Physics-informed neural networks for blood flow inverse problems

Physics-informed neural networks (PINNs) have emerged as a powerful tool for solving inverse problems, especially in cases where no complete information about the system is known and scatter measurements are available. This is especially useful in hemodynamics since the boundary information is often difficult to model, and high-quality blood flow measurements are generally hard to obtain. In this work, we use the PINNs methodology for estimating reduced-order model parameters and the full velocity field from scatter 2D noisy measurements in the ascending aorta. The results show stable and accurate parameter estimations when using the method with simulated data, while the velocity reconstruction shows dependence on the measurement quality and the flow pattern complexity. The method allows for solving clinical-relevant inverse problems in hemodynamics and complex coupled physical systems

Probabilistic learning of the Purkinje network from the electrocardiogram

The identification of the Purkinje conduction system in the heart is a challenging task, yet essential for a correct definition of cardiac digital twins for precision cardiology. Here, we propose a probabilistic approach for identifying the Purkinje network from non-invasive clinical data such as the standard electrocardiogram (ECG). We use cardiac imaging to build an anatomically accurate model of the ventricles; we algorithmically generate a rule-based Purkinje network tailored to the anatomy; we simulate physiological electrocardiograms with a fast model; we identify the geometrical and electrical parameters of the Purkinje-ECG model with Bayesian optimization and approximate Bayesian computation. The proposed approach is inherently probabilistic and generates a population of plausible Purkinje networks, all fitting the ECG within a given tolerance. In this way, we can estimate the uncertainty of the parameters, thus providing reliable predictions. We test our methodology in physiological and pathological scenarios, showing that we are able to accurately recover the ECG with our model. We propagate the uncertainty in the Purkinje network parameters in a simulation of conduction system pacing therapy. Our methodology is a step forward in creation of digital twins from non-invasive data in precision medicine. An open source implementation can be found at http://github.com/fsahli/purkinje-learningComment: 18 pages, 9 figure

Generative Hyperelasticity with Physics-Informed Probabilistic Diffusion Fields

Many natural materials exhibit highly complex, nonlinear, anisotropic, and heterogeneous mechanical properties. Recently, it has been demonstrated that data-driven strain energy functions possess the flexibility to capture the behavior of these complex materials with high accuracy while satisfying physics-based constraints. However, most of these approaches disregard the uncertainty in the estimates and the spatial heterogeneity of these materials. In this work, we leverage recent advances in generative models to address these issues. We use as building block neural ordinary equations (NODE) that -- by construction -- create polyconvex strain energy functions, a key property of realistic hyperelastic material models. We combine this approach with probabilistic diffusion models to generate new samples of strain energy functions. This technique allows us to sample a vector of Gaussian white noise and translate it to NODE parameters thereby representing plausible strain energy functions. We extend our approach to spatially correlated diffusion resulting in heterogeneous material properties for arbitrary geometries. We extensively test our method with synthetic and experimental data on biological tissues and run finite element simulations with various degrees of spatial heterogeneity. We believe this approach is a major step forward including uncertainty in predictive, data-driven models of hyperelasticityComment: 22 pages, 11 figure

WarpPINN: Cine-MR image registration with physics-informed neural networks

Heart failure is typically diagnosed with a global function assessment, such as ejection fraction. However, these metrics have low discriminate power, failing to distinguish different types of this disease. Quantifying local deformations in the form of cardiac strain can provide helpful information, but it remains a challenge. In this work, we introduce WarpPINN, a physics-informed neural network to perform image registration to obtain local metrics of the heart deformation. We apply this method to cine magnetic resonance images to estimate the motion during the cardiac cycle. We inform our neural network of near-incompressibility of cardiac tissue by penalizing the jacobian of the deformation field. The loss function has two components: an intensity-based similarity term between the reference and the warped template images, and a regularizer that represents the hyperelastic behavior of the tissue. The architecture of the neural network allows us to easily compute the strain via automatic differentiation to assess cardiac activity. We use Fourier feature mappings to overcome the spectral bias of neural networks, allowing us to capture discontinuities in the strain field. We test our algorithm on a synthetic example and on a cine-MRI benchmark of 15 healthy volunteers. We outperform current methodologies both landmark tracking and strain estimation. We expect that WarpPINN will enable more precise diagnostics of heart failure based on local deformation information. Source code is available at https://github.com/fsahli/WarpPINN.Comment: 18 pages, 10 figure

Shape of my heart: Cardiac models through learned signed distance functions

The efficient construction of an anatomical model is one of the major challenges of patient-specific in-silico models of the human heart. Current methods frequently rely on linear statistical models, allowing no advanced topological changes, or requiring medical image segmentation followed by a meshing pipeline, which strongly depends on image resolution, quality, and modality. These approaches are therefore limited in their transferability to other imaging domains. In this work, the cardiac shape is reconstructed by means of three-dimensional deep signed distance functions with Lipschitz regularity. For this purpose, the shapes of cardiac MRI reconstructions are learned from public databases to model the spatial relation of multiple chambers in Cartesian space. We demonstrate that this approach is also capable of reconstructing anatomical models from partial data, such as point clouds from a single ventricle, or modalities different from the trained MRI, such as electroanatomical mapping, and in addition, allows us to generate new anatomical shapes by randomly sampling latent vectors

Physics-informed neural networks to learn cardiac fiber orientation from multiple electroanatomical maps

We propose FiberNet, a method to estimate \emph{in-vivo} the cardiac fiber architecture of the human atria from multiple catheter recordings of the electrical activation. Cardiac fibers play a central role in the electro-mechanical function of the heart, yet they are difficult to determine in-vivo, and hence rarely truly patient-specific in existing cardiac models. FiberNet learns the fiber arrangement by solving an inverse problem with physics-informed neural networks. The inverse problem amounts to identifying the conduction velocity tensor of a cardiac propagation model from a set of sparse activation maps. The use of multiple maps enables the simultaneous identification of all the components of the conduction velocity tensor, including the local fiber angle. We extensively test FiberNet on synthetic 2-D and 3-D examples, diffusion tensor fibers, and a patient-specific case. We show that 3 maps are sufficient to accurately capture the fibers, also in the presence of noise. With fewer maps, the role of regularization becomes prominent. Moreover, we show that the fitted model can robustly reproduce unseen activation maps. We envision that FiberNet will help the creation of patient-specific models for personalized medicine. The full code is available at http://github.com/fsahli/FiberNet.Comment: 29 pages, 11 figure