Surface Masked AutoEncoder: Self-Supervision for Cortical Imaging Data

Self-supervision has been widely explored as a means of addressing the lack of inductive biases in vision transformer architectures, which limits generalisation when networks are trained on small datasets. This is crucial in the context of cortical imaging, where phenotypes are complex and heterogeneous, but the available datasets are limited in size. This paper builds upon recent advancements in translating vision transformers to surface meshes and investigates the potential of Masked AutoEncoder (MAE) self-supervision for cortical surface learning. By reconstructing surface data from a masked version of the input, the proposed method effectively models cortical structure to learn strong representations that translate to improved performance in downstream tasks. We evaluate our approach on cortical phenotype regression using the developing Human Connectome Project (dHCP) and demonstrate that pre-training leads to a 26\% improvement in performance, with an 80\% faster convergence, compared to models trained from scratch. Furthermore, we establish that pre-training vision transformer models on large datasets, such as the UK Biobank (UKB), enables the acquisition of robust representations for finetuning in low-data scenarios. Our code and pre-trained models are publicly available at \url{https://github.com/metrics-lab/surface-vision-transformers}.

Unlocking the Diagnostic Potential of ECG through Knowledge Transfer from Cardiac MRI

The electrocardiogram (ECG) is a widely available diagnostic tool that allows for a cost-effective and fast assessment of the cardiovascular health. However, more detailed examination with expensive cardiac magnetic resonance (CMR) imaging is often preferred for the diagnosis of cardiovascular diseases. While providing detailed visualization of the cardiac anatomy, CMR imaging is not widely available due to long scan times and high costs. To address this issue, we propose the first self-supervised contrastive approach that transfers domain-specific information from CMR images to ECG embeddings. Our approach combines multimodal contrastive learning with masked data modeling to enable holistic cardiac screening solely from ECG data. In extensive experiments using data from 40,044 UK Biobank subjects, we demonstrate the utility and generalizability of our method. We predict the subject-specific risk of various cardiovascular diseases and determine distinct cardiac phenotypes solely from ECG data. In a qualitative analysis, we demonstrate that our learned ECG embeddings incorporate information from CMR image regions of interest. We make our entire pipeline publicly available, including the source code and pre-trained model weights.

Metrics to Quantify Global Consistency in Synthetic Medical Images

Image synthesis is increasingly being adopted in medical image processing, for example for data augmentation or inter-modality image translation. In these critical applications, the generated images must fulfill a high standard of biological correctness. A particular requirement for these images is global consistency, i.e an image being overall coherent and structured so that all parts of the image fit together in a realistic and meaningful way. Yet, established image quality metrics do not explicitly quantify this property of synthetic images. In this work, we introduce two metrics that can measure the global consistency of synthetic images on a per-image basis. To measure the global consistency, we presume that a realistic image exhibits consistent properties, e.g., a person's body fat in a whole-body MRI, throughout the depicted object or scene. Hence, we quantify global consistency by predicting and comparing explicit attributes of images on patches using supervised trained neural networks. Next, we adapt this strategy to an unlabeled setting by measuring the similarity of implicit image features predicted by a self-supervised trained network. Our results demonstrate that predicting explicit attributes of synthetic images on patches can distinguish globally consistent from inconsistent images. Implicit representations of images are less sensitive to assess global consistency but are still serviceable when labeled data is unavailable. Compared to established metrics, such as the FID, our method can explicitly measure global consistency on a per-image basis, enabling a dedicated analysis of the biological plausibility of single synthetic images.

Pretrained Deep 2.5D Models for Efficient Predictive Modeling from Retinal OCT

In the field of medical imaging, 3D deep learning models play a crucial role in building powerful predictive models of disease progression. However, the size of these models presents significant challenges, both in terms of computational resources and data requirements. Moreover, achieving high-quality pretraining of 3D models proves to be even more challenging. To address these issues, hybrid 2.5D approaches provide an effective solution for utilizing 3D volumetric data efficiently using 2D models. Combining 2D and 3D techniques offers a promising avenue for optimizing performance while minimizing memory requirements. In this paper, we explore 2.5D architectures based on a combination of convolutional neural networks (CNNs), long short-term memory (LSTM), and Transformers. In addition, leveraging the benefits of recent non-contrastive pretraining approaches in 2D, we enhanced the performance and data efficiency of 2.5D techniques even further. We demonstrate the effectiveness of architectures and associated pretraining on a task of predicting progression to wet age-related macular degeneration (AMD) within a six-month period on two large longitudinal OCT datasets.

Global k-Space Interpolation for Dynamic MRI Reconstruction using Masked Image Modeling

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

Conditional Temporal Attention Networks for Neonatal Cortical Surface Reconstruction

Cortical surface reconstruction plays a fundamental role in modeling the rapid brain development during the perinatal period. In this work, we propose Conditional Temporal Attention Network (CoTAN), a fast end-to-end framework for diffeomorphic neonatal cortical surface reconstruction. CoTAN predicts multi-resolution stationary velocity fields (SVF) from neonatal brain magnetic resonance images (MRI). Instead of integrating multiple SVFs, CoTAN introduces attention mechanisms to learn a conditional time-varying velocity field (CTVF) by computing the weighted sum of all SVFs at each integration step. The importance of each SVF, which is estimated by learned attention maps, is conditioned on the age of the neonates and varies with the time step of integration. The proposed CTVF defines a diffeomorphic surface deformation, which reduces mesh self-intersection errors effectively. It only requires 0.21 seconds to deform an initial template mesh to cortical white matter and pial surfaces for each brain hemisphere. CoTAN is validated on the Developing Human Connectome Project (dHCP) dataset with 877 3D brain MR images acquired from preterm and term born neonates. Compared to state-of-the-art baselines, CoTAN achieves superior performance with only 0.12mm geometric error and 0.07% self-intersecting faces. The visualization of our attention maps illustrates that CoTAN indeed learns coarse-to-fine surface deformations automatically without intermediate supervision.

Multimodal brain age estimation using interpretable adaptive population-graph learning

Brain age estimation is clinically important as it can provide valuable information in the context of neurodegenerative diseases such as Alzheimer's. Population graphs, which include multimodal imaging information of the subjects along with the relationships among the population, have been used in literature along with Graph Convolutional Networks (GCNs) and have proved beneficial for a variety of medical imaging tasks. A population graph is usually static and constructed manually using non-imaging information. However, graph construction is not a trivial task and might significantly affect the performance of the GCN, which is inherently very sensitive to the graph structure. In this work, we propose a framework that learns a population graph structure optimized for the downstream task. An attention mechanism assigns weights to a set of imaging and non-imaging features (phenotypes), which are then used for edge extraction. The resulting graph is used to train the GCN. The entire pipeline can be trained end-to-end. Additionally, by visualizing the attention weights that were the most important for the graph construction, we increase the interpretability of the graph. We use the UK Biobank, which provides a large variety of neuroimaging and non-imaging phenotypes, to evaluate our method on brain age regression and classification. The proposed method outperforms competing static graph approaches and other state-of-the-art adaptive methods. We further show that the assigned attention scores indicate that there are both imaging and non-imaging phenotypes that are informative for brain age estimation and are in agreement with the relevant literature.

Atlas-Based Interpretable Age Prediction

Age prediction is an important part of medical assessments and research. It can aid in detecting diseases as well as abnormal ageing by highlighting the discrepancy between chronological and biological age. To gain a comprehensive understanding of age-related changes observed in various body parts, we investigate them on a larger scale by using whole-body images. We utilise the Grad-CAM interpretability method to determine the body areas most predictive of a person's age. We expand our analysis beyond individual subjects by employing registration techniques to generate population-wide interpretability maps. Furthermore, we set state-of-the-art whole-body age prediction with a model that achieves a mean absolute error of 2.76 years. Our findings reveal three primary areas of interest: the spine, the autochthonous back muscles, and the cardiac region, which exhibits the highest importance.

Privacy-Utility Trade-offs in Neural Networks for Medical Population Graphs: Insights from Differential Privacy and Graph Structure

We initiate an empirical investigation into differentially private graph neural networks on population graphs from the medical domain by examining privacy-utility trade-offs at different privacy levels on both real-world and synthetic datasets and performing auditing through membership inference attacks. Our findings highlight the potential and the challenges of this specific DP application area. Moreover, we find evidence that the underlying graph structure constitutes a potential factor for larger performance gaps by showing a correlation between the degree of graph homophily and the accuracy of the trained model.

Body Fat Estimation from Surface Meshes using Graph Neural Networks

Body fat volume and distribution can be a strong indication for a person's overall health and the risk for developing diseases like type 2 diabetes and cardiovascular diseases. Frequently used measures for fat estimation are the body mass index (BMI), waist circumference, or the waist-hip-ratio. However, those are rather imprecise measures that do not allow for a discrimination between different types of fat or between fat and muscle tissue. The estimation of visceral (VAT) and abdominal subcutaneous (ASAT) adipose tissue volume has shown to be a more accurate measure for named risk factors. In this work, we show that triangulated body surface meshes can be used to accurately predict VAT and ASAT volumes using graph neural networks. Our methods achieve high performance while reducing training time and required resources compared to state-of-the-art convolutional neural networks in this area. We furthermore envision this method to be applicable to cheaper and easily accessible medical surface scans instead of expensive medical images.