Machine learning prediction of obstructive coronary artery disease using opportunistic coronary calcium and epicardial fat assessments from CT calcium scoring scans

Non-contrast computed tomography calcium scoring (CTCS) is a cost-effective imaging modality widely used to detect coronary artery calcifications. This study aimed to develop an advanced machine learning framework that utilizes quantitative analyses of coronary calcium and epicardial fat from CTCS images to predict obstructive coronary artery disease (CAD). The study population consisted of 1,324 patients from the SCOT-HEART clinical trial who underwent both CTCS and coronary CT angiography. We extracted and analyzed a broad range of features, including 24 clinical variables, 189 calcium-omics, and 211 epicardial fat-omics features from the CTCS images. Feature selection was conducted using the CatBoost algorithm combined with SHapley Additive exPlanation (SHAP) values. Predictive modeling utilized the CatBoost gradient boosting method, focusing on the most informative features. From an initial set of 424 candidate features, 14 were identified as most predictive through the CatBoost-SHAP method. The top two predictive features originated from fat-omics, with the remaining 12 features derived from calcium-omics. The optimized model achieved robust predictive capabilities, demonstrating a sensitivity of 83.1+/-4.6%, specificity of 93.8+/-1.7%, accuracy of 85.3+/-2.0%, and an F1 score of 73.9+/-3.3%. Inclusion of calcium-omics and fat-omics data significantly improved predictive performance. Notably, the model also showed reliable predictive accuracy in patients with diverse coronary calcium scores, including cases with obstructive CAD despite a zero-calcium score. This innovative approach holds promise for improving clinical decision-making and potentially reducing dependence on contrast-enhanced or invasive diagnostic procedures, particularly within low-to intermediate-risk patient groups.

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

Whole Heart Anatomical Refinement from CCTA using Extrapolation and Parcellation

Coronary computed tomography angiography (CCTA) provides detailed an-atomical information on all chambers of the heart. Existing segmentation tools can label the gross anatomy, but addition of application-specific labels can require detailed and often manual refinement. We developed a U-Net based framework to i) extrapolate a new label from existing labels, and ii) parcellate one label into multiple labels, both using label-to-label mapping, to create a desired segmentation that could then be learnt directly from the image (image- to-label mapping). This approach only required manual correction in a small subset of cases (80 for extrapolation, 50 for parcella-tion, compared with 260 for initial labels). An initial 6-label segmentation (left ventricle, left ventricular myocardium, right ventricle, left atrium, right atrium and aorta) was refined to a 10-label segmentation that added a label for the pulmonary artery and divided the left atrium label into body, left and right veins and appendage components. The final method was tested using 30 cases, 10 each from Philips, Siemens and Toshiba scanners. In addition to the new labels, the median Dice scores were improved for all the initial 6 labels to be above 95% in the 10-label segmentation, e.g. from 91% to 97% for the left atrium body and from 92% to 96% for the right ventricle. This method provides a simple framework for flexible refinement of anatomical labels. The code and executables are available at cemrg.com.