arXiv subjects

Francisco Sahli Costabal

Publications and source records attributed to Francisco Sahli Costabal.

At least 19 recordsLinked to original sources

arXiv2026

Operator-informed initialization for Fourier features physics-informed neural networks

Physics-Informed Neural Networks (PINNs) typically exhibit spectral bias, where some frequencies of the target function converge more slowly than others. In this work, we analyze the training dynamics of Fourier Feature PINNs in the Neural Tangent Kernel regime to address this limitation. We derive an explicit evolution equation to estimate the residual error in the frequency domain, demonstrating that the convergence rate of specific frequencies is primarily governed by the product of the differential operator's symbol and the spectral density of the initialization weights. Leveraging this theoretical insight, we propose an informative initialization strategy that tailors the initial weight distribution to the specific PDE being solved. With this method, we can diminish the operator-induced spectral bias, balancing the convergence rates across the frequency spectrum and achieving better prediction accuracy. Numerical experiments on linear and nonlinear partial differential equations confirm that this initialization strategy improves learning dynamics and approximation accuracy across frequencies compared to standard initialization methods, with no additional training cost.

cs.LG↗

arXiv2026

iLogMap: Geodesic Polar Coordinates Parameterization with the Magnetic Laplacian

Geodesic polar coordinates (GPCs) provide an intrinsic parameterization over curved surfaces, but their accurate estimation remains challenging, particularly in the presence of anisotropic metrics, high curvature and complex topology. We introduce iLogMap, a method for computing GPCs in curved domains that recasts the angular component of the logarithmic map to a ground-state magnetic eigenproblem over the circumferential direction field of geodesic distance. Our method effortlessly extends to anisotropic metric tensors and solid volumes, enabling cylindrical and spherical parameterizations in tetrahedral meshes. Experiments on diverse shapes with varying genus confirm competitive angular accuracy and reduced metric distortion relative to heat-based methods, with improved performance on surfaces with boundary and domains with anisotropy. We demonstrate the utility of iLogMap in computational cardiology applications, where we use it to initialize spiral phases on atrial surfaces and estimate local activation patterns in ventricular models.

cs.CG↗

arXiv2026

Uncertainty Quantification for Cardiac Shape Reconstruction with Deep Signed Distance Functions via MCMC methods

Atlas-based approaches allow high-quality, patient-specific shape reconstructions of cardiac anatomy from sparse and/or noisy data such as point clouds. However, these methods are mainly prior-driven, so the impact of uncertainty can be large, limiting their clinical reliability. We propose a probabilistic framework for uncertainty-aware cardiac shape reconstruction that combines Deep Signed Distance Functions (DeepSDFs) with Markov Chain Monte Carlo (MCMC) sampling. Cardiac geometries are modeled implicitly as zero-level sets of a neural network conditioned on learned latent codes, enabling multi-surface reconstruction of the left and right ventricles. By interpreting the reconstruction loss as a log-likelihood, we perform Bayesian inference in the latent space to obtain both maximum a posteriori (MAP) and posterior-sampled reconstructions. Experiments on a public cardiac dataset show that our approach produces accurate reconstructions and well-calibrated uncertainty estimates.

eess.IV↗

arXiv2025

WarpPINN-fibers: improved cardiac strain estimation from cine-MR with physics-informed neural networks

The contractile motion of the heart is strongly determined by the distribution of the fibers that constitute cardiac tissue. Strain analysis informed with the orientation of fibers allows to describe several pathologies that are typically associated with impaired mechanics of the myocardium, such as cardiovascular disease. Several methods have been developed to estimate strain-derived metrics from traditional imaging techniques. However, the physical models underlying these methods do not include fiber mechanics, restricting their capacity to accurately explain cardiac function. In this work, we introduce WarpPINN-fibers, a physics-informed neural network framework to accurately obtain cardiac motion and strains enhanced by fiber information. We train our neural network to satisfy a hyper-elastic model and promote fiber contraction with the goal to predict the deformation field of the heart from cine magnetic resonance images. For this purpose, we build a loss function composed of three terms: a data-similarity loss between the reference and the warped template images, a regularizer enforcing near-incompressibility of cardiac tissue and a fiber-stretch penalization that controls strain in the direction of synthetically produced fibers. We show that our neural network improves the former WarpPINN model and effectively controls fiber stretch in a synthetic phantom experiment. Then, we demonstrate that WarpPINN-fibers outperforms alternative methodologies in landmark-tracking and strain curve prediction for a cine-MRI benchmark with a cohort of 15 healthy volunteers. We expect that our method will enable a more precise quantification of cardiac strains through accurate deformation fields that are consistent with fiber physiology, without requiring imaging techniques more sophisticated than MRI.

eess.IV↗

arXiv2025

Fully data-driven inverse hyperelasticity with hyper-network neural ODE fields

We propose a new framework for identifying mechanical properties of heterogeneous materials without a closed-form constitutive equation. Given a full-field measurement of the displacement field, for instance as obtained from digital image correlation (DIC), a continuous approximation of the strain field is obtained by training a neural network that incorporates Fourier features to effectively capture sharp gradients in the data. A physics-based data-driven method built upon ordinary neural differential equations (NODEs) is employed to discover constitutive equations. The NODE framework can represent arbitrary materials while satisfying constraints in the theory of constitutive equations by default. To account for heterogeneity, a hyper-network is defined, where the input is the material coordinate system, and the output is the NODE-based constitutive equation. The parameters of the hyper-network are optimized by minimizing a multi-objective loss function that includes penalty terms for violations of the strong form of the equilibrium equations of elasticity and the associated Neumann boundary conditions. We showcase the framework with several numerical examples, including heterogeneity arising from variations in material parameters, spatial transitions from isotropy to anisotropy, material identification in the presence of noise, and, ultimately, application to experimental data. As the numerical results suggest, the proposed approach is robust and general in identifying the mechanical properties of heterogeneous materials with very few assumptions, making it a suitable alternative to classical inverse methods.

cs.LG↗

arXiv2025

$Δ$-PINNs: physics-informed neural networks on complex geometries

Physics-informed neural networks (PINNs) have demonstrated promise in solving forward and inverse problems involving partial differential equations. Despite recent progress on expanding the class of problems that can be tackled by PINNs, most of existing use-cases involve simple geometric domains. To date, there is no clear way to inform PINNs about the topology of the domain where the problem is being solved. In this work, we propose a novel positional encoding mechanism for PINNs based on the eigenfunctions of the Laplace-Beltrami operator. This technique allows to create an input space for the neural network that represents the geometry of a given object. We approximate the eigenfunctions as well as the operators involved in the partial differential equations with finite elements. We extensively test and compare the proposed methodology against traditional PINNs in complex shapes, such as a coil, a heat sink and a bunny, with different physics, such as the Eikonal equation and heat transfer. We also study the sensitivity of our method to the number of eigenfunctions used, as well as the discretization used for the eigenfunctions and the underlying operators. Our results show excellent agreement with the ground truth data in cases where traditional PINNs fail to produce a meaningful solution. We envision this new technique will expand the effectiveness of PINNs to more realistic applications.

cs.LG↗

arXiv2025

Image Velocimetry using Direct Displacement Field estimation with Neural Networks for Fluids

An important tool for experimental fluids mechanics research is Particle Image Velocimetry (PIV). Several robust methodologies have been proposed to perform the estimation of velocity field from the images, however, alternative methods are still needed to increase the spatial resolution of the results. This work presents a novel approach for estimating fluid flow fields using neural networks and the optical flow equation to predict displacement vectors between sequential images. The result is a continuous representation of the displacement, that can be evaluated on the full spatial resolution of the image. The methodology was validated on synthetic and experimental images. Accurate results were obtained in terms of the estimation of instantaneous velocity fields, and of the determined time average turbulence quantities and power spectral density. The methodology proposed differs of previous attempts of using machine learning for this task: it does not require any previous training, and could be directly used in any pair of images.

cs.CV↗

arXiv2025

PISCO: Self-Supervised k-Space Regularization for Improved Neural Implicit k-Space Representations of Dynamic MRI

Neural implicit k-space representations (NIK) have shown promising results for dynamic magnetic resonance imaging (MRI) at high temporal resolutions. Yet, reducing acquisition time, and thereby available training data, results in severe performance drops due to overfitting. To address this, we introduce a novel self-supervised k-space loss function $\mathcal{L}_\mathrm{PISCO}$, applicable for regularization of NIK-based reconstructions. The proposed loss function is based on the concept of parallel imaging-inspired self-consistency (PISCO), enforcing a consistent global k-space neighborhood relationship without requiring additional data. Quantitative and qualitative evaluations on static and dynamic MR reconstructions show that integrating PISCO significantly improves NIK representations. Particularly for high acceleration factors (R$\geq$54), NIK with PISCO achieves superior spatio-temporal reconstruction quality compared to state-of-the-art methods. Furthermore, an extensive analysis of the loss assumptions and stability shows PISCO's potential as versatile self-supervised k-space loss function for further applications and architectures. Code is available at: https://github.com/compai-lab/2025-pisco-spieker

eess.IV↗

arXiv2024

Ensemble learning of the atrial fiber orientation with physics-informed neural networks

The anisotropic structure of the myocardium is a key determinant of the cardiac function. To date, there is no imaging modality to assess in-vivo the cardiac fiber structure. We recently proposed Fibernet, a method for the automatic identification of the anisotropic conduction -- and thus fibers -- in the atria from local electrical recordings. Fibernet uses cardiac activation as recorded during electroanatomical mappings to infer local conduction properties using physics-informed neural networks. In this work, we extend Fibernet to cope with the uncertainty in the estimated fiber field. Specifically, we use an ensemble of neural networks to produce multiple samples, all fitting the observed data, and compute posterior statistics. We also introduce a methodology to select the best fiber orientation members and define the input of the neural networks directly on the atrial surface. With these improvements, we outperform the previous methodology in terms of fiber orientation error in 8 different atrial anatomies. Currently, our approach can estimate the fiber orientation and conduction velocities in under 7 minutes with quantified uncertainty, which opens the door to its application in clinical practice. We hope the proposed methodology will enable further personalization of cardiac digital twins for precision medicine.

cs.LG↗

arXiv2024

An eikonal model with re-excitability for fast simulations in cardiac electrophysiology

Precision cardiology based on cardiac digital twins requires accurate simulations of cardiac arrhythmias. However, detailed models, such as the monodomain model, are computationally costly and have limited applicability in practice. Thus, it desirable to have fast models that can still represent the main physiological features presented during cardiac arrhythmias. The eikonal model is an approximation of the monodomain model that is widely used to describe the arrival times of the electrical wave. However, the standard eikonal model does not generalize to the complex re-entrant dynamics that characterize the cardiac arrhythmias. In this work, we propose an eikonal model that includes the tissue re-excitability, which allows to describe re-entries. The re-excitability properties are inferred from the monodomain model. Our eikonal model also handles the tissue anisotropy and heterogeneity. We compare the eikonal model to the monodomain model in various numerical experiments in the atria and the ventricles. The eikonal model is qualitatively accurate in the simulation of re-entries and can be potentially ran in real-time, opening the door to its clinical applicability.

cs.CE↗

arXiv2024

Understanding the dynamics of the frequency bias in neural networks

Recent works have shown that traditional Neural Network (NN) architectures display a marked frequency bias in the learning process. Namely, the NN first learns the low-frequency features before learning the high-frequency ones. In this study, we rigorously develop a partial differential equation (PDE) that unravels the frequency dynamics of the error for a 2-layer NN in the Neural Tangent Kernel regime. Furthermore, using this insight, we explicitly demonstrate how an appropriate choice of distributions for the initialization weights can eliminate or control the frequency bias. We focus our study on the Fourier Features model, an NN where the first layer has sine and cosine activation functions, with frequencies sampled from a prescribed distribution. In this setup, we experimentally validate our theoretical results and compare the NN dynamics to the solution of the PDE using the finite element method. Finally, we empirically show that the same principle extends to multi-layer NNs.

cs.LG↗

arXiv2024

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

The efficient construction of anatomical models 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 to model the spatial relation of multiple chambers. 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 the electroanatomical mapping (EAM).

eess.IV↗

arXiv2024

Self-Supervised k-Space Regularization for Motion-Resolved Abdominal MRI Using Neural Implicit k-Space Representation

Neural implicit k-space representations have shown promising results for dynamic MRI at high temporal resolutions. Yet, their exclusive training in k-space limits the application of common image regularization methods to improve the final reconstruction. In this work, we introduce the concept of parallel imaging-inspired self-consistency (PISCO), which we incorporate as novel self-supervised k-space regularization enforcing a consistent neighborhood relationship. At no additional data cost, the proposed regularization significantly improves neural implicit k-space reconstructions on simulated data. Abdominal in-vivo reconstructions using PISCO result in enhanced spatio-temporal image quality compared to state-of-the-art methods. Code is available at https://github.com/vjspi/PISCO-NIK.

eess.IV↗

arXiv2023

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-learning

stat.ML↗

arXiv2023

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 hyperelasticity

cs.CE↗

arXiv2023

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.

cs.CE↗

arXiv2023

Unsupervised reconstruction of accelerated cardiac cine MRI using Neural Fields

Cardiac cine MRI is the gold standard for cardiac functional assessment, but the inherently slow acquisition process creates the necessity of reconstruction approaches for accelerated undersampled acquisitions. Several regularization approaches that exploit spatial-temporal redundancy have been proposed to reconstruct undersampled cardiac cine MRI. More recently, methods based on supervised deep learning have been also proposed to further accelerate acquisition and reconstruction. However, these techniques rely on usually large dataset for training, which are not always available. In this work, we propose an unsupervised approach based on implicit neural field representations for cardiac cine MRI (so called NF-cMRI). The proposed method was evaluated in in-vivo undersampled golden-angle radial multi-coil acquisitions for undersampling factors of 26x and 52x, achieving good image quality, and comparable spatial and improved temporal depiction than a state-of-the-art reconstruction technique.

eess.IV↗

arXiv2022

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.

eess.IV↗