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NEURAL NETWORK-ENHANCED hr-ADAPTIVE FINITE ELEMENT ALGORITHM FOR PARABOLIC EQUATIONS

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arXiv 2025年

作者： Hao, Jiaxiong Huang, Yunqing Yi, Nianyu Yin, Peimeng Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China National Center for Applied Mathematics in Hunan Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education Xiangtan University Hunan Xiangtan411105 China Department of Mathematical Sciences University of Texas at El Paso El PasoTX79968 United States

In this paper, we present a novel enhancement to the conventional hr-adaptive finite element methods for parabolic equations, integrating traditional h-adaptive and r-adaptive methods via neural networks. A major challenge in hr-adaptive finite element methods lies in projecting the previous step’s finite element solution onto the updated mesh. This projection depends on the new mesh and must be recomputed for each adaptive iteration. To address this, we introduce a neural network to construct a mesh-free surrogate of the previous step finite element solution. Since the neural network is mesh-free, it only requires training once per time step, with its parameters initialized using the optimizer from the previous time step. This approach effectively overcomes the interpolation challenges associated with non-nested meshes in computation, making node insertion and movement more convenient and efficient. The new algorithm also emphasizes SIZING and GENERATE, allowing each refinement to roughly double the number of mesh nodes of the previous iteration and then redistribute them to form a new mesh that effectively captures the singularities. It significantly reduces the time required for repeated refinement and achieves the desired accuracy in no more than seven space-adaptive iterations per time step. Numerical experiments confirm the efficiency of the proposed algorithm in capturing dynamic changes of *** Codes 92B20, 65M60, 35K57 © 2025, CC BY.

关键词： Interpolation

Error Analysis of Virtual Element Method for the Poisson-Boltzmann Equation

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arXiv 2023年

作者： Huang, Linghan Shu, Shi Yang, Ying Guangxi Guilin541004 China School of Mathematics and Computational Science Xiangtan University Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing Ministry of Education Hunan Xiangtan411105 China Guangxi541004 China

The Poisson-Boltzmann equation is a nonlinear elliptic equation with Dirac distribution sources, which has been widely applied to the prediction of electrostatics potential of biological biomolecular systems in solution. In this paper, we discuss and analysis the virtual element method for the Poisson-Boltzmann equation on general polyhedral meshes. Under the low regularity of the solution of the whole domain, nearly optimal error estimates in both L2-norm and H1-norm for the virtual element approximation are obtained. The numerical experiment on different polyhedral meshes shows the efficiency of the virtual element method and verifies the proposed theoretical prediction. Copyright © 2023, The Authors. All rights reserved.

关键词： Poisson equation

The interior penalty virtual element method for fourth-order singular perturbation problems

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arXiv 2023年

作者： Feng, Fang Yu, Yue School of Mathematics and Statistics Nanjing University of Science and Technology Nanjing China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing Ministry of Education Xiangtan University Hunan Xiangtan411105 China

This paper is dedicated to the numerical solution of a fourth-order singular perturbation problem using the interior penalty virtual element method (IPVEM) proposed in [42]. The study introduces modifications to the jumps and averages in the penalty term, as well as presents an automated mesh-dependent selection of the penalty parameter. Drawing inspiration from the modified Morley finite element methods, we leverage the conforming interpolation technique to handle the lower part of the bilinear form. Through our analysis, we establish optimal convergence in the energy norm and provide a rigorous proof of uniform convergence concerning the perturbation parameter in the lowest-order case. © 2023, CC BY-NC-ND.

关键词： Numerical methods

Efficient numerical methods for computing stationary states of spherical Landau-Brazovskii model

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arXiv 2025年

作者： Qiu, Qun Si, Wei Ji, Guanghua Jiang, Kai School of Mathematical Sciences Beijing Normal University Beijing100875 China School of Mathematics Sciences Peking University Beijing100871 China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan Xiangtan411105 China

In this paper, we develop a set of efficient methods to compute stationary states of the spherical Landau-Brazovskii (LB) model in a discretization-then-optimization way. First, we discretize the spherical LB energy functional into a finite-dimensional energy function by the spherical harmonic expansion. Then five optimization methods are developed to compute stationary states of the discretized energy function, including the accelerated adaptive Bregman proximal gradient, Nesterov, adaptive Nesterov, adaptive nonlinear conjugate gradient and adaptive gradient descent methods. To speed up the convergence, we propose a principal mode analysis (PMA) method to estimate good initial configurations and sphere radius. The PMA method also reveals the relationship between the optimal sphere radius and the dominant degree of spherical harmonics. Numerical experiments show that our approaches significantly reduce the number of iterations and the computational time. Copyright © 2025, The Authors. All rights reserved.

关键词： Conjugate gradient method

Identifying possible lncRNA-disease associations based on deep learning and positive-unlabeled learning

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Identifying possible lncRNA-disease associations based on de...

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Lihong Peng Liangliang Huang Yuankang Lu Guangyi Liu Min Chen Guosheng Han School of Computer Science Hunan University of Technology Zhuzhou China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan China

ISBN: (数字)9781665468190

ISBN: (纸本)9781665468206

lncRNAs are involved in many biological processes, and their mutations and disorders are closely related to many diseases. Identification of LncRNA-Disease Associations (LDAs) helps us understand the pathogenesis of diseases and improve their diagnosis and treatment. However, experiments to determine LDAs are expensive, so it is essential to exploit effective computational methods to screen possible LDAs. In this study, we developed an LDA prediction model (LDA-DLPU) based on deep learning and positive-unlabeled (PU) learning. First, LDA-DLPU extracted features of lncRNAs and diseases based on singular value decomposition and regression model. Second, it selected negative LDAs based on PU learning and graph autoencoder. Finally, it classified unknown lncRNA-disease pairs based on deep neural network. LDA-DLPU obtained the best performance on two datasets. We predict that BCYRN1 and IFNG-AS1 may associate with leukemia.

关键词： Deep learning computational modeling Neural networks Biological processes Predictive models Feature extraction Bioinformatics

Two-Relaxation-Time Regularized Lattice Boltzmann Model for Navier-Stokes Equations

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SSRN

SSRN 2024年

作者： Yu, Yuan Qin, Zuojian Chen, Siwei Shu, Shi Yuan, Hai-Zhuan aSchool of Mathematics and Computational Science Xiangtan University Xiangtan 411105 China bNational Center for Applied Mathematics in Hunan Xiangtan 411105 China cHunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan 411105 China

In this paper, we propose a novel two-relaxation-time regularized lattice Boltzmann (TRTRLB) model for simulating weakly compressible isothermal flows. A free relaxation parameter, τs,2, is employed to relax the regularized non-equilibrium third-order terms. ChapmanEnskog analysis reveals that our model can accurately recover the Navier-Stokes equations (NSEs). Theoretical analysis of the Poiseuille flow problem demonstrates that the slip velocity magnitude in the proposed model is controlled by a magic parameter, which can be entirely eliminated under specific values, consistent with the classical TRT model. Our simulations of the double shear layer problem, Taylor-Green vortex flow, and force-driven Poiseuille flow confirm that the stability and accuracy of our model significantly surpass those of both the regularized lattice Boltzmann (RLB) and two-relaxation-time (TRT) models, even under super-high Reynolds numbers as Re = 107. Concurrently, the TRT-RLB model exhibits superior performance in very high viscosity scenarios. The simulations of creeping flow around a square cylinder demonstrates the model’s capability to accurately compute ultra-low Reynolds numbers as Re = 10−7. This study establishes the TRT-RLB model as a flexible and robust tool in computational fluid dynamics. © 2024, The Authors. All rights reserved.

关键词： Navier Stokes equations

Phase Behaviour of X-Shaped Liquid Crystalline Molecules

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arXiv 2024年

作者： Wei, Dan He, Zhijuan Huang, Yunqing Shi, An-Chang Jiang, Kai Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing Ministry of Education School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China Department of Physics and Astronomy McMaster University HamiltonONL8S 4M1 Canada

X-shaped liquid crystalline molecules (XLCMs) are obtained by tethering two flexible end A-blocks and two flexible side B-blocks to a rigid backbone (R). A rich array of ordered structures can be formed from XLCMs, driven by the competition between the interactions between the chemically distinct blocks and the molecular connectivity. Here, we report a theoretical study on the phase behaviour of XLCMs with symmetric and asymmetric side blocks by using the self-consistent field theory (SCFT). A large number of ordered structures, including stable smectic-A, triangle-square, pentagon and giant polygon, are obtained as solutions of the SCFT equations. Phase diagrams of XLCMs as a function of the total length and asymmetric ratio of the side chains are constructed. For XLCMs with symmetric side blocks, the theoretically predicted phase transition sequence is in good agreement with experiments. For XLCMs with a fixed total side chain length, transitions between layered structure to polygonal phases, as well as between different polygonal phases, could be induced by varying the asymmetry of the side chains. The free energy density, domain size, side-chain stretching, and molecular orientation are analyzed to elucidate mechanisms stabilizing the different ordered phases. © 2024, CC BY.

关键词： Free energy

Irrational-window-filter projection method and application to quasiperiodic Schrödinger eigenproblems

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arXiv 2024年

作者： Jiang, Kai Li, Xueyang Ma, Yao Zhang, Juan Zhang, Pingwen Zhou, Qi Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing Ministry of Education School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China School of Mathematics and Statistics Wuhan University Wuhan430072 China School of Mathematical Sciences Peking University Beijing100871 China

In this paper, we propose a new algorithm, the irrational-window-filter projection method (IWFPM), for quasiperiodic systems with concentrated spectral point distribution. Based on the projection method (PM), IWFPM filters out dominant spectral points by defining an irrational window and uses a corresponding index-shift transform to make the FFT available. The error analysis on the function approximation level is also given. We apply IWFPM to 1D, 2D, and 3D quasiperiodic Schrödinger eigenproblems (QSEs) to demonstrate its accuracy and efficiency. IWFPM exhibits a significant computational advantage over PM for both extended and localized quantum states. More importantly, by using IWFPM, the existence of Anderson localization in 2D and 3D QSEs is numerically *** Codes 35P05, 35J10, 65D15, 65T50, 81-08 © 2024, CC BY-NC-SA.

关键词： Wiener filtering

PROJECTION METHOD FOR QUASIPERIODIC ELLIPTIC EQUATIONS AND APPLICATION TO QUASIPERIODIC HOMOGENIZATION

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arXiv 2024年

作者： Jiang, Kai Li, Meng Zhang, Juan Zhang, Lei Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China School of Mathematical Sciences Institute of Natural Sciences MOE-LSC Shanghai Jiao Tong University Shanghai200240 China

In this study, we address the challenge of solving elliptic equations with quasiperiodic coefficients. To achieve accurate and efficient computation, we introduce the projection method, which enables the embedding of quasiperiodic systems into higher-dimensional periodic systems. To enhance the computational efficiency, we propose a compressed storage strategy for the stiffness matrix by its multi-level block circulant structure, significantly reducing memory requirements. Furthermore, we design a diagonal preconditioner to efficiently solve the resulting high-dimensional linear system by reducing the condition number of the stiffness matrix. These techniques collectively contribute to the computational effectiveness of our proposed approach. Convergence analysis shows the spectral accuracy of the proposed method. We demonstrate the effectiveness and accuracy of our approach through a series of numerical examples. Moreover, we apply our method to achieve a highly accurate computation of the homogenized coefficients for a quasiperiodic multiscale elliptic *** Codes 65D05, 65D15, 65F08, 35B15, 35B27 Copyright © 2024, The Authors. All rights reserved.

关键词： Stiffness matrix