Cheng Ouyang

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.

Zeju Li, Konstantinos Kamnitsas, Cheng Ouyang et al.

Background samples provide key contextual information for segmenting regions of interest (ROIs). However, they always cover a diverse set of structures, causing difficulties for the segmentation model to learn good decision boundaries with high sensitivity and precision. The issue concerns the highly heterogeneous nature of the background class, resulting in multi-modal distributions. Empirically, we find that neural networks trained with heterogeneous background struggle to map the corresponding contextual samples to compact clusters in feature space. As a result, the distribution over background logit activations may shift across the decision boundary, leading to systematic over-segmentation across different datasets and tasks. In this study, we propose context label learning (CoLab) to improve the context representations by decomposing the background class into several subclasses. Specifically, we train an auxiliary network as a task generator, along with the primary segmentation model, to automatically generate context labels that positively affect the ROI segmentation accuracy. Extensive experiments are conducted on several challenging segmentation tasks and datasets. The results demonstrate that CoLab can guide the segmentation model to map the logits of background samples away from the decision boundary, resulting in significantly improved segmentation accuracy. Code is available.

Cheng Ouyang, Shuo Wang, Chen Chen et al.

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.

Shuo Wang, Chen Qin, Chengyan Wang et al.

The quality of cardiac magnetic resonance (CMR) imaging is susceptible to respiratory motion artifacts. The model robustness of automated segmentation techniques in face of real-world respiratory motion artifacts is unclear. This manuscript describes the design of extreme cardiac MRI analysis challenge under respiratory motion (CMRxMotion Challenge). The challenge aims to establish a public benchmark dataset to assess the effects of respiratory motion on image quality and examine the robustness of segmentation models. The challenge recruited 40 healthy volunteers to perform different breath-hold behaviors during one imaging visit, obtaining paired cine imaging with artifacts. Radiologists assessed the image quality and annotated the level of respiratory motion artifacts. For those images with diagnostic quality, radiologists further segmented the left ventricle, left ventricle myocardium and right ventricle. The images of training set (20 volunteers) along with the annotations are released to the challenge participants, to develop an automated image quality assessment model (Task 1) and an automated segmentation model (Task 2). The images of validation set (5 volunteers) are released to the challenge participants but the annotations are withheld for online evaluation of submitted predictions. Both the images and annotations of the test set (15 volunteers) were withheld and only used for offline evaluation of submitted containerized dockers. The image quality assessment task is quantitatively evaluated by the Cohen's kappa statistics and the segmentation task is evaluated by the Dice scores and Hausdorff distances.

Jiazhen Pan, Che Liu, Junde Wu et al.

Reasoning is a critical frontier for advancing medical image analysis, where transparency and trustworthiness play a central role in both clinician trust and regulatory approval. Although Medical Visual Language Models (VLMs) show promise for radiological tasks, most existing VLMs merely produce final answers without revealing the underlying reasoning. To address this gap, we introduce MedVLM-R1, a medical VLM that explicitly generates natural language reasoning to enhance transparency and trustworthiness. Instead of relying on supervised fine-tuning (SFT), which often suffers from overfitting to training distributions and fails to foster genuine reasoning, MedVLM-R1 employs a reinforcement learning framework that incentivizes the model to discover human-interpretable reasoning paths without using any reasoning references. Despite limited training data (600 visual question answering samples) and model parameters (2B), MedVLM-R1 boosts accuracy from 55.11% to 78.22% across MRI, CT, and X-ray benchmarks, outperforming larger models trained on over a million samples. It also demonstrates robust domain generalization under out-of-distribution tasks. By unifying medical image analysis with explicit reasoning, MedVLM-R1 marks a pivotal step toward trustworthy and interpretable AI in clinical practice. Inference model is available at: https://huggingface.co/JZPeterPan/MedVLM-R1.

Che Liu, Zhongwei Wan, Cheng Ouyang et al.

Electrocardiograms (ECGs) are non-invasive diagnostic tools crucial for detecting cardiac arrhythmic diseases in clinical practice. While ECG Self-supervised Learning (eSSL) methods show promise in representation learning from unannotated ECG data, they often overlook the clinical knowledge that can be found in reports. This oversight and the requirement for annotated samples for downstream tasks limit eSSL's versatility. In this work, we address these issues with the Multimodal ECG Representation Learning (MERL}) framework. Through multimodal learning on ECG records and associated reports, MERL is capable of performing zero-shot ECG classification with text prompts, eliminating the need for training data in downstream tasks. At test time, we propose the Clinical Knowledge Enhanced Prompt Engineering (CKEPE) approach, which uses Large Language Models (LLMs) to exploit external expert-verified clinical knowledge databases, generating more descriptive prompts and reducing hallucinations in LLM-generated content to boost zero-shot classification. Based on MERL, we perform the first benchmark across six public ECG datasets, showing the superior performance of MERL compared against eSSL methods. Notably, MERL achieves an average AUC score of 75.2% in zero-shot classification (without training data), 3.2% higher than linear probed eSSL methods with 10\% annotated training data, averaged across all six datasets. Code and models are available at https://github.com/cheliu-computation/MERL

Cheng Ouyang, Moeen Ul Islam, Dong Chen et al.

Soft robots offer significant advantages in safety and adaptability, yet achieving precise and dynamic control remains a major challenge due to their inherently complex and nonlinear dynamics. Recently, Data-enabled Predictive Control (DeePC) has emerged as a promising model-free approach that bypasses explicit system identification by directly leveraging input-output data. While DeePC has shown success in other domains, its application to soft robots remains underexplored, particularly for three-dimensional (3D) soft robotic systems. This paper addresses this gap by developing and experimentally validating an effective DeePC framework on a 3D, cable-driven soft arm. Specifically, we design and fabricate a soft robotic arm with a thick tubing backbone for stability, a dense silicone body with large cavities for strength and flexibility, and rigid endcaps for secure termination. Using this platform, we implement DeePC with singular value decomposition (SVD)-based dimension reduction for two key control tasks: fixed-point regulation and trajectory tracking in 3D space. Comparative experiments with a baseline model-based controller demonstrate DeePC's superior accuracy, robustness, and adaptability, highlighting its potential as a practical solution for dynamic control of soft robots.

Liu Li, Hanchun Wang, Matthew Baugh et al.

Although existing medical image segmentation methods provide impressive pixel-wise accuracy, they often neglect topological correctness, making their segmentations unusable for many downstream tasks. One option is to retrain such models whilst including a topology-driven loss component. However, this is computationally expensive and often impractical. A better solution would be to have a versatile plug-and-play topology refinement method that is compatible with any domain-specific segmentation pipeline. Directly training a post-processing model to mitigate topological errors often fails as such models tend to be biased towards the topological errors of a target segmentation network. The diversity of these errors is confined to the information provided by a labelled training set, which is especially problematic for small datasets. Our method solves this problem by training a model-agnostic topology refinement network with synthetic segmentations that cover a wide variety of topological errors. Inspired by the Stone-Weierstrass theorem, we synthesize topology-perturbation masks with randomly sampled coefficients of orthogonal polynomial bases, which ensures a complete and unbiased representation. Practically, we verified the efficiency and effectiveness of our methods as being compatible with multiple families of polynomial bases, and show evidence that our universal plug-and-play topology refinement network outperforms both existing topology-driven learning-based and post-processing methods. We also show that combining our method with learning-based models provides an effortless add-on, which can further improve the performance of existing approaches.

Yuyuan Liu, Can Peng, Yingyu Yang et al.

Recent progress in deep learning has significantly advanced CT image analysis, particularly for segmentation tasks. However, these advances are largely confined to image-level pattern recognition, with most methods lacking explicit anatomical or contextual reasoning. Large vision-language models introduce linguistic context into image analysis, yet most approaches typically focus on a single task, which is insufficient for clinical workflow analysis that requires multiple fine-grained types of analysis, such as anatomy detection and segmentation. In this paper, we propose a unified autoregressive framework that integrates language-guided visual reasoning into CT interpretation. Our method introduces task-routing tokens that trigger detection and segmentation heads conditioned on the hidden states of a large vision-language model, enabling coherent generation of visual outputs (e.g., masks and bounding boxes) and textual reasonings. To progressively enhance localisation accuracy and semantic clarity, we further design a "closer-look" mechanism that allows the model to perform progressive coarse-to-fine visits to regions of interest under refined fields of view. To support model training and evaluation, we curated a new multimodal CT dataset containing pixel-wise masks, bounding boxes, spatial prompts, and structured descriptions for visual objects constructed through an AI-assisted annotation process with human verification. Experiments on public benchmarks demonstrate consistent improvements over the SoTA, achieving up to 1.0% Dice on BTCV and 1.7% Dice on MosMed+, while additionally providing appearance reasoning outputs. The code and dataset will be available.

Jiazhen Pan, Bailiang Jian, Paul Hager et al.

Ensuring the safety and reliability of large language models (LLMs) in clinical practice is critical to prevent patient harm and promote trustworthy healthcare applications of AI. However, LLMs are advancing so rapidly that static safety benchmarks often become obsolete upon publication, yielding only an incomplete and sometimes misleading picture of model trustworthiness. We demonstrate that a Dynamic, Automatic, and Systematic (DAS) red-teaming framework that continuously stress-tests LLMs can reveal significant weaknesses of current LLMs across four safety-critical domains: robustness, privacy, bias/fairness, and hallucination. A suite of adversarial agents is applied to autonomously mutate test cases, identify/evolve unsafe-triggering strategies, and evaluate responses, uncovering vulnerabilities in real time without human intervention. Applying DAS to 15 proprietary and open-source LLMs revealed a stark contrast between static benchmark performance and vulnerability under adversarial pressure. Despite a median MedQA accuracy exceeding 80\%, 94\% of previously correct answers failed our dynamic robustness tests. We observed similarly high failure rates across other domains: privacy leaks were elicited in 86\% of scenarios, cognitive-bias priming altered clinical recommendations in 81\% of fairness tests, and we identified hallucination rates exceeding 66\% in widely used models. Such profound residual risks are incompatible with routine clinical practice. By converting red-teaming from a static checklist into a dynamic stress-test audit, DAS red-teaming offers the surveillance that hospitals/regulators/technology vendors require as LLMs become embedded in patient chatbots, decision-support dashboards, and broader healthcare workflows. Our framework delivers an evolvable, scalable, and reliable safeguard for the next generation of medical AI.

Pramit Saha, Joshua Strong, Divyanshu Mishra et al.

Federated learning (FL) allows collaborative model training across healthcare sites without sharing sensitive patient data. However, real-world FL deployment is often hindered by complex operational challenges that demand substantial human efforts. This includes: (a) selecting appropriate clients (hospitals), (b) coordinating between the central server and clients, (c) client-level data pre-processing, (d) harmonizing non-standardized data and labels across clients, and (e) selecting FL algorithms based on user instructions and cross-client data characteristics. However, the existing FL works overlook these practical orchestration challenges. These operational bottlenecks motivate the need for autonomous, agent-driven FL systems, where intelligent agents at each hospital client and the central server agent collaboratively manage FL setup and model training with minimal human intervention. To this end, we first introduce an agent-driven FL framework that captures key phases of real-world FL workflows from client selection to training completion and a benchmark dubbed FedAgentBench that evaluates the ability of LLM agents to autonomously coordinate healthcare FL. Our framework incorporates 40 FL algorithms, each tailored to address diverse task-specific requirements and cross-client characteristics. Furthermore, we introduce a diverse set of complex tasks across 201 carefully curated datasets, simulating 6 modality-specific real-world healthcare environments, viz., Dermatoscopy, Ultrasound, Fundus, Histopathology, MRI, and X-Ray. We assess the agentic performance of 14 open-source and 10 proprietary LLMs spanning small, medium, and large model scales. While some agent cores such as GPT-4.1 and DeepSeek V3 can automate various stages of the FL pipeline, our results reveal that more complex, interdependent tasks based on implicit goals remain challenging for even the strongest models.

Jinming Duan, Jo Schlemper, Chen Qin et al.

In this work, we propose a deep learning approach for parallel magnetic resonance imaging (MRI) reconstruction, termed a variable splitting network (VS-Net), for an efficient, high-quality reconstruction of undersampled multi-coil MR data. We formulate the generalized parallel compressed sensing reconstruction as an energy minimization problem, for which a variable splitting optimization method is derived. Based on this formulation we propose a novel, end-to-end trainable deep neural network architecture by unrolling the resulting iterative process of such variable splitting scheme. VS-Net is evaluated on complex valued multi-coil knee images for 4-fold and 6-fold acceleration factors. We show that VS-Net outperforms state-of-the-art deep learning reconstruction algorithms, in terms of reconstruction accuracy and perceptual quality. Our code is publicly available at https://github.com/j-duan/VS-Net.

Xinru Zhang, Ni Ou, Berke Doga Basaran et al.

Brain lesion segmentation plays an essential role in neurological research and diagnosis. As brain lesions can be caused by various pathological alterations, different types of brain lesions tend to manifest with different characteristics on different imaging modalities. Due to this complexity, brain lesion segmentation methods are often developed in a task-specific manner. A specific segmentation model is developed for a particular lesion type and imaging modality. However, the use of task-specific models requires predetermination of the lesion type and imaging modality, which complicates their deployment in real-world scenarios. In this work, we propose a universal foundation model for 3D brain lesion segmentation, which can automatically segment different types of brain lesions for input data of various imaging modalities. We formulate a novel Mixture of Modality Experts (MoME) framework with multiple expert networks attending to different imaging modalities. A hierarchical gating network combines the expert predictions and fosters expertise collaboration. Furthermore, we introduce a curriculum learning strategy during training to avoid the degeneration of each expert network and preserve their specialization. We evaluated the proposed method on nine brain lesion datasets, encompassing five imaging modalities and eight lesion types. The results show that our model outperforms state-of-the-art universal models and provides promising generalization to unseen datasets.

Che Liu, Yinda Chen, Haoyuan Shi et al.

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 specialized domains remains such as medical imaging remains an open question. This report investigates whether DINOv3, a state-of-the-art self-supervised vision transformer (ViT) that features strong capability in dense prediction tasks, can directly serve as a powerful, unified encoder for medical vision tasks without domain-specific pre-training. To answer this, we benchmark DINOv3 across common medical vision tasks, including 2D/3D classification and segmentation on a wide range of medical imaging modalities. We systematically analyze 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 specialization, such as in Whole-Slide Pathological Images (WSIs), Electron Microscopy (EM), and Positron Emission Tomography (PET). Furthermore, we observe that DINOv3 does not consistently obey scaling law in the medical domain; performance does not reliably increase with larger models or finer feature resolutions, showing diverse scaling behaviors across tasks. Ultimately, our work establishes DINOv3 as a strong baseline, whose powerful visual features can serve as a robust prior for multiple complex medical tasks. This opens promising future directions, such as leveraging its features to enforce multiview consistency in 3D reconstruction.

Che Liu, Cheng Ouyang, Zhongwei Wan et al.

Recent advances in multimodal ECG representation learning center on aligning ECG signals with paired free-text reports. However, suboptimal alignment persists due to the complexity of medical language and the reliance on a full 12-lead setup, which is often unavailable in under-resourced settings. To tackle these issues, we propose **K-MERL**, a knowledge-enhanced multimodal ECG representation learning framework. **K-MERL** leverages large language models to extract structured knowledge from free-text reports and employs a lead-aware ECG encoder with dynamic lead masking to accommodate arbitrary lead inputs. Evaluations on six external ECG datasets show that **K-MERL** achieves state-of-the-art performance in zero-shot classification and linear probing tasks, while delivering an average **16%** AUC improvement over existing methods in partial-lead zero-shot classification.

Kang Wang, Chen Qin, Zhang Shi et al.

Deep learning models have achieved state-of-the-art performance in automated Cardiac Magnetic Resonance (CMR) analysis. However, the efficacy of these models is highly dependent on the availability of high-quality, artifact-free images. In clinical practice, CMR acquisitions are frequently degraded by respiratory motion, yet the robustness of deep learning models against such artifacts remains an underexplored problem. To promote research in this domain, we organized the MICCAI CMRxMotion challenge. We curated and publicly released a dataset of 320 CMR cine series from 40 healthy volunteers who performed specific breathing protocols to induce a controlled spectrum of motion artifacts. The challenge comprised two tasks: 1) automated image quality assessment to classify images based on motion severity, and 2) robust myocardial segmentation in the presence of motion artifacts. A total of 22 algorithms were submitted and evaluated on the two designated tasks. This paper presents a comprehensive overview of the challenge design and dataset, reports the evaluation results for the top-performing methods, and further investigates the impact of motion artifacts on five clinically relevant biomarkers. All resources and code are publicly available at: https://github.com/CMRxMotion

Liu Li, Qiang Ma, Cheng Ouyang et al.

Deep learning-based medical image segmentation techniques have shown promising results when evaluated based on conventional metrics such as the Dice score or Intersection-over-Union. However, these fully automatic methods often fail to meet clinically acceptable accuracy, especially when topological constraints should be observed, e.g., continuous boundaries or closed surfaces. In medical image segmentation, the correctness of a segmentation in terms of the required topological genus sometimes is even more important than the pixel-wise accuracy. Existing topology-aware approaches commonly estimate and constrain the topological structure via the concept of persistent homology (PH). However, these methods are difficult to implement for high dimensional data due to their polynomial computational complexity. To overcome this problem, we propose a novel and fast approach for topology-aware segmentation based on the Euler Characteristic ($χ$). First, we propose a fast formulation for $χ$ computation in both 2D and 3D. The scalar $χ$ error between the prediction and ground-truth serves as the topological evaluation metric. Then we estimate the spatial topology correctness of any segmentation network via a so-called topological violation map, i.e., a detailed map that highlights regions with $χ$ errors. Finally, the segmentation results from the arbitrary network are refined based on the topological violation maps by a topology-aware correction network. Our experiments are conducted on both 2D and 3D datasets and show that our method can significantly improve topological correctness while preserving pixel-wise segmentation accuracy.

Zhe Li, Sarah Cechnicka, Cheng Ouyang et al.

As deep learning models grow in complexity and the volume of training data increases, reducing storage and computational costs becomes increasingly important. Dataset distillation addresses this challenge by synthesizing a compact set of synthetic data that can effectively replace the original dataset in downstream classification tasks. While existing methods typically rely on mapping data from pixel space to the latent space of a generative model, we propose a novel stochastic approach that models the joint distribution of latent features. This allows our method to better capture spatial structures and produce diverse synthetic samples, which benefits model training. Specifically, we introduce a low-rank multivariate normal distribution parameterized by a lightweight network. This design maintains low computational complexity and is compatible with various matching networks used in dataset distillation. After distillation, synthetic images are generated by feeding the learned latent features into a pretrained generator. These synthetic images are then used to train classification models, and performance is evaluated on real test set. We validate our method on several benchmarks, including ImageNet subsets, CIFAR-10, and the MedMNIST histopathological dataset. Our approach achieves state-of-the-art cross architecture performance across a range of backbone architectures, demonstrating its generality and effectiveness.

Joshua Strong, Pramit Saha, Yasin Ibrahim et al.

Learning to Defer (L2D) trains autonomous systems to handle straightforward cases while deferring uncertain ones to human experts. Recent advancements in this field have introduced methods that offer flexibility to unseen experts at test time. However, we find these approaches struggle to generalise to experts with behaviours not seen during training, require extensive human annotation, and lack mechanisms for incorporating prior knowledge of expert capabilities. To address these challenges, we introduce Expert-Agnostic Learning to Defer (EA-L2D), a novel L2D framework that employs a Bayesian approach to model expert behaviour in an \textit{expert-agnostic} fashion. Across benchmark medical imaging datasets (HAM10000, Blood Cells, Retinal OCT, and Liver Tumours), EA-L2D significantly outperforms prior methods on unseen experts, achieving up to a 28\% relative improvement, while also matching or exceeding state-of-the-art performance on seen experts.

Jiayuan Zhu, Junde Wu, Cheng Ouyang et al.

Medical image segmentation data inherently contain uncertainty. This can stem from both imperfect image quality and variability in labeling preferences on ambiguous pixels, which depend on annotator expertise and the clinical context of the annotations. For instance, a boundary pixel might be labeled as tumor in diagnosis to avoid under-estimation of severity, but as normal tissue in radiotherapy to prevent damage to sensitive structures. As segmentation preferences vary across downstream applications, it is often desirable for an image segmentation model to offer user-adaptable predictions rather than a fixed output. While prior uncertainty-aware and interactive methods offer adaptability, they are inefficient at test time: uncertainty-aware models require users to choose from numerous similar outputs, while interactive models demand significant user input through click or box prompts to refine segmentation. To address these challenges, we propose \textbf{SPA}, a new \textbf{S}egmentation \textbf{P}reference \textbf{A}lignment framework that efficiently adapts to diverse test-time preferences with minimal human interaction. By presenting users with a select few, distinct segmentation candidates that best capture uncertainties, it reduces the user workload to reach the preferred segmentation. To accommodate user preference, we introduce a probabilistic mechanism that leverages user feedback to adapt a model's segmentation preference. The proposed framework is evaluated on several medical image segmentation tasks: color fundus images, lung lesion and kidney CT scans, MRI scans of brain and prostate. SPA shows 1) a significant reduction in user time and effort compared to existing interactive segmentation approaches, 2) strong adaptability based on human feedback, and 3) state-of-the-art image segmentation performance across different imaging modalities and semantic labels.

Can Peng, Qianhui Men, Pramit Saha et al.

Federated learning seeks to foster collaboration among distributed clients while preserving the privacy of their local data. Traditionally, federated learning methods assume a fixed setting in which client data and learning objectives remain constant. However, in real-world scenarios, new clients may join, and existing clients may expand the segmentation label set as task requirements evolve. In such a dynamic federated analysis setup, the conventional federated communication strategy of model aggregation per communication round is suboptimal. As new clients join, this strategy requires retraining, linearly increasing communication and computation overhead. It also imposes requirements for synchronized communication, which is difficult to achieve among distributed clients. In this paper, we propose a federated continual learning strategy that employs a one-time model aggregation at the server through multi-model distillation. This approach builds and updates the global model while eliminating the need for frequent server communication. When integrating new data streams or onboarding new clients, this approach efficiently reuses previous client models, avoiding the need to retrain the global model across the entire federation. By minimizing communication load and bypassing the need to put unchanged clients online, our approach relaxes synchronization requirements among clients, providing an efficient and scalable federated analysis framework suited for real-world applications. Using multi-class 3D abdominal CT segmentation as an application task, we demonstrate the effectiveness of the proposed approach.

Zi Wang, Fanwen Wang, Chen Qin et al.

Cardiac magnetic resonance imaging (MRI) has emerged as a clinically gold-standard technique for diagnosing cardiac diseases, thanks to its ability to provide diverse information with multiple modalities and anatomical views. Accelerated cardiac MRI is highly expected to achieve time-efficient and patient-friendly imaging, and then advanced image reconstruction approaches are required to recover high-quality, clinically interpretable images from undersampled measurements. However, the lack of publicly available cardiac MRI k-space dataset in terms of both quantity and diversity has severely hindered substantial technological progress, particularly for data-driven artificial intelligence. Here, we provide a standardized, diverse, and high-quality CMRxRecon2024 dataset to facilitate the technical development, fair evaluation, and clinical transfer of cardiac MRI reconstruction approaches, towards promoting the universal frameworks that enable fast and robust reconstructions across different cardiac MRI protocols in clinical practice. To the best of our knowledge, the CMRxRecon2024 dataset is the largest and most protocal-diverse publicly available cardiac k-space dataset. It is acquired from 330 healthy volunteers, covering commonly used modalities, anatomical views, and acquisition trajectories in clinical cardiac MRI workflows. Besides, an open platform with tutorials, benchmarks, and data processing tools is provided to facilitate data usage, advanced method development, and fair performance evaluation.

Weitong Zhang, Chengqi Zang, Liu Li et al.

Inverse problems describe the process of estimating the causal factors from a set of measurements or data. Mapping of often incomplete or degraded data to parameters is ill-posed, thus data-driven iterative solutions are required, for example when reconstructing clean images from poor signals. Diffusion models have shown promise as potent generative tools for solving inverse problems due to their superior reconstruction quality and their compatibility with iterative solvers. However, most existing approaches are limited to linear inverse problems represented as Stochastic Differential Equations (SDEs). This simplification falls short of addressing the challenging nature of real-world problems, leading to amplified cumulative errors and biases. We provide an explanation for this gap through the lens of measure-preserving dynamics of Random Dynamical Systems (RDS) with which we analyse Temporal Distribution Discrepancy and thus introduce a theoretical framework based on RDS for SDE diffusion models. We uncover several strategies that inherently enhance the stability and generalizability of diffusion models for inverse problems and introduce a novel score-based diffusion framework, the \textbf{D}ynamics-aware S\textbf{D}E \textbf{D}iffusion \textbf{G}enerative \textbf{M}odel (D$^3$GM). The \textit{Measure-preserving property} can return the degraded measurement to the original state despite complex degradation with the RDS concept of \textit{stability}. Our extensive experimental results corroborate the effectiveness of D$^3$GM across multiple benchmarks including a prominent application for inverse problems, magnetic resonance imaging. Code and data will be publicly available.

Cheng Ouyang, Chen Chen, Surui Li et al.

Deep learning models usually suffer from domain shift issues, where models trained on one source domain do not generalize well to other unseen domains. In this work, we investigate the single-source domain generalization problem: training a deep network that is robust to unseen domains, under the condition that training data is only available from one source domain, which is common in medical imaging applications. We tackle this problem in the context of cross-domain medical image segmentation. Under this scenario, domain shifts are mainly caused by different acquisition processes. We propose a simple causality-inspired data augmentation approach to expose a segmentation model to synthesized domain-shifted training examples. Specifically, 1) to make the deep model robust to discrepancies in image intensities and textures, we employ a family of randomly-weighted shallow networks. They augment training images using diverse appearance transformations. 2) Further we show that spurious correlations among objects in an image are detrimental to domain robustness. These correlations might be taken by the network as domain-specific clues for making predictions, and they may break on unseen domains. We remove these spurious correlations via causal intervention. This is achieved by resampling the appearances of potentially correlated objects independently. The proposed approach is validated on three cross-domain segmentation tasks: cross-modality (CT-MRI) abdominal image segmentation, cross-sequence (bSSFP-LGE) cardiac MRI segmentation, and cross-center prostate MRI segmentation. The proposed approach yields consistent performance gains compared with competitive methods when tested on unseen domains.

Chen Chen, Chen Qin, Cheng Ouyang et al.

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.

Chen Chen, Kerstin Hammernik, Cheng Ouyang et al.

Deep learning-based segmentation methods are vulnerable to unforeseen data distribution shifts during deployment, e.g. change of image appearances or contrasts caused by different scanners, unexpected imaging artifacts etc. In this paper, we present a cooperative framework for training image segmentation models and a latent space augmentation method for generating hard examples. Both contributions improve model generalization and robustness with limited data. The cooperative training framework consists of a fast-thinking network (FTN) and a slow-thinking network (STN). The FTN learns decoupled image features and shape features for image reconstruction and segmentation tasks. The STN learns shape priors for segmentation correction and refinement. The two networks are trained in a cooperative manner. The latent space augmentation generates challenging examples for training by masking the decoupled latent space in both channel-wise and spatial-wise manners. We performed extensive experiments on public cardiac imaging datasets. Using only 10 subjects from a single site for training, we demonstrated improved cross-site segmentation performance and increased robustness against various unforeseen imaging artifacts compared to strong baseline methods. Particularly, cooperative training with latent space data augmentation yields 15% improvement in terms of average Dice score when compared to a standard training method.

Cheng Ouyang, Carlo Biffi, Chen Chen et al.

Few-shot semantic segmentation (FSS) has great potential for medical imaging applications. Most of the existing FSS techniques require abundant annotated semantic classes for training. However, these methods may not be applicable for medical images due to the lack of annotations. To address this problem we make several contributions: (1) A novel self-supervised FSS framework for medical images in order to eliminate the requirement for annotations during training. Additionally, superpixel-based pseudo-labels are generated to provide supervision; (2) An adaptive local prototype pooling module plugged into prototypical networks, to solve the common challenging foreground-background imbalance problem in medical image segmentation; (3) We demonstrate the general applicability of the proposed approach for medical images using three different tasks: abdominal organ segmentation for CT and MRI, as well as cardiac segmentation for MRI. Our results show that, for medical image segmentation, the proposed method outperforms conventional FSS methods which require manual annotations for training.

Chen Chen, Chen Qin, Huaqi Qiu et al.

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.

Xiahai Zhuang, Jiahang Xu, Xinzhe Luo et al.

Accurate computing, analysis and modeling of the ventricles and myocardium from medical images are important, especially in the diagnosis and treatment management for patients suffering from myocardial infarction (MI). Late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) provides an important protocol to visualize MI. However, automated segmentation of LGE CMR is still challenging, due to the indistinguishable boundaries, heterogeneous intensity distribution and complex enhancement patterns of pathological myocardium from LGE CMR. Furthermore, compared with the other sequences LGE CMR images with gold standard labels are particularly limited, which represents another obstacle for developing novel algorithms for automatic segmentation of LGE CMR. This paper presents the selective results from the Multi-Sequence Cardiac MR (MS-CMR) Segmentation challenge, in conjunction with MICCAI 2019. The challenge offered a data set of paired MS-CMR images, including auxiliary CMR sequences as well as LGE CMR, from 45 patients who underwent cardiomyopathy. It was aimed to develop new algorithms, as well as benchmark existing ones for LGE CMR segmentation and compare them objectively. In addition, the paired MS-CMR images could enable algorithms to combine the complementary information from the other sequences for the segmentation of LGE CMR. Nine representative works were selected for evaluation and comparisons, among which three methods are unsupervised methods and the other six are supervised. The results showed that the average performance of the nine methods was comparable to the inter-observer variations. The success of these methods was mainly attributed to the inclusion of the auxiliary sequences from the MS-CMR images, which provide important label information for the training of deep neural networks.

Jo Schlemper, Jinming Duan, Cheng Ouyang et al.

We present simple reconstruction networks for multi-coil data by extending deep cascade of CNN's and exploiting the data consistency layer. In particular, we propose two variants, where one is inspired by POCSENSE and the other is calibration-less. We show that the proposed approaches are competitive relative to the state of the art both quantitatively and qualitatively.

Chen Chen, Cheng Ouyang, Giacomo Tarroni et al.

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.

Cheng Ouyang, Konstantinos Kamnitsas, Carlo Biffi et al.

Deep learning models trained on medical images from a source domain (e.g. imaging modality) often fail when deployed on images from a different target domain, despite imaging common anatomical structures. Deep unsupervised domain adaptation (UDA) aims to improve the performance of a deep neural network model on a target domain, using solely unlabelled target domain data and labelled source domain data. However, current state-of-the-art methods exhibit reduced performance when target data is scarce. In this work, we introduce a new data efficient UDA method for multi-domain medical image segmentation. The proposed method combines a novel VAE-based feature prior matching, which is data-efficient, and domain adversarial training to learn a shared domain-invariant latent space which is exploited during segmentation. Our method is evaluated on a public multi-modality cardiac image segmentation dataset by adapting from the labelled source domain (3D MRI) to the unlabelled target domain (3D CT). We show that by using only one single unlabelled 3D CT scan, the proposed architecture outperforms the state-of-the-art in the same setting. Finally, we perform ablation studies on prior matching and domain adversarial training to shed light on the theoretical grounding of the proposed method.

Cheng Ouyang, Jo Schlemper, Carlo Biffi et al.

We look into the robustness of deep learning based MRI reconstruction when tested on unseen contrasts and organs. We then propose to generalize the network by training with large publicly-available natural image datasets with synthesized phase information to achieve high cross-domain reconstruction performance which is competitive with domain-specific training. To explain its generalization mechanism, we have also analyzed patch sets for different training datasets.

Qi Dou, Cheng Ouyang, Cheng Chen et al.

Deep convolutional networks have demonstrated the state-of-the-art performance on various medical image computing tasks. Leveraging images from different modalities for the same analysis task holds clinical benefits. However, the generalization capability of deep models on test data with different distributions remain as a major challenge. In this paper, we propose the PnPAdaNet (plug-and-play adversarial domain adaptation network) for adapting segmentation networks between different modalities of medical images, e.g., MRI and CT. We propose to tackle the significant domain shift by aligning the feature spaces of source and target domains in an unsupervised manner. Specifically, a domain adaptation module flexibly replaces the early encoder layers of the source network, and the higher layers are shared between domains. With adversarial learning, we build two discriminators whose inputs are respectively multi-level features and predicted segmentation masks. We have validated our domain adaptation method on cardiac structure segmentation in unpaired MRI and CT. The experimental results with comprehensive ablation studies demonstrate the excellent efficacy of our proposed PnP-AdaNet. Moreover, we introduce a novel benchmark on the cardiac dataset for the task of unsupervised cross-modality domain adaptation. We will make our code and database publicly available, aiming to promote future studies on this challenging yet important research topic in medical imaging.

Qi Dou, Cheng Ouyang, Cheng Chen et al.

Convolutional networks (ConvNets) have achieved great successes in various challenging vision tasks. However, the performance of ConvNets would degrade when encountering the domain shift. The domain adaptation is more significant while challenging in the field of biomedical image analysis, where cross-modality data have largely different distributions. Given that annotating the medical data is especially expensive, the supervised transfer learning approaches are not quite optimal. In this paper, we propose an unsupervised domain adaptation framework with adversarial learning for cross-modality biomedical image segmentations. Specifically, our model is based on a dilated fully convolutional network for pixel-wise prediction. Moreover, we build a plug-and-play domain adaptation module (DAM) to map the target input to features which are aligned with source domain feature space. A domain critic module (DCM) is set up for discriminating the feature space of both domains. We optimize the DAM and DCM via an adversarial loss without using any target domain label. Our proposed method is validated by adapting a ConvNet trained with MRI images to unpaired CT data for cardiac structures segmentations, and achieved very promising results.