SegHeD: Segmentation of Heterogeneous Data for Multiple Sclerosis Lesions with Anatomical Constraints

Assessment of lesions and their longitudinal progression from brain magnetic resonance (MR) images plays a crucial role in diagnosing and monitoring multiple sclerosis (MS). Machine learning models have demonstrated a great potential for automated MS lesion segmentation. Training such models typically requires large-scale high-quality datasets that are consistently annotated. However, MS imaging datasets are often small, segregated across multiple sites, with different formats (cross-sectional or longitudinal), and diverse annotation styles. This poses a significant challenge to train a unified MS lesion segmentation model. To tackle this challenge, we present SegHeD, a novel multi-dataset multi-task segmentation model that can incorporate heterogeneous data as input and perform all-lesion, new-lesion, as well as vanishing-lesion segmentation. Furthermore, we account for domain knowledge about MS lesions, incorporating longitudinal, spatial, and volumetric constraints into the segmentation model. SegHeD is assessed on five MS datasets and achieves a high performance in all, new, and vanishing-lesion segmentation, outperforming several state-of-the-art methods in this field.

A Personalised 3D+t Mesh Generative Model for Unveiling Normal Heart Dynamics

Understanding the structure and motion of the heart is crucial for diagnosing and managing cardiovascular diseases, the leading cause of global death. There is wide variation in cardiac shape and motion patterns, that are influenced by demographic, anthropometric and disease factors. Unravelling the normal patterns of shape and motion, as well as understanding how each individual deviates from the norm, would facilitate accurate diagnosis and personalised treatment strategies. To this end, we developed a novel conditional generative model, MeshHeart, to learn the distribution of cardiac shape and motion patterns. MeshHeart is capable of generating 3D+t cardiac mesh sequences, taking into account clinical factors such as age, sex, weight and height. To model the high-dimensional and complex spatio-temporal mesh data, MeshHeart employs a geometric encoder to represent cardiac meshes in a latent space, followed by a temporal Transformer to model the motion dynamics of latent representations. Based on MeshHeart, we investigate the latent space of 3D+t cardiac mesh sequences and propose a novel distance metric termed latent delta, which quantifies the deviation of a real heart from its personalised normative pattern in the latent space. In experiments using a large dataset of 38,309 subjects, MeshHeart demonstrates a high performance in cardiac mesh sequence reconstruction and generation. Features defined in the latent space are highly discriminative for cardiac disease classification, whereas the latent delta exhibits strong correlation with clinical phenotypes in phenome-wide association studies. The codes and models of this study will be released to benefit further research on digital heart modelling.

Quantifying the Impact of Population Shift Across Age and Sex for Abdominal Organ Segmentation

Deep learning-based medical image segmentation has seen tremendous progress over the last decade, but there is still relatively little transfer into clinical practice. One of the main barriers is the challenge of domain generalisation, which requires segmentation models to maintain high performance across a wide distribution of image data. This challenge is amplified by the many factors that contribute to the diverse appearance of medical images, such as acquisition conditions and patient characteristics. The impact of shifting patient characteristics such as age and sex on segmentation performance remains relatively under-studied, especially for abdominal organs, despite that this is crucial for ensuring the fairness of the segmentation model. We perform the first study to determine the impact of population shift with respect to age and sex on abdominal CT image segmentation, by leveraging two large public datasets, and introduce a novel metric to quantify the impact. We find that population shift is a challenge similar in magnitude to cross-dataset shift for abdominal organ segmentation, and that the effect is asymmetric and dataset-dependent. We conclude that dataset diversity in terms of known patient characteristics is not necessarily equivalent to dataset diversity in terms of image features. This implies that simple population matching to ensure good generalisation and fairness may be insufficient, and we recommend that fairness research should be directed towards better understanding and quantifying medical image dataset diversity in terms of performance-relevant characteristics such as organ morphology.

TIP: Tabular-Image Pre-training for Multimodal Classification with Incomplete Data

Images and structured tables are essential parts of real-world databases. Though tabular-image representation learning is promising to create new insights, it remains a challenging task, as tabular data is typically heterogeneous and incomplete, presenting significant modality disparities with images. Earlier works have mainly focused on simple modality fusion strategies in complete data scenarios, without considering the missing data issue, and thus are limited in practice. In this paper, we propose TIP, a novel tabular-image pre-training framework for learning multimodal representations robust to incomplete tabular data. Specifically, TIP investigates a novel self-supervised learning (SSL) strategy, including a masked tabular reconstruction task for tackling data missingness, and image-tabular matching and contrastive learning objectives to capture multimodal information. Moreover, TIP proposes a versatile tabular encoder tailored for incomplete, heterogeneous tabular data and a multimodal interaction module for inter-modality representation learning. Experiments are performed on downstream multimodal classification tasks using both natural and medical image datasets. The results show that TIP outperforms state-of-the-art supervised/SSL image/multimodal algorithms in both complete and incomplete data scenarios. Our code is available at https://github.com/siyi-wind/TIP.

CMRxRecon2024: A Multi-Modality, Multi-View K-Space Dataset Boosting Universal Machine Learning for Accelerated Cardiac MRI

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 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.

A Foundation Model for Brain Lesion Segmentation with Mixture of Modality Experts

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.

The state-of-the-art in Cardiac MRI Reconstruction: Results of the CMRxRecon Challenge in MICCAI 2023

Cardiac MRI, crucial for evaluating heart structure and function, faces limitations like slow imaging and motion artifacts. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on MICCAI. CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techniques, physical modeling, and model complexity, thereby providing valuable insights for further developments in this field.

Zero-Shot ECG Classification with Multimodal Learning and Test-time Clinical Knowledge Enhancement

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.

T3D: Towards 3D Medical Image Understanding through Vision-Language Pre-training

Expert annotation of 3D medical image for downstream analysis is resource-intensive, posing challenges in clinical applications. Visual self-supervised learning (vSSL), though effective for learning visual invariance, neglects the incorporation of domain knowledge from medicine. To incorporate medical knowledge into visual representation learning, vision-language pre-training (VLP) has shown promising results in 2D image. However, existing VLP approaches become generally impractical when applied to high-resolution 3D medical images due to GPU hardware constraints and the potential loss of critical details caused by downsampling, which is the intuitive solution to hardware constraints. To address the above limitations, we introduce T3D, the first VLP framework designed for high-resolution 3D medical images. T3D incorporates two text-informed pretext tasks: (\lowerromannumeral{1}) text-informed contrastive learning; (\lowerromannumeral{2}) text-informed image restoration. These tasks focus on learning 3D visual representations from high-resolution 3D medical images and integrating clinical knowledge from radiology reports, without distorting information through forced alignment of downsampled volumes with detailed anatomical text. Trained on a newly curated large-scale dataset of 3D medical images and radiology reports, T3D significantly outperforms current vSSL methods in tasks like organ and tumor segmentation, as well as disease classification. This underlines T3D's potential in representation learning for 3D medical image analysis. All data and code will be available upon acceptance.

G2D: From Global to Dense Radiography Representation Learning via Vision-Language Pre-training

Recently, medical vision-language pre-training (VLP) has reached substantial progress to learn global visual representation from medical images and their paired radiology reports. However, medical imaging tasks in real world usually require finer granularity in visual features. These tasks include visual localization tasks (e.g., semantic segmentation, object detection) and visual grounding task. Yet, current medical VLP methods face challenges in learning these fine-grained features, as they primarily focus on brute-force alignment between image patches and individual text tokens for local visual feature learning, which is suboptimal for downstream dense prediction tasks. In this work, we propose a new VLP framework, named \textbf{G}lobal to \textbf{D}ense level representation learning (G2D) that achieves significantly improved granularity and more accurate grounding for the learned features, compared to existing medical VLP approaches. In particular, G2D learns dense and semantically-grounded image representations via a pseudo segmentation task parallel with the global vision-language alignment. Notably, generating pseudo segmentation targets does not incur extra trainable parameters: they are obtained on the fly during VLP with a parameter-free processor. G2D achieves superior performance across 6 medical imaging tasks and 25 diseases, particularly in semantic segmentation, which necessitates fine-grained, semantically-grounded image features. In this task, G2D surpasses peer models even when fine-tuned with just 1\% of the training data, compared to the 100\% used by these models. The code will be released upon acceptance.