Searcharxiv⌕ Search

arXiv subjects

Paola F. Antonietti

Publications and source records attributed to Paola F. Antonietti.

At least 37 records · Page 2Linked to original sources

Deep Learning Accelerated Algebraic Multigrid Methods for Polytopal Discretizations of Second-Order Differential Problems

Algebraic Multigrid (AMG) methods are state-of-the-art algebraic solvers for partial differential equations. Still, their efficiency depends heavily on the choice of suitable parameters and/or ingredients. Paradigmatic examples include the so-called strong threshold parameter $θ$, which controls the algebraic coarse-grid hierarchy, as well as the smoother, i.e., the relaxation methods used on the fine grid to damp out high-frequency errors. In AMG, since the coarse grids are constructed algebraically (without geometric intuition), the smoother's performance is even more critical. For the linear systems stemming from polytopal discretizations, such as Polytopal Discontinuous Galerkin (PolyDG) and Virtual Element Methods (VEM), AMG sensitivity to such choices is even more critical due to the significant variability of the underlying meshes, which results in algebraic systems with different sparsity patterns. We propose a novel deep learning approach that automatically tunes the strong threshold parameter, as well as the smoother choice in AMG solvers, for linear systems of equations arising from polytopal discretizations, thereby maximizing AMG performance. We interpret the sparse matrix resulting from polytopal discretization as a grayscale image, and by applying pooling, our neural network extracts compact features that preserve the necessary information at a low computational cost. We test various differential problems in both two- and three-dimensional settings, with heterogeneous coefficients and polygonal/polyhedral meshes, and demonstrate that the proposed approach generalizes well. In practice, we demonstrate that we can reduce AMG solver time by up to $27\%$ with minimal changes to existing PolyDG and VEM codes.

math.NA↗

A massively parallel non-overlapping Schwarz preconditioner for PolyDG methods in brain electrophysiology

We investigate non-overlapping Schwarz preconditioners for the algebraic systems stemming from high-order discretizations of the coupled monodomain and Barreto-Cressman models, with applications to brain electrophysiology. The spatial discretization is based on a high-order Polytopal Discontinuous Galerkin (PolyDG) method, coupled with the Crank-Nicolson time discretization scheme with explicit extrapolation of the ion term. To improve solver efficiency, we consider additive Schwarz preconditioners within the PolyDG framework, which combines (massively parallel) local subdomain solvers with a coarse-grid correction. Numerical experiments demonstrate robustness with respect to the discretization parameters, as well as a significant reduction in iteration counts compared to the unpreconditioned solver. These features make the proposed approach well-suited for parallel large-scale simulations in brain electrophysiology.

math.NA↗

MAGNET: an open-source library for mesh agglomeration by Graph Neural Networks

We introduce MAGNET, an open-source Python library designed for mesh agglomeration in both two- and three-dimensions, based on employing Graph Neural Networks (GNN). MAGNET serves as a comprehensive solution for training a variety of GNN models, integrating deep learning and other advanced algorithms such as METIS and k-means to facilitate mesh agglomeration and quality metric computation. The library's introduction is outlined through its code structure and primary features. The GNN framework adopts a graph bisection methodology that capitalizes on connectivity and geometric mesh information via SAGE convolutional layers, in line with the methodology proposed by Antonietti et al. (2024). Additionally, the proposed MAGNET library incorporates reinforcement learning to enhance the accuracy and robustness of the model for predicting coarse partitions within a multilevel framework. A detailed tutorial is provided to guide the user through the process of mesh agglomeration and the training of a GNN bisection model. We present several examples of mesh agglomeration conducted by MAGNET, demonstrating the library's applicability across various scenarios. Furthermore, the performance of the newly introduced models is contrasted with that of METIS and k-means, illustrating that the proposed GNN models are competitive regarding partition quality and computational efficiency. Finally, we exhibit the versatility of MAGNET's interface through its integration with Lymph, an open-source library implementing discontinuous Galerkin methods on polytopal grids for the numerical discretization of multiphysics differential problems.

math.NA↗

A structure-preserving LDG discretization of the Fisher-Kolmogorov equation for modeling neurodegenerative diseases

This work presents a structure-preserving, high-order, unconditionally stable numerical method for approximating the solution to the Fisher-Kolmogorov equation on polytopic meshes, with a particular focus on its application in simulating misfolded protein spreading in neurodegenerative diseases. The model problem is reformulated using an entropy variable to guarantee solution positivity, boundedness, and satisfaction of a discrete entropy-stability inequality at the numerical level. The scheme combines a local discontinuous Galerkin method on polytopal meshes for the space discretization with a $ν$-step backward differentiation formula for the time integration. Implementation details are discussed, including a detailed derivation of the linear systems arising from Newton's iteration. The accuracy and robustness of the proposed method are demonstrated through extensive numerical tests. Finally, the method's practical performance is demonstrated through simulations of $α$-synuclein propagation in a two-dimensional brain geometry segmented from MRI data, providing a relevant computational framework for modeling synucleopathies (such as Parkinson's disease) and, more generally, neurodegenerative diseases.

math.NA↗

Polytopal mesh agglomeration via geometrical deep learning for three-dimensional heterogeneous domains

Agglomeration techniques can be successfully employed to reduce the computational costs of numerical simulations and stand at the basis of multilevel algebraic solvers. To automatically perform mesh agglomeration, we propose a novel Geometrical Deep Learning-based algorithm that can exploit the geometrical and physical information of the underlying computational domain to construct the agglomerated grid and -- simultaneously -- guarantee the agglomerated grid's quality. In particular, we propose a bisection model based on Graph Neural Networks (GNNs) to partition a suitable connectivity graph of computational three-dimensional meshes. The new approach has a high online inference speed. It can simultaneously process the graph structure of the mesh, the geometrical information of the mesh (e.g., elements' volumes, centers' coordinates), and the physical information of the domain (e.g., physical parameters). Taking advantage of this new approach, our algorithm can agglomerate meshes of a domain composed of heterogeneous media, automatically respecting the underlying heterogeneities. The proposed GNN approach is compared with the k-means algorithm and METIS, which are widely employed approaches for graph partitioning and are meant to process only the connectivity information on the mesh. We demonstrate that the performance of our algorithms outperforms the k-means and METIS algorithms in terms of quality metrics and runtimes. Moreover, we demonstrate that our algorithm also shows a good level of generalization when applied to complex geometries, such as three-dimensional geometries reconstructed from medical images. Finally, the model's capability to perform agglomeration in heterogeneous domains is evaluated when integrated into a polytopal discontinuous Galerkin finite element solver.

math.NA↗

A review of discontinuous Galerkin time-stepping methods for wave propagation problems

This chapter reviews and compares discontinuous Galerkin time-stepping methods for the numerical approximation of second-order ordinary differential equations, particularly those stemming from space finite element discretization of wave propagation problems. Two formulations, tailored for second- and first-order systems of ordinary differential equations, are discussed within a generalized framework, assessing their stability, accuracy, and computational efficiency. Theoretical results are supported by various illustrative examples that validate the findings, enhancing the understanding and applicability of these methods in practical scenarios.

math.NA↗

A p-adaptive polytopal discontinuous Galerkin method for high-order approximation of brain electrophysiology

Multiscale mathematical models have shown great promise in computational brain electrophysiology but are still hindered by high computational costs due to fast dynamics and complex brain geometries, requiring very fine spatio-temporal resolution. This paper introduces a novel p-adaptive discontinuous Galerkin method on polytopal grids (PolyDG) coupled with Crank-Nicolson time integration to approximate such models efficiently. The p-adaptive method enhances local accuracy via dynamic, element-wise polynomial refinement/de-refinement guided by a-posteriori error estimators. A novel clustering algorithm automatizes the selection of elements for adaptive updates, further improving efficiency. A wide set of numerical tests, including epileptic seizure simulations in a sagittal section of a human brain stem, demonstrate the method's ability to reduce computational load while maintaining the accuracy of the numerical solution in capturing the dynamics of multiple wavefronts.

math.NA↗

A coupled mathematical and numerical model for protein spreading and tissue atrophy, applied to Alzheimer's disease

The aim of this paper is to introduce, analyse and test in practice a new mathematical model describing the interplay between biological tissue atrophy driven by pathogen diffusion, with applications to neurodegenerative disorders. This study introduces a novel mathematical and computational model comprising a Fisher-Kolmogorov equation for species diffusion coupled with an elasticity equation governing mass loss. These equations intertwine through a logistic law dictating the reduction of the medium's mass. One potential application of this model lies in understanding the onset and development of Alzheimer's disease. Here, the equations can describe the propagation of misfolded tau-proteins and the ensuing brain atrophy characteristic of the disease. To address numerically the inherited complexities, we propose a Polygonal Discontinuous Galerkin method on polygonal/polyhedral grids for spatial discretization, while time integration relies on the theta-method. We present the mathematical model, delving into its characteristics and propose discretization applied. Furthermore, convergence results are presented to validate the model, accompanied by simulations illustrating the application scenario of the onset of Alzheimer's disease.

math.NA↗

lymph: discontinuous poLYtopal methods for Multi-PHysics differential problems

We present the library lymph for the finite element numerical discretization of coupled multi-physics problems. lymph is a Matlab library for the discretization of partial differential equations based on high-order discontinuous Galerkin methods on polytopal grids (PolyDG) for spatial discretization coupled with suitable finite-difference time marching schemes. The objective of the paper is to introduce the library by describing it in terms of installation, input/output data, and code structure, highlighting - when necessary - key implementation aspects related to the method. A user guide, proceeding step-by-step in the implementation and solution of a Poisson problem, is also provided. In the last part of the paper, we show the results obtained for several differential problems, namely the Poisson problem, the heat equation, the elastodynamics system, and a multiphysics problem coupling poroelasticity and acoustic equations. Through these examples, we show the convergence properties and highlight some of the main features of the proposed method, i.e. geometric flexibility, high-order accuracy, and robustness with respect to heterogeneous physical parameters.

math.NA↗

Discontinuous Galerkin approximations of the heterodimer model for protein-protein interaction

Mathematical models of protein-protein dynamics, such as the heterodimer model, play a crucial role in understanding many physical phenomena. This model is a system of two semilinear parabolic partial differential equations describing the evolution and mutual interaction of biological species. An example is the neurodegenerative disease progression in some significant pathologies, such as Alzheimer's and Parkinson's diseases, characterized by the accumulation and propagation of toxic prionic proteins. This article presents and analyzes a flexible high-order discretization method for the numerical approximation of the heterodimer model. We propose a space discretization based on a Discontinuous Galerkin method on polygonal/polyhedral grids, which provides flexibility in handling complex geometries. Concerning the semi-discrete formulation, we prove stability and a-priori error estimates for the first time. Next, we adopt a $θ$-method scheme as a time integration scheme. Convergence tests are carried out to demonstrate the theoretical bounds and the ability of the method to approximate traveling wave solutions, considering also complex geometries such as brain sections reconstructed from medical images. Finally, the proposed scheme is tested in a practical test case stemming from neuroscience applications, namely the simulation of the spread of $α$-synuclein in a realistic test case of Parkinson's disease in a two-dimensional sagittal brain section geometry reconstructed from medical images.

math.NA↗

A polytopal discontinuous Galerkin method for the pseudo-stress formulation of the unsteady Stokes problem

This work aims to construct and analyze a discontinuous Galerkin method on polytopal grids (PolydG) to solve the pseudo-stress formulation of the unsteady Stokes problem. The pseudo-stress variable is introduced due to the growing interest in non-Newtonian flows and coupled interface problems, where stress assumes a fundamental role. The space-time discretization of the problem is achieved by combining the PolydG approach with the implicit theta-method time integration scheme. For both the semi- and fully-discrete problems we present a detailed stability analysis. Moreover, we derive convergence estimates for the fully discrete space-time discretization. A set of verification tests is presented to verify the theoretical estimates and the application of the method to cases of engineering interest.

math.NA↗

Discovering Artificial Viscosity Models for Discontinuous Galerkin Approximation of Conservation Laws using Physics-Informed Machine Learning

Finite element-based high-order solvers of conservation laws offer large accuracy but face challenges near discontinuities due to the Gibbs phenomenon. Artificial viscosity is a popular and effective solution to this problem based on physical insight. In this work, we present a physics-informed machine learning algorithm to automate the discovery of artificial viscosity models in a non-supervised paradigm. The algorithm is inspired by reinforcement learning and trains a neural network acting cell-by-cell (the viscosity model) by minimizing a loss defined as the difference with respect to a reference solution thanks to automatic differentiation. This enables a dataset-free training procedure. We prove that the algorithm is effective by integrating it into a state-of-the-art Runge-Kutta discontinuous Galerkin solver. We showcase several numerical tests on scalar and vectorial problems, such as Burgers' and Euler's equations in one and two dimensions. Results demonstrate that the proposed approach trains a model that is able to outperform classical viscosity models. Moreover, we show that the learnt artificial viscosity model is able to generalize across different problems and parameters.

math.NA↗

Iterative solution to the biharmonic equation in mixed form discretized by the Hybrid High-Order method

We consider the solution to the biharmonic equation in mixed form discretized by the Hybrid High-Order (HHO) methods. The two resulting second-order elliptic problems can be decoupled via the introduction of a new unknown, corresponding to the boundary value of the solution of the first Laplacian problem. This technique yields a global linear problem that can be solved iteratively via a Krylov-type method. More precisely, at each iteration of the scheme, two second-order elliptic problems have to be solved, and a normal derivative on the boundary has to be computed. In this work, we specialize this scheme for the HHO discretization. To this aim, an explicit technique to compute the discrete normal derivative of an HHO solution of a Laplacian problem is proposed. Moreover, we show that the resulting discrete scheme is well-posed. Finally, a new preconditioner is designed to speed up the convergence of the Krylov method. Numerical experiments assessing the performance of the proposed iterative algorithm on both two- and three-dimensional test cases are presented.

math.NA↗

A discontinuous Galerkin method for the three-dimensional heterodimer model with application to prion-like proteins' dynamics

Neurocognitive disorders, such as Alzheimer's and Parkinson's, have a wide social impact. These proteinopathies involve misfolded proteins accumulating into neurotoxic aggregates. Mathematical and computational models describing the prion-like dynamics offer an analytical basis to study the diseases' evolution and a computational framework for exploring potential therapies. This work focuses on the heterodimer model in a three-dimensional setting, a reactive-diffusive system of nonlinear partial differential equations describing the evolution of both healthy and misfolded proteins. We investigate traveling wave solutions and diffusion-driven instabilities as a mechanism of neurotoxic pattern formation. For the considered mathematical model, we propose a space discretization, relying on the Discontinuous Galerkin method on polytopal/polyhedral grids, allowing high-order accuracy and flexible handling of the complicated brain's geometry. Further, we present a priori error estimates for the semi-discrete formulation and we perform convergence tests to verify the theoretical results. Finally, we conduct simulations using realistic data on a three-dimensional brain mesh reconstructed from medical images.

math.NA↗

High-order Discontinuous Galerkin Methods for the Monodomain and Bidomain Models

This work aims at presenting a Discontinuous Galerkin (DG) formulation employing a spectral basis for two important models employed in cardiac electrophysiology, namely the monodomain and bidomain models. The use of DG methods is motivated by the characteristic of the mathematical solution of such equations which often corresponds to a highly steep wavefront. Hence, the built-in flexibility of discontinuous methods in developing adaptive approaches, combined with the high-order accuracy, can well represent the underlying physics. The choice of a semi-implicit time integration allows for a fast solution at each time step. The article includes some numerical tests to verify the convergence properties and the physiological behaviour of the numerical solution. Also, a pseudo-realistic simulation turns out to fully reconstruct the propagation of the electric potential, comprising the phases of depolarization and repolarization, by overcoming the typical issues related to the steepness of the wave front.

math.NA↗

Numerical modelling of protein misfolding in neurodegenerative diseases: a computational study

The spreading of misfolded proteins is a known hallmark in some neurodegenerative diseases, known as proteinopathies. A significant example is the tau protein, associated with many pathologies, such as Alzheimer's. In this work, we discuss and compare two different models for the mathematical modelling of protein misfolding, namely the heterodimer model and the Fisher-Kolmogorov model, as well as their numerical discretizations. We introduce a discontinuous Galerkin method on polygonal and polyhedral grids for space discretization to accurately simulate the wavefronts typically observed in the prionic spreading. Starting from the semidiscrete formulations, we use a Crank-Nicolson scheme to advance in time. Finally, we simulate the spreading of the misfolded tau protein in a two-dimensional brain slice in the sagittal plane with a polygonal agglomerated grid. The simulation is performed using both the presented models, and we compare the results and the differences deriving from the modelling choices.

math.NA↗

A high-order discontinuous Galerkin method for the numerical modeling of epileptic seizures

Epilepsy is a clinical neurological disorder characterized by recurrent and spontaneous seizures consisting of abnormal high-frequency electrical activity in the brain. In this condition, the transmembrane potential dynamics are characterized by rapid and sharp wavefronts traveling along the heterogeneous and anisotropic conduction pathways of the brain. This work employs the monodomain model, coupled with specific neuronal ionic models characterizing ion concentration dynamics, to mathematically describe brain tissue electrophysiology in grey and white matter at the organ scale. This multiscale model is discretized in space with the high-order discontinuous Galerkin method on polygonal and polyhedral grids (PolyDG) and advanced in time with a Crank-Nicolson scheme. This ensures, on the one hand, efficient and accurate simulations of the high-frequency electrical activity that is responsible for epileptic seizure and, on the other hand, keeps reasonably low the computational costs by a suitable combination of high-order approximations and agglomerated polytopal meshes. We numerically investigate synthetic test cases on a two-dimensional heterogeneous squared domain discretized with a polygonal grid, and on a two-dimensional brainstem in a sagittal plane with an agglomerated polygonal grid that takes full advantage of the flexibility of the PolyDG approximation of the semidiscrete formulation. Finally, we provide a theoretical analysis of stability and an a-priori convergence analysis for a simplified mathematical problem.

math.NA↗

Robust discontinuous Galerkin-based scheme for the fully-coupled non-linear thermo-hydro-mechanical problem

We present and analyze a discontinuous Galerkin method for the numerical modeling of the non-linear fully-coupled thermo-hydro-mechanic problem. We propose a high-order symmetric weighted interior penalty scheme that supports general polytopal grids and is robust with respect to strong heteorgeneities in the model coefficients. We focus on the treatment of the non-linear convective transport term in the energy conservation equation and we propose suitable stabilization techniques that make the scheme robust for advection-dominated regimes. The stability analysis of the problem and the convergence of the fixed-point linearization strategy are addressed theoretically under mild requirements on the problem's data. A complete set of numerical simulations is presented in order to assess the convergence and robustness properties of the proposed method.

math.NA↗