arXiv subjects

Wenrui Hao

Publications and source records attributed to Wenrui Hao.

At least 37 records · Page 2Linked to original sources

arXiv2025

Laplacian Eigenfunction-Based Neural Operator for Learning Nonlinear Reaction-Diffusion Dynamics

Learning reaction-diffusion equations has become increasingly important across scientific and engineering disciplines, including fluid dynamics, materials science, and biological systems. In this work, we propose the Laplacian Eigenfunction-Based Neural Operator (LE-NO), a novel framework designed to efficiently learn nonlinear reaction terms in reaction-diffusion equations. LE-NO models the nonlinear operator on the right-hand side using a data-driven approach, with Laplacian eigenfunctions serving as the basis. This spectral representation enables efficient approximation of the nonlinear terms, reduces computational complexity through direct inversion of the Laplacian matrix, and alleviates challenges associated with limited data and large neural network architectures-issues commonly encountered in operator learning. We demonstrate that LE-NO generalizes well across varying boundary conditions and provides interpretable representations of learned dynamics. Numerical experiments in mathematical physics showcase the effectiveness of LE-NO in capturing complex nonlinear behavior, offering a powerful and robust tool for the discovery and prediction of reaction-diffusion dynamics.

math-ph↗

arXiv2025

Learning Patient-Specific Spatial Biomarker Dynamics via Operator Learning for Alzheimer's Disease Progression

Alzheimer's disease (AD) is a complex, multifactorial neurodegenerative disorder with substantial heterogeneity in progression and treatment response. Despite recent therapeutic advances, predictive models capable of accurately forecasting individualized disease trajectories remain limited. Here, we present a machine learning-based operator learning framework for personalized modeling of AD progression, integrating longitudinal multimodal imaging, biomarker, and clinical data. Unlike conventional models with prespecified dynamics, our approach directly learns patient-specific disease operators governing the spatiotemporal evolution of amyloid, tau, and neurodegeneration biomarkers. Using Laplacian eigenfunction bases, we construct geometry-aware neural operators capable of capturing complex brain dynamics. Embedded within a digital twin paradigm, the framework enables individualized predictions, simulation of therapeutic interventions, and in silico clinical trials. Applied to AD clinical data, our method achieves high prediction accuracy exceeding 90% across multiple biomarkers, substantially outperforming existing approaches. This work offers a scalable, interpretable platform for precision modeling and personalized therapeutic optimization in neurodegenerative diseases.

cs.LG↗

arXiv2025

A Systematic Computational Framework for Practical Identifiability Analysis in Mathematical Models Arising from Biology

Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models of biological systems. Starting with a rigorous mathematical definition of practical identifiability, we demonstrate its equivalence to the invertibility of the Fisher Information Matrix. Our framework establishes the relationship between practical identifiability and coordinate identifiability, introducing a novel metric that simplifies and accelerates the evaluation of parameter identifiability compared to the profile likelihood method. Additionally, we introduce new regularization terms to address non-identifiable parameters, enabling uncertainty quantification and improving model reliability. To guide experimental design, we present an optimal data collection algorithm that ensures all model parameters are practically identifiable. Applications to Hill functions, neural networks, and dynamic biological models demonstrate the feasibility and efficiency of the proposed computational framework in uncovering critical biological processes and identifying key observable variables.

q-bio.QM↗

arXiv2025

Accelerating Causal Network Discovery of Alzheimer Disease Biomarkers via Scientific Literature-based Retrieval Augmented Generation

The causal relationships between biomarkers are essential for disease diagnosis and medical treatment planning. One notable application is Alzheimer's disease (AD) diagnosis, where certain biomarkers may influence the presence of others, enabling early detection, precise disease staging, targeted treatments, and improved monitoring of disease progression. However, understanding these causal relationships is complex and requires extensive research. Constructing a comprehensive causal network of biomarkers demands significant effort from human experts, who must analyze a vast number of research papers, and have bias in understanding diseases' biomarkers and their relation. This raises an important question: Can advanced large language models (LLMs), such as those utilizing retrieval-augmented generation (RAG), assist in building causal networks of biomarkers for further medical analysis? To explore this, we collected 200 AD-related research papers published over the past 25 years and then integrated scientific literature with RAG to extract AD biomarkers and generate causal relations among them. Given the high-risk nature of the medical diagnosis, we applied uncertainty estimation to assess the reliability of the generated causal edges and examined the faithfulness and scientificness of LLM reasoning using both automatic and human evaluation. We find that RAG enhances the ability of LLMs to generate more accurate causal networks from scientific papers. However, the overall performance of LLMs in identifying causal relations of AD biomarkers is still limited. We hope this study will inspire further foundational research on AI-driven analysis of AD biomarkers causal network discovery.

cs.IR↗

arXiv2025

Learn Singularly Perturbed Solutions via Homotopy Dynamics

Solving partial differential equations (PDEs) using neural networks has become a central focus in scientific machine learning. Training neural networks for singularly perturbed problems is particularly challenging due to certain parameters in the PDEs that introduce near-singularities in the loss function. In this study, we overcome this challenge by introducing a novel method based on homotopy dynamics to effectively manipulate these parameters. From a theoretical perspective, we analyze the effects of these parameters on training difficulty in these singularly perturbed problems and establish the convergence of the proposed homotopy dynamics method. Experimentally, we demonstrate that our approach significantly accelerates convergence and improves the accuracy of these singularly perturbed problems. These findings present an efficient optimization strategy leveraging homotopy dynamics, offering a robust framework to extend the applicability of neural networks for solving singularly perturbed differential equations.

cs.LG↗

arXiv2025

On pattern formation in the thermodynamically-consistent variational Gray-Scott model

In this paper, we explore pattern formation in a four-species variational Gary-Scott model, which includes all reverse reactions and introduces a virtual species to describe the birth-death process in the classical Gray-Scott model. This modification transforms the classical Gray-Scott model into a thermodynamically consistent closed system. The classical two-species Gray-Scott model can be viewed as a subsystem of the variational model in the limiting case when the small parameter $ε$, related to the reaction rate of the reverse reactions, approaches zero. We numerically explore pattern formation in this physically more complete Gray-Scott model in one spatial dimension, using non-uniform steady states of the classical model as initial conditions. By decreasing $ε$, we observed that the stationary pattern in the classical Gray-Scott model can be stabilized as the transient state in the variational model for a significantly small $ε$. Additionally, the variational model admits oscillating and traveling-wave-like patterns for small $ε$. The persistent time of these patterns is on the order of $O(ε^{-1})$. We also analyze the energy stability of two uniform steady states in the variational Gary-Scott model for fixed $ε$. Although both states are stable in a certain sense, the gradient flow type dynamics of the variational model exhibit a selection effect based on the initial conditions, with pattern formation occurring only if the initial condition does not converge to the boundary steady state, which corresponds to the trivial uniform steady state in the classical Gray-Scott model.

math.NA↗

arXiv2025

An Efficient Quasi-Newton Method with Tensor Product Implementation for Solving Quasi-Linear Elliptic Equations and Systems

In this paper, we introduce a quasi-Newton method optimized for efficiently solving quasi-linear elliptic equations and systems, with a specific focus on GPU-based computation. By approximating the Jacobian matrix with a combination of linear Laplacian and simplified nonlinear terms, our method reduces the computational overhead typical of traditional Newton methods while handling the large, sparse matrices generated from discretized PDEs. We also provide a convergence analysis demonstrating local convergence to the exact solution under optimal choices for the regularization parameter, ensuring stability and efficiency in each iteration. Numerical experiments in two- and three-dimensional domains validate the proposed method's robustness and computational gains with tensor-product implementation. This approach offers a promising pathway for accelerating quasi-linear elliptic equation and system solvers, expanding the feasibility of complex simulations in physics, engineering, and other fields leveraging advanced hardware capabilities.

math.NA↗

arXiv2025

Automatic Differentiation is Essential in Training Neural Networks for Solving Differential Equations

Neural network-based approaches have recently shown significant promise in solving partial differential equations (PDEs) in science and engineering, especially in scenarios featuring complex domains or incorporation of empirical data. One advantage of the neural network methods for PDEs lies in its automatic differentiation (AD), which necessitates only the sample points themselves, unlike traditional finite difference (FD) approximations that require nearby local points to compute derivatives. In this paper, we quantitatively demonstrate the advantage of AD in training neural networks. The concept of truncated entropy is introduced to characterize the training property. Specifically, through comprehensive experimental and theoretical analyses conducted on random feature models and two-layer neural networks, we discover that the defined truncated entropy serves as a reliable metric for quantifying the residual loss of random feature models and the training speed of neural networks for both AD and FD methods. Our experimental and theoretical analyses demonstrate that, from a training perspective, AD outperforms FD in solving PDEs.

cs.LG↗

arXiv2025

Data-Driven Modeling of Amyloid-beta Targeted Antibodies for Alzheimer's Disease

Alzheimer's disease (AD) is driven by the accumulation of amyloid-beta (Abeta) proteins in the brain, leading to memory loss and cognitive decline. While monoclonal antibodies targeting Abetahave been approved, optimizing their use to maximize benefits while minimizing side effects remains a challenge. This study develops a mathematical model to describe Abeta aggregation, capturing its progression from monomers to toxic oligomers, protofibrils, and fibrils using mass-action kinetics and coarse-grained modeling. The model is calibrated with experimental data, incorporating parameter estimation and sensitivity analysis to ensure accuracy. An optimal control framework is introduced to determine the best drug dosing strategy that reduces toxic Abeta aggregates while minimizing adverse effects, such as amyloid-related imaging abnormalities (ARIA). Results indicate that Donanemab achieves the greatest reduction in fibrils. This work provides a quantitative framework for optimizing AD treatment strategies, offering insights into balancing therapeutic efficacy and safety.

q-bio.QM↗

arXiv2025

An Imbalanced Learning-based Sampling Method for Physics-informed Neural Networks

This paper introduces Residual-based Smote (RSmote), an innovative local adaptive sampling technique tailored to improve the performance of Physics-Informed Neural Networks (PINNs) through imbalanced learning strategies. Traditional residual-based adaptive sampling methods, while effective in enhancing PINN accuracy, often struggle with efficiency and high memory consumption, particularly in high-dimensional problems. RSmote addresses these challenges by targeting regions with high residuals and employing oversampling techniques from imbalanced learning to refine the sampling process. Our approach is underpinned by a rigorous theoretical analysis that supports the effectiveness of RSmote in managing computational resources more efficiently. Through extensive evaluations, we benchmark RSmote against the state-of-the-art Residual-based Adaptive Distribution (RAD) method across a variety of dimensions and differential equations. The results demonstrate that RSmote not only achieves or exceeds the accuracy of RAD but also significantly reduces memory usage, making it particularly advantageous in high-dimensional scenarios. These contributions position RSmote as a robust and resource-efficient solution for solving complex partial differential equations, especially when computational constraints are a critical consideration.

cs.LG↗

arXiv2024

Homotopy Relaxation Training Algorithms for Infinite-Width Two-Layer ReLU Neural Networks

In this paper, we present a novel training approach called the Homotopy Relaxation Training Algorithm (HRTA), aimed at accelerating the training process in contrast to traditional methods. Our algorithm incorporates two key mechanisms: one involves building a homotopy activation function that seamlessly connects the linear activation function with the ReLU activation function; the other technique entails relaxing the homotopy parameter to enhance the training refinement process. We have conducted an in-depth analysis of this novel method within the context of the neural tangent kernel (NTK), revealing significantly improved convergence rates. Our experimental results, especially when considering networks with larger widths, validate the theoretical conclusions. This proposed HRTA exhibits the potential for other activation functions and deep neural networks.

cs.LG↗

arXiv2024

Stability and Robustness of Time-discretization Schemes for the Allen-Cahn Equation via Bifurcation and Perturbation Analysis

The Allen-Cahn equation is a fundamental model for phase transitions, offering critical insights into the dynamics of interface evolution in various physical systems. This paper investigates the stability and robustness of frequently utilized time-discretization numerical schemes for solving the Allen-Cahn equation, with focuses on the Backward Euler, Crank-Nicolson (CN), convex splitting of modified CN, and Diagonally Implicit Runge-Kutta (DIRK) methods. Our stability analysis reveals that the Convex Splitting of the Modified CN scheme exhibits unconditional stability, allowing greater flexibility in time step selection, while the other schemes are conditionally stable. Additionally, our robustness analysis highlights that the Backward Euler method converges to correct physical solutions regardless of initial conditions. In contrast, the other methods studied in this work show sensitivity to initial conditions and may converge to incorrect physical solutions if the initial conditions are not carefully chosen. This study introduces a comprehensive approach to assessing stability and robustness in numerical methods for solving the Allen-Cahn equation, providing a new perspective for evaluating numerical techniques for general nonlinear differential equations.

math.NA↗

arXiv2024

Newton Informed Neural Operator for Computing Multiple Solutions of Nonlinear Partials Differential Equations

Solving nonlinear partial differential equations (PDEs) with multiple solutions using neural networks has found widespread applications in various fields such as physics, biology, and engineering. However, classical neural network methods for solving nonlinear PDEs, such as Physics-Informed Neural Networks (PINN), Deep Ritz methods, and DeepONet, often encounter challenges when confronted with the presence of multiple solutions inherent in the nonlinear problem. These methods may encounter ill-posedness issues. In this paper, we propose a novel approach called the Newton Informed Neural Operator, which builds upon existing neural network techniques to tackle nonlinearities. Our method combines classical Newton methods, addressing well-posed problems, and efficiently learns multiple solutions in a single learning process while requiring fewer supervised data points compared to existing neural network methods.

cs.LG↗

arXiv2024

Gauss Newton method for solving variational problems of PDEs with neural network discretizaitons

The numerical solution of differential equations using machine learning-based approaches has gained significant popularity. Neural network-based discretization has emerged as a powerful tool for solving differential equations by parameterizing a set of functions. Various approaches, such as the deep Ritz method and physics-informed neural networks, have been developed for numerical solutions. Training algorithms, including gradient descent and greedy algorithms, have been proposed to solve the resulting optimization problems. In this paper, we focus on the variational formulation of the problem and propose a Gauss- Newton method for computing the numerical solution. We provide a comprehensive analysis of the superlinear convergence properties of this method, along with a discussion on semi-regular zeros of the vanishing gradient. Numerical examples are presented to demonstrate the efficiency of the proposed Gauss-Newton method.

math.NA↗

arXiv2024

HomPINNs: homotopy physics-informed neural networks for solving the inverse problems of nonlinear differential equations with multiple solutions

Due to the complex behavior arising from non-uniqueness, symmetry, and bifurcations in the solution space, solving inverse problems of nonlinear differential equations (DEs) with multiple solutions is a challenging task. To address this, we propose homotopy physics-informed neural networks (HomPINNs), a novel framework that leverages homotopy continuation and neural networks (NNs) to solve inverse problems. The proposed framework begins with the use of NNs to simultaneously approximate unlabeled observations across diverse solutions while adhering to DE constraints. Through homotopy continuation, the proposed method solves the inverse problem by tracing the observations and identifying multiple solutions. The experiments involve testing the performance of the proposed method on one-dimensional DEs and applying it to solve a two-dimensional Gray-Scott simulation. Our findings demonstrate that the proposed method is scalable and adaptable, providing an effective solution for solving DEs with multiple solutions and unknown parameters. Moreover, it has significant potential for various applications in scientific computing, such as modeling complex systems and solving inverse problems in physics, chemistry, biology, etc.

cs.LG↗

arXiv2023

A numerical method for solving elliptic equations on real closed algebraic curves and surfaces

There are many numerical methods for solving partial different equations (PDEs) on manifolds such as classical implicit, finite difference, finite element, and isogeometric analysis methods which aim at improving the interoperability between finite element method and computer aided design (CAD) software. However, these approaches have difficulty when the domain has singularities since the solution at the singularity may be multivalued. This paper develops a novel numerical approach to solve elliptic PDEs on real, closed, connected, orientable, and almost smooth algebraic curves and surfaces. Our method integrates numerical algebraic geometry, differential geometry, and a finite difference scheme which is demonstrated on several examples.

math.NA↗

arXiv2023

Companion-Based Multi-Level Finite Element Method for Computing Multiple Solutions of Nonlinear Differential Equations

The use of nonlinear PDEs has led to significant advancements in various fields, such as physics, biology, ecology, and quantum mechanics. However, finding multiple solutions for nonlinear PDEs can be a challenging task, especially when suitable initial guesses are difficult to obtain. In this paper, we introduce a novel approach called the Companion-Based Multilevel finite element method (CBMFEM), which can efficiently and accurately generate multiple initial guesses for solving nonlinear elliptic semi-linear equations with polynomial nonlinear terms using finite element methods with conforming elements. We provide a theoretical analysis of the error estimate of finite element methods using an appropriate notion of isolated solutions, for the nonlinear elliptic equation with multiple solutions and present numerical results obtained using CBMFEM which are consistent with the theoretical analysis.

math.NA↗

arXiv2023

Greedy Training Algorithms for Neural Networks and Applications to PDEs

Recently, neural networks have been widely applied for solving partial differential equations (PDEs). Although such methods have been proven remarkably successful on practical engineering problems, they have not been shown, theoretically or empirically, to converge to the underlying PDE solution with arbitrarily high accuracy. The primary difficulty lies in solving the highly non-convex optimization problems resulting from the neural network discretization, which are difficult to treat both theoretically and practically. It is our goal in this work to take a step toward remedying this. For this purpose, we develop a novel greedy training algorithm for shallow neural networks. Our method is applicable to both the variational formulation of the PDE and also to the residual minimization formulation pioneered by physics informed neural networks (PINNs). We analyze the method and obtain a priori error bounds when solving PDEs from the function class defined by shallow networks, which rigorously establishes the convergence of the method as the network size increases. Finally, we test the algorithm on several benchmark examples, including high dimensional PDEs, to confirm the theoretical convergence rate. Although the method is expensive relative to traditional approaches such as finite element methods, we view this work as a proof of concept for neural network-based methods, which shows that numerical methods based upon neural networks can be shown to rigorously converge.

math.NA↗