Active Learning for Deep Learning-Based Hemodynamic Parameter Estimation

Hemodynamic parameters such as pressure and wall shear stress play an important role in diagnosis, prognosis, and treatment planning in cardiovascular diseases. These parameters can be accurately computed using computational fluid dynamics (CFD), but CFD is computationally intensive. Hence, deep learning methods have been adopted as a surrogate to rapidly estimate CFD outcomes. A drawback of such data-driven models is the need for time-consuming reference CFD simulations for training. In this work, we introduce an active learning framework to reduce the number of CFD simulations required for the training of surrogate models, lowering the barriers to their deployment in new applications. We propose three distinct querying strategies to determine for which unlabeled samples CFD simulations should be obtained. These querying strategies are based on geometrical variance, ensemble uncertainty, and adherence to the physics governing fluid dynamics. We benchmark these methods on velocity field estimation in synthetic coronary artery bifurcations and find that they allow for substantial reductions in annotation cost. Notably, we find that our strategies reduce the number of samples required by up to 50% and make the trained models more robust to difficult cases. Our results show that active learning is a feasible strategy to increase the potential of deep learning-based CFD surrogates.

Learning Hemodynamic Scalar Fields on Coronary Artery Meshes: A Benchmark of Geometric Deep Learning Models

Coronary artery disease, caused by the narrowing of coronary vessels due to atherosclerosis, is the leading cause of death worldwide. The diagnostic gold standard, fractional flow reserve (FFR), measures the trans-stenotic pressure ratio during maximal vasodilation but is invasive and costly. This has driven the development of virtual FFR (vFFR) using computational fluid dynamics (CFD) to simulate coronary flow. Geometric deep learning algorithms have shown promise for learning features on meshes, including cardiovascular research applications. This study empirically analyzes various backends for predicting vFFR fields in coronary arteries as CFD surrogates, comparing six backends for learning hemodynamics on meshes using CFD solutions as ground truth. The study has two parts: i) Using 1,500 synthetic left coronary artery bifurcations, models were trained to predict pressure-related fields for vFFR reconstruction, comparing different learning variables. ii) Using 427 patient-specific CFD simulations, experiments were repeated focusing on the best-performing learning variable from the synthetic dataset. Most backends performed well on the synthetic dataset, especially when predicting pressure drop over the manifold. Transformer-based backends outperformed others when predicting pressure and vFFR fields and were the only models achieving strong performance on patient-specific data, excelling in both average per-point error and vFFR accuracy in stenotic lesions. These results suggest geometric deep learning backends can effectively replace CFD for simple geometries, while transformer-based networks are superior for complex, heterogeneous datasets. Pressure drop was identified as the optimal network output for learning pressure-related fields.

Deep vectorised operators for pulsatile hemodynamics estimation in coronary arteries from a steady-state prior

Cardiovascular hemodynamic fields provide valuable medical decision markers for coronary artery disease. Computational fluid dynamics (CFD) is the gold standard for accurate, non-invasive evaluation of these quantities in vivo. In this work, we propose a time-efficient surrogate model, powered by machine learning, for the estimation of pulsatile hemodynamics based on steady-state priors. We introduce deep vectorised operators, a modelling framework for discretisation independent learning on infinite-dimensional function spaces. The underlying neural architecture is a neural field conditioned on hemodynamic boundary conditions. Importantly, we show how relaxing the requirement of point-wise action to permutation-equivariance leads to a family of models that can be parametrised by message passing and self-attention layers. We evaluate our approach on a dataset of 74 stenotic coronary arteries extracted from coronary computed tomography angiography (CCTA) with patient-specific pulsatile CFD simulations as ground truth. We show that our model produces accurate estimates of the pulsatile velocity and pressure while being agnostic to re-sampling of the source domain (discretisation independence). This shows that deep vectorised operators are a powerful modelling tool for cardiovascular hemodynamics estimation in coronary arteries and beyond.

ICML Topological Deep Learning Challenge 2024: Beyond the Graph Domain

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings.

Neural Fields for Continuous Periodic Motion Estimation in 4D Cardiovascular Imaging

Time-resolved three-dimensional flow MRI (4D flow MRI) provides a unique non-invasive solution to visualize and quantify hemodynamics in blood vessels such as the aortic arch. However, most current analysis methods for arterial 4D flow MRI use static artery walls because of the difficulty in obtaining a full cycle segmentation. To overcome this limitation, we propose a neural fields-based method that directly estimates continuous periodic wall deformations throughout the cardiac cycle. For a 3D + time imaging dataset, we optimize an implicit neural representation (INR) that represents a time-dependent velocity vector field (VVF). An ODE solver is used to integrate the VVF into a deformation vector field (DVF), that can deform images, segmentation masks, or meshes over time, thereby visualizing and quantifying local wall motion patterns. To properly reflect the periodic nature of 3D + time cardiovascular data, we impose periodicity in two ways. First, by periodically encoding the time input to the INR, and hence VVF. Second, by regularizing the DVF. We demonstrate the effectiveness of this approach on synthetic data with different periodic patterns, ECG-gated CT, and 4D flow MRI data. The obtained method could be used to improve 4D flow MRI analysis.

Global Control for Local SO-Equivariant Scale-Invariant Vessel Segmentation

Personalized 3D vascular models can aid in a range of diagnostic, prognostic, and treatment-planning tasks relevant to cardiovascular disease management. Deep learning provides a means to automatically obtain such models. Ideally, a user should have control over the exact region of interest (ROI) to be included in a vascular model, and the model should be watertight and highly accurate. To this end, we propose a combination of a global controller leveraging voxel mask segmentations to provide boundary conditions for vessels of interest to a local, iterative vessel segmentation model. We introduce the preservation of scale- and rotational symmetries in the local segmentation model, leading to generalisation to vessels of unseen sizes and orientations. Combined with the global controller, this enables flexible 3D vascular model building, without additional retraining. We demonstrate the potential of our method on a dataset containing abdominal aortic aneurysms (AAAs). Our method performs on par with a state-of-the-art segmentation model in the segmentation of AAAs, iliac arteries and renal arteries, while providing a watertight, smooth surface segmentation. Moreover, we demonstrate that by adapting the global controller, we can easily extend vessel sections in the 3D model.