coordinates are parameterized via a learnable Lipschitz-continuous deformation network. This provides theoretical guarantees for the prevention of self-intersections. CortexODE can be integrated to an automatic learning-based pipeline, which reconstructs cortical surfaces efficiently in less than 5 seconds. The pipeline utilizes a 3D U-Net to predict a white matter segmentation from brain Magnetic Resonance Imaging (MRI) scans, and further generates a signed distance function that represents an initial surface. Fast topology correction is introduced to guarantee homeomorphism to a sphere. Following the isosurface extraction step, two CortexODE models are trained to deform the initial surface to white matter and pial surfaces respectively. The proposed pipeline is evaluated on large-scale neuroimage datasets in various age groups including neonates (25-45 weeks), young adults (22-36 years) and elderly subjects (55-90 years). Our experiments demonstrate that the CortexODE-based pipeline can achieve less than 0.2mm average geometric error while being orders of magnitude faster compared to conventional processing pipelines.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Data and Physics Driven Learning Models for Fast MRI -- Fundamentals and Methodologies from CNN, GAN to Attention and Transformers

Research studies have shown no qualms about using data driven deep learning models for downstream tasks in medical image analysis, e.g., anatomy segmentation and lesion detection, disease diagnosis and prognosis, and treatment planning. However, deep learning models are not the sovereign remedy for medical image analysis when the upstream imaging is not being conducted properly (with artefacts). This has been manifested in MRI studies, where the scanning is typically slow, prone to motion artefacts, with a relatively low signal to noise ratio, and poor spatial and/or temporal resolution. Recent studies have witnessed substantial growth in the development of deep learning techniques for propelling fast MRI. This article aims to (1) introduce the deep learning based data driven techniques for fast MRI including convolutional neural network and generative adversarial network based methods, (2) survey the attention and transformer based models for speeding up MRI reconstruction, and (3) detail the research in coupling physics and data driven models for MRI acceleration. Finally, we will demonstrate through a few clinical applications, explain the importance of data harmonisation and explainable models for such fast MRI techniques in multicentre and multi-scanner studies, and discuss common pitfalls in current research and recommendations for future research directions.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Differentially private training of residual networks with scale normalisation

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Embedding Gradient-based Optimization in Image Registration Networks

Deep learning (DL) image registration methods amortize the costly pair-wise iterative optimization by training deep neural networks to predict the optimal transformation in one fast forward-pass. In this work, we bridge the gap between traditional iterative energy optimization-based registration and network-based registration, and propose Gradient Descent Network for Image Registration (GraDIRN). Our proposed approach trains a DL network that embeds unrolled multiresolution gradient-based energy optimization in its forward pass, which explicitly enforces image dissimilarity minimization in its update steps. Extensive evaluations were performed on registration tasks using 2D cardiac MR and 3D brain MR images. We demonstrate that our approach achieved state-of-the-art registration performance while using fewer learned parameters, with good data efficiency and domain robustness.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Enhancing MR Image Segmentation with Realistic Adversarial Data Augmentation

The success of neural networks on medical image segmentation tasks typically relies on large labeled datasets for model training. However, acquiring and manually labeling a large medical image set is resource-intensive, expensive, and sometimes impractical due to data sharing and privacy issues. To address this challenge, we propose AdvChain, a generic adversarial data augmentation framework, aiming at improving both the diversity and effectiveness of training data for medical image segmentation tasks. AdvChain augments data with dynamic data augmentation, generating randomly chained photo-metric and geometric transformations to resemble realistic yet challenging imaging variations to expand training data. By jointly optimizing the data augmentation model and a segmentation network during training, challenging examples are generated to enhance network generalizability for the downstream task. The proposed adversarial data augmentation does not rely on generative networks and can be used as a plug-in module in general segmentation networks. It is computationally efficient and applicable for both low-shot supervised and semi-supervised learning. We analyze and evaluate the method on two MR image segmentation tasks: cardiac segmentation and prostate segmentation with limited labeled data. Results show that the proposed approach can alleviate the need for labeled data while improving model generalization ability, indicating its practical value in medical imaging applications.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Faster Diffusion Cardiac MRI with Deep Learning-based breath hold reduction

Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) enables us to probe the microstructural arrangement of cardiomyocytes within the myocardium in vivo and non-invasively, which no other imaging modality allows. This innovative technology could revolutionise the ability to perform cardiac clinical diagnosis, risk stratification, prognosis and therapy follow-up. However, DT-CMR is currently inefficient with over six minutes needed to acquire a single 2D static image. Therefore, DT-CMR is currently confined to research but not used clinically. We propose to reduce the number of repetitions needed to produce DT-CMR datasets and subsequently de-noise them, decreasing the acquisition time by a linear factor while maintaining acceptable image quality. Our proposed approach, based on Generative Adversarial Networks, Vision Transformers, and Ensemble Learning, performs significantly and considerably better than previous proposed approaches, bringing single breath-hold DT-CMR closer to reality.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

FedNorm: Modality-Based Normalization in Federated Learning for Multi-Modal Liver Segmentation

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Generative Myocardial Motion Tracking via Latent Space Exploration with Biomechanics-informed Prior

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Improved post-hoc probability calibration for out-of-domain MRI segmentation

Probability calibration for deep models is highly desirable in safety-critical applications such as medical imaging. It makes output probabilities of deep networks interpretable, by aligning prediction probability with the actual accuracy in test data. In image segmentation, well-calibrated probabilities allow radiologists to identify regions where model-predicted segmentations are unreliable. These unreliable predictions often occur to out-of-domain (OOD) images that are caused by imaging artifacts or unseen imaging protocols. Unfortunately, most previous calibration methods for image segmentation perform sub-optimally on OOD images. To reduce the calibration error when confronted with OOD images, we propose a novel post-hoc calibration model. Our model leverages the pixel susceptibility against perturbations at the local level, and the shape prior information at the global level. The model is tested on cardiac MRI segmentation datasets that contain unseen imaging artifacts and images from an unseen imaging protocol. We demonstrate reduced calibration errors compared with the state-of-the-art calibration algorithm.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Learning-based and unrolled motion-compensated reconstruction for cardiac MR CINE imaging

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

MaxStyle: Adversarial Style Composition for Robust Medical Image Segmentation

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Multi-modal unsupervised brain image registration using edge maps

Diffeomorphic deformable multi-modal image registration is a challenging task which aims to bring images acquired by different modalities to the same coordinate space and at the same time to preserve the topology and the invertibility of the transformation. Recent research has focused on leveraging deep learning approaches for this task as these have been shown to achieve competitive registration accuracy while being computationally more efficient than traditional iterative registration methods. In this work, we propose a simple yet effective unsupervised deep learning-based {\em multi-modal} image registration approach that benefits from auxiliary information coming from the gradient magnitude of the image, i.e. the image edges, during the training. The intuition behind this is that image locations with a strong gradient are assumed to denote a transition of tissues, which are locations of high information value able to act as a geometry constraint. The task is similar to using segmentation maps to drive the training, but the edge maps are easier and faster to acquire and do not require annotations. We evaluate our approach in the context of registering multi-modal (T1w to T2w) magnetic resonance (MR) brain images of different subjects using three different loss functions that are said to assist multi-modal registration, showing that in all cases the auxiliary information leads to better results without compromising the runtime.

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preprint2022arXiv

MulViMotion: Shape-aware 3D Myocardial Motion Tracking from Multi-View Cardiac MRI

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.

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preprint2022arXiv

Placenta Segmentation in Ultrasound Imaging: Addressing Sources of Uncertainty and Limited Field-of-View

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.

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preprint2022arXiv

Privacy: An axiomatic approach

The increasing prevalence of large-scale data collection in modern society represents a potential threat to individual privacy. Addressing this threat, for example through privacy-enhancing technologies (PETs), requires a rigorous definition of what exactly is being protected, that is, of privacy itself. In this work, we formulate an axiomatic definition of privacy based on quantifiable and irreducible information flows. Our definition synthesizes prior work from the domain of social science with a contemporary understanding of PETs such as differential privacy (DP). Our work highlights the fact that the inevitable difficulties of protecting privacy in practice are fundamentally information-theoretic. Moreover, it enables quantitative reasoning about PETs based on what they are protecting, thus fostering objective policy discourse about their societal implementation.

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preprint2022arXiv

SmoothNets: Optimizing CNN architecture design for differentially private deep learning

The arguably most widely employed algorithm to train deep neural networks with Differential Privacy is DPSGD, which requires clipping and noising of per-sample gradients. This introduces a reduction in model utility compared to non-private training. Empirically, it can be observed that this accuracy degradation is strongly dependent on the model architecture. We investigated this phenomenon and, by combining components which exhibit good individual performance, distilled a new model architecture termed SmoothNet, which is characterised by increased robustness to the challenges of DP-SGD training. Experimentally, we benchmark SmoothNet against standard architectures on two benchmark datasets and observe that our architecture outperforms others, reaching an accuracy of 73.5\% on CIFAR-10 at $\varepsilon=7.0$ and 69.2\% at $\varepsilon=7.0$ on ImageNette, a state-of-the-art result compared to prior architectural modifications for DP.

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preprint2022arXiv

SoK: Differential Privacy on Graph-Structured Data

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.

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preprint2022arXiv

Surface Analysis with Vision Transformers

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

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preprint2022arXiv

Surface Vision Transformers: Flexible Attention-Based Modelling of Biomedical Surfaces

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

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preprint2021arXiv

A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises

Since its renaissance, deep learning has been widely used in various medical imaging tasks and has achieved remarkable success in many medical imaging applications, thereby propelling us into the so-called artificial intelligence (AI) era. It is known that the success of AI is mostly attributed to the availability of big data with annotations for a single task and the advances in high performance computing. However, medical imaging presents unique challenges that confront deep learning approaches. In this survey paper, we first present traits of medical imaging, highlight both clinical needs and technical challenges in medical imaging, and describe how emerging trends in deep learning are addressing these issues. We cover the topics of network architecture, sparse and noisy labels, federating learning, interpretability, uncertainty quantification, etc. Then, we present several case studies that are commonly found in clinical practice, including digital pathology and chest, brain, cardiovascular, and abdominal imaging. Rather than presenting an exhaustive literature survey, we instead describe some prominent research highlights related to these case study applications. We conclude with a discussion and presentation of promising future directions.

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preprint2021arXiv

FedDis: Disentangled Federated Learning for Unsupervised Brain Pathology Segmentation

In recent years, data-driven machine learning (ML) methods have revolutionized the computer vision community by providing novel efficient solutions to many unsolved (medical) image analysis problems. However, due to the increasing privacy concerns and data fragmentation on many different sites, existing medical data are not fully utilized, thus limiting the potential of ML. Federated learning (FL) enables multiple parties to collaboratively train a ML model without exchanging local data. However, data heterogeneity (non-IID) among the distributed clients is yet a challenge. To this end, we propose a novel federated method, denoted Federated Disentanglement (FedDis), to disentangle the parameter space into shape and appearance, and only share the shape parameter with the clients. FedDis is based on the assumption that the anatomical structure in brain MRI images is similar across multiple institutions, and sharing the shape knowledge would be beneficial in anomaly detection. In this paper, we leverage healthy brain scans of 623 subjects from multiple sites with real data (OASIS, ADNI) in a privacy-preserving fashion to learn a model of normal anatomy, that allows to segment abnormal structures. We demonstrate a superior performance of FedDis on real pathological databases containing 109 subjects; two publicly available MS Lesions (MSLUB, MSISBI), and an in-house database with MS and Glioblastoma (MSI and GBI). FedDis achieved an average dice performance of 0.38, outperforming the state-of-the-art (SOTA) auto-encoder by 42% and the SOTA federated method by 11%. Further, we illustrate that FedDis learns a shape embedding that is orthogonal to the appearance and consistent under different intensity augmentations.

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preprint2021arXiv

Personalized Federated Deep Learning for Pain Estimation From Face Images

Standard machine learning approaches require centralizing the users' data in one computer or a shared database, which raises data privacy and confidentiality concerns. Therefore, limiting central access is important, especially in healthcare settings, where data regulations are strict. A potential approach to tackling this is Federated Learning (FL), which enables multiple parties to collaboratively learn a shared prediction model by using parameters of locally trained models while keeping raw training data locally. In the context of AI-assisted pain-monitoring, we wish to enable confidentiality-preserving and unobtrusive pain estimation for long-term pain-monitoring and reduce the burden on the nursing staff who perform frequent routine check-ups. To this end, we propose a novel Personalized Federated Deep Learning (PFDL) approach for pain estimation from face images. PFDL performs collaborative training of a deep model, implemented using a lightweight CNN architecture, across different clients (i.e., subjects) without sharing their face images. Instead of sharing all parameters of the model, as in standard FL, PFDL retains the last layer locally (used to personalize the pain estimates). This (i) adds another layer of data confidentiality, making it difficult for an adversary to infer pain levels of the target subject, while (ii) personalizing the pain estimation to each subject through local parameter tuning. We show using a publicly available dataset of face videos of pain (UNBC-McMaster Shoulder Pain Database), that PFDL performs comparably or better than the standard centralized and FL algorithms, while further enhancing data privacy. This, has the potential to improve traditional pain monitoring by making it more secure, computationally efficient, and scalable to a large number of individuals (e.g., for in-home pain monitoring), providing timely and unobtrusive pain measurement.

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preprint2021arXiv

Video Summarization through Reinforcement Learning with a 3D Spatio-Temporal U-Net

Intelligent video summarization algorithms allow to quickly convey the most relevant information in videos through the identification of the most essential and explanatory content while removing redundant video frames. In this paper, we introduce the 3DST-UNet-RL framework for video summarization. A 3D spatio-temporal U-Net is used to efficiently encode spatio-temporal information of the input videos for downstream reinforcement learning (RL). An RL agent learns from spatio-temporal latent scores and predicts actions for keeping or rejecting a video frame in a video summary. We investigate if real/inflated 3D spatio-temporal CNN features are better suited to learn representations from videos than commonly used 2D image features. Our framework can operate in both, a fully unsupervised mode and a supervised training mode. We analyse the impact of prescribed summary lengths and show experimental evidence for the effectiveness of 3DST-UNet-RL on two commonly used general video summarization benchmarks. We also applied our method on a medical video summarization task. The proposed video summarization method has the potential to save storage costs of ultrasound screening videos as well as to increase efficiency when browsing patient video data during retrospective analysis or audit without loosing essential information

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preprint2020arXiv

3D Probabilistic Segmentation and Volumetry from 2D projection images

X-Ray imaging is quick, cheap and useful for front-line care assessment and intra-operative real-time imaging (e.g., C-Arm Fluoroscopy). However, it suffers from projective information loss and lacks vital volumetric information on which many essential diagnostic biomarkers are based on. In this paper we explore probabilistic methods to reconstruct 3D volumetric images from 2D imaging modalities and measure the models' performance and confidence. We show our models' performance on large connected structures and we test for limitations regarding fine structures and image domain sensitivity. We utilize fast end-to-end training of a 2D-3D convolutional networks, evaluate our method on 117 CT scans segmenting 3D structures from digitally reconstructed radiographs (DRRs) with a Dice score of $0.91 \pm 0.0013$. Source code will be made available by the time of the conference.

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preprint2020arXiv

A Global Benchmark of Algorithms for Segmenting Late Gadolinium-Enhanced Cardiac Magnetic Resonance Imaging

Segmentation of cardiac images, particularly late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) widely used for visualizing diseased cardiac structures, is a crucial first step for clinical diagnosis and treatment. However, direct segmentation of LGE-MRIs is challenging due to its attenuated contrast. Since most clinical studies have relied on manual and labor-intensive approaches, automatic methods are of high interest, particularly optimized machine learning approaches. To address this, we organized the "2018 Left Atrium Segmentation Challenge" using 154 3D LGE-MRIs, currently the world's largest cardiac LGE-MRI dataset, and associated labels of the left atrium segmented by three medical experts, ultimately attracting the participation of 27 international teams. In this paper, extensive analysis of the submitted algorithms using technical and biological metrics was performed by undergoing subgroup analysis and conducting hyper-parameter analysis, offering an overall picture of the major design choices of convolutional neural networks (CNNs) and practical considerations for achieving state-of-the-art left atrium segmentation. Results show the top method achieved a dice score of 93.2% and a mean surface to a surface distance of 0.7 mm, significantly outperforming prior state-of-the-art. Particularly, our analysis demonstrated that double, sequentially used CNNs, in which a first CNN is used for automatic region-of-interest localization and a subsequent CNN is used for refined regional segmentation, achieved far superior results than traditional methods and pipelines containing single CNNs. This large-scale benchmarking study makes a significant step towards much-improved segmentation methods for cardiac LGE-MRIs, and will serve as an important benchmark for evaluating and comparing the future works in the field.

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preprint2020arXiv

Automated Detection of Congenital Heart Disease in Fetal Ultrasound Screening

Prenatal screening with ultrasound can lower neonatal mortality significantly for selected cardiac abnormalities. However, the need for human expertise, coupled with the high volume of screening cases, limits the practically achievable detection rates. In this paper we discuss the potential for deep learning techniques to aid in the detection of congenital heart disease (CHD) in fetal ultrasound. We propose a pipeline for automated data curation and classification. During both training and inference, we exploit an auxiliary view classification task to bias features toward relevant cardiac structures. This bias helps to improve in F1-scores from 0.72 and 0.77 to 0.87 and 0.85 for healthy and CHD classes respectively.

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preprint2020arXiv

Biomechanics-informed Neural Networks for Myocardial Motion Tracking in MRI

Image registration is an ill-posed inverse problem which often requires regularisation on the solution space. In contrast to most of the current approaches which impose explicit regularisation terms such as smoothness, in this paper we propose a novel method that can implicitly learn biomechanics-informed regularisation. Such an approach can incorporate application-specific prior knowledge into deep learning based registration. Particularly, the proposed biomechanics-informed regularisation leverages a variational autoencoder (VAE) to learn a manifold for biomechanically plausible deformations and to implicitly capture their underlying properties via reconstructing biomechanical simulations. The learnt VAE regulariser then can be coupled with any deep learning based registration network to regularise the solution space to be biomechanically plausible. The proposed method is validated in the context of myocardial motion tracking on 2D stacks of cardiac MRI data from two different datasets. The results show that it can achieve better performance against other competing methods in terms of motion tracking accuracy and has the ability to learn biomechanical properties such as incompressibility and strains. The method has also been shown to have better generalisability to unseen domains compared with commonly used L2 regularisation schemes.

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preprint2020arXiv

Causal Future Prediction in a Minkowski Space-Time

Estimating future events is a difficult task. Unlike humans, machine learning approaches are not regularized by a natural understanding of physics. In the wild, a plausible succession of events is governed by the rules of causality, which cannot easily be derived from a finite training set. In this paper we propose a novel theoretical framework to perform causal future prediction by embedding spatiotemporal information on a Minkowski space-time. We utilize the concept of a light cone from special relativity to restrict and traverse the latent space of an arbitrary model. We demonstrate successful applications in causal image synthesis and future video frame prediction on a dataset of images. Our framework is architecture- and task-independent and comes with strong theoretical guarantees of causal capabilities.

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preprint2020arXiv

Deep Network Interpolation for Accelerated Parallel MR Image Reconstruction

We present a deep network interpolation strategy for accelerated parallel MR image reconstruction. In particular, we examine the network interpolation in parameter space between a source model that is formulated in an unrolled scheme with L1 and SSIM losses and its counterpart that is trained with an adversarial loss. We show that by interpolating between the two different models of the same network structure, the new interpolated network can model a trade-off between perceptual quality and fidelity.

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preprint2020arXiv

Explainable Anatomical Shape Analysis through Deep Hierarchical Generative Models

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer's disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating high-throughput analysis of normal anatomy and pathology in large-scale studies of volumetric imaging.

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preprint2020arXiv

Learning Cross-domain Generalizable Features by Representation Disentanglement

Deep learning models exhibit limited generalizability across different domains. Specifically, transferring knowledge from available entangled domain features(source/target domain) and categorical features to new unseen categorical features in a target domain is an interesting and difficult problem that is rarely discussed in the current literature. This problem is essential for many real-world applications such as improving diagnostic classification or prediction in medical imaging. To address this problem, we propose Mutual-Information-based Disentangled Neural Networks (MIDNet) to extract generalizable features that enable transferring knowledge to unseen categorical features in target domains. The proposed MIDNet is developed as a semi-supervised learning paradigm to alleviate the dependency on labeled data. This is important for practical applications where data annotation requires rare expertise as well as intense time and labor. We demonstrate our method on handwritten digits datasets and a fetal ultrasound dataset for image classification tasks. Experiments show that our method outperforms the state-of-the-art and achieve expected performance with sparsely labeled data.

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preprint2020arXiv

Realistic Adversarial Data Augmentation for MR Image Segmentation

Neural network-based approaches can achieve high accuracy in various medical image segmentation tasks. However, they generally require large labelled datasets for supervised learning. Acquiring and manually labelling a large medical dataset is expensive and sometimes impractical due to data sharing and privacy issues. In this work, we propose an adversarial data augmentation method for training neural networks for medical image segmentation. Instead of generating pixel-wise adversarial attacks, our model generates plausible and realistic signal corruptions, which models the intensity inhomogeneities caused by a common type of artefacts in MR imaging: bias field. The proposed method does not rely on generative networks, and can be used as a plug-in module for general segmentation networks in both supervised and semi-supervised learning. Using cardiac MR imaging we show that such an approach can improve the generalization ability and robustness of models as well as provide significant improvements in low-data scenarios.

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preprint2020arXiv

Regression Forest-Based Atlas Localization and Direction Specific Atlas Generation for Pancreas Segmentation

This paper proposes a fully automated atlas-based pancreas segmentation method from CT volumes utilizing atlas localization by regression forest and atlas generation using blood vessel information. Previous probabilistic atlas-based pancreas segmentation methods cannot deal with spatial variations that are commonly found in the pancreas well. Also, shape variations are not represented by an averaged atlas. We propose a fully automated pancreas segmentation method that deals with two types of variations mentioned above. The position and size of the pancreas is estimated using a regression forest technique. After localization, a patient-specific probabilistic atlas is generated based on a new image similarity that reflects the blood vessel position and direction information around the pancreas. We segment it using the EM algorithm with the atlas as prior followed by the graph-cut. In evaluation results using 147 CT volumes, the Jaccard index and the Dice overlap of the proposed method were 62.1% and 75.1%, respectively. Although we automated all of the segmentation processes, segmentation results were superior to the other state-of-the-art methods in the Dice overlap.

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preprint2020arXiv

Robust Aggregation for Adaptive Privacy Preserving Federated Learning in Healthcare

Federated learning (FL) has enabled training models collaboratively from multiple data owning parties without sharing their data. Given the privacy regulations of patient's healthcare data, learning-based systems in healthcare can greatly benefit from privacy-preserving FL approaches. However, typical model aggregation methods in FL are sensitive to local model updates, which may lead to failure in learning a robust and accurate global model. In this work, we implement and evaluate different robust aggregation methods in FL applied to healthcare data. Furthermore, we show that such methods can detect and discard faulty or malicious local clients during training. We run two sets of experiments using two real-world healthcare datasets for training medical diagnosis classification tasks. Each dataset is used to simulate the performance of three different robust FL aggregation strategies when facing different poisoning attacks. The results show that privacy preserving methods can be successfully applied alongside Byzantine-robust aggregation techniques. We observed in particular how using differential privacy (DP) did not significantly impact the final learning convergence of the different aggregation strategies.

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preprint2020arXiv

Ultrasound Video Summarization using Deep Reinforcement Learning

Video is an essential imaging modality for diagnostics, e.g. in ultrasound imaging, for endoscopy, or movement assessment. However, video hasn't received a lot of attention in the medical image analysis community. In the clinical practice, it is challenging to utilise raw diagnostic video data efficiently as video data takes a long time to process, annotate or audit. In this paper we introduce a novel, fully automatic video summarization method that is tailored to the needs of medical video data. Our approach is framed as reinforcement learning problem and produces agents focusing on the preservation of important diagnostic information. We evaluate our method on videos from fetal ultrasound screening, where commonly only a small amount of the recorded data is used diagnostically. We show that our method is superior to alternative video summarization methods and that it preserves essential information required by clinical diagnostic standards.

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preprint2020arXiv

Unsupervised Cross-domain Image Classification by Distance Metric Guided Feature Alignment

Learning deep neural networks that are generalizable across different domains remains a challenge due to the problem of domain shift. Unsupervised domain adaptation is a promising avenue which transfers knowledge from a source domain to a target domain without using any labels in the target domain. Contemporary techniques focus on extracting domain-invariant features using domain adversarial training. However, these techniques neglect to learn discriminative class boundaries in the latent representation space on a target domain and yield limited adaptation performance. To address this problem, we propose distance metric guided feature alignment (MetFA) to extract discriminative as well as domain-invariant features on both source and target domains. The proposed MetFA method explicitly and directly learns the latent representation without using domain adversarial training. Our model integrates class distribution alignment to transfer semantic knowledge from a source domain to a target domain. We evaluate the proposed method on fetal ultrasound datasets for cross-device image classification. Experimental results demonstrate that the proposed method outperforms the state-of-the-art and enables model generalization.

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preprint2019arXiv

Deep learning for cardiac image segmentation: A review

Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.

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preprint2019arXiv

Improving the generalizability of convolutional neural network-based segmentation on CMR images

Convolutional neural network (CNN) based segmentation methods provide an efficient and automated way for clinicians to assess the structure and function of the heart in cardiac MR images. While CNNs can generally perform the segmentation tasks with high accuracy when training and test images come from the same domain (e.g. same scanner or site), their performance often degrades dramatically on images from different scanners or clinical sites. We propose a simple yet effective way for improving the network generalization ability by carefully designing data normalization and augmentation strategies to accommodate common scenarios in multi-site, multi-scanner clinical imaging data sets. We demonstrate that a neural network trained on a single-site single-scanner dataset from the UK Biobank can be successfully applied to segmenting cardiac MR images across different sites and different scanners without substantial loss of accuracy. Specifically, the method was trained on a large set of 3,975 subjects from the UK Biobank. It was then directly tested on 600 different subjects from the UK Biobank for intra-domain testing and two other sets for cross-domain testing: the ACDC dataset (100 subjects, 1 site, 2 scanners) and the BSCMR-AS dataset (599 subjects, 6 sites, 9 scanners). The proposed method produces promising segmentation results on the UK Biobank test set which are comparable to previously reported values in the literature, while also performing well on cross-domain test sets, achieving a mean Dice metric of 0.90 for the left ventricle, 0.81 for the myocardium and 0.82 for the right ventricle on the ACDC dataset; and 0.89 for the left ventricle, 0.83 for the myocardium on the BSCMR-AS dataset. The proposed method offers a potential solution to improve CNN-based model generalizability for the cross-scanner and cross-site cardiac MR image segmentation task.

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preprint2019arXiv

Unsupervised Multi-modal Style Transfer for Cardiac MR Segmentation

In this work, we present a fully automatic method to segment cardiac structures from late-gadolinium enhanced (LGE) images without using labelled LGE data for training, but instead by transferring the anatomical knowledge and features learned on annotated balanced steady-state free precession (bSSFP) images, which are easier to acquire. Our framework mainly consists of two neural networks: a multi-modal image translation network for style transfer and a cascaded segmentation network for image segmentation. The multi-modal image translation network generates realistic and diverse synthetic LGE images conditioned on a single annotated bSSFP image, forming a synthetic LGE training set. This set is then utilized to fine-tune the segmentation network pre-trained on labelled bSSFP images, achieving the goal of unsupervised LGE image segmentation. In particular, the proposed cascaded segmentation network is able to produce accurate segmentation by taking both shape prior and image appearance into account, achieving an average Dice score of 0.92 for the left ventricle, 0.83 for the myocardium, and 0.88 for the right ventricle on the test set.

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