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Inferring microRNA-disease association by hybrid recommendation algorithm and unbalanced bi-random walk on heterogeneous network

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Scientific reports 2019年第1期9卷 2474页

作者： Dong-Ling Yu Yuan-Lin Ma Zu-Guo Yu Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. yuzuguo@***. School of Electrical Engineering and Computer Science Queensland University of Technology Brisbane Q4001 Australia. yuzuguo@***.

More and more research works have indicated that microRNAs (miRNAs) play indispensable roles in exploring the pathogenesis of diseases. Detecting miRNA-disease associations by experimental techniques in biology is expensive and time-consuming. Hence, it is important to propose reliable and accurate computational methods to exploring potential miRNAs related diseases. In our work, we develop a novel method (BRWHNHA) to uncover potential miRNAs associated with diseases based on hybrid recommendation algorithm and unbalanced bi-random walk. We first integrate the Gaussian interaction profile kernel similarity into the miRNA functional similarity network and the disease semantic similarity network. Then we calculate the transition probability matrix of bipartite network by using hybrid recommendation algorithm. Finally, we adopt unbalanced bi-random walk on the heterogeneous network to infer undiscovered miRNA-disease relationships. We tested BRWHNHA on 22 diseases based on five-fold cross-validation and achieves reliable performance with average AUC of 0.857, which an area under the ROC curve ranging from 0.807 to 0.924. As a result, BRWHNHA significantly improves the performance of inferring potential miRNA-disease association compared with previous methods. Moreover, the case studies on lung neoplasms and prostate neoplasms also illustrate that BRWHNHA is superior to previous prediction methods and is more advantageous in exploring potential miRNAs related diseases. All source codes can be downloaded from https://***/myl446/BRWHNHA .

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Parallel-in-Time with Fully Finite Element Multigrid for 2-D Space-fractional Diffusion Equations

arXiv

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arXiv 2018年

作者： Yue, X.Q. Shu, S. Xu, X.W. Bu, W.P. Pan, K.J. School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan411105 China Institute of Applied Physics and Computational Mathematics Beijing100088 China School of Mathematics and Statistics Central South University Hunan410083 China

The paper investigates a non-intrusive parallel time integration with multigrid for space-fractional diffusion equations in two spatial dimensions. We firstly obtain a fully discrete scheme via using the linear finite element method to discretize spatial and temporal derivatives to propagate solutions. Next, we present a non-intrusive time-parallelization and its two-level convergence analysis, where we algorithmically and theoretically generalize the MGRIT to time-dependent fine time-grid propagators. Finally, numerical illustrations show that the obtained numerical scheme possesses the saturation error order, theoretical results of the two-level variant deliver good predictions, and significant speedups can be achieved when compared to parareal and the sequential time-stepping approach. Copyright © 2018, The Authors. All rights reserved.

关键词： Finite element method

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Enhancement of photoluminescence efficiency in GeSe ultrathin slab by thermal treatment and annealing: experiment and first-principles molecular dynamics simulations

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Scientific reports 2018年第1期8卷 17671页

作者： Yuliang Mao Xin Mao Hongquan Zhao Nandi Zhang Xuan Shi Jianmei Yuan Hunan Key Laboratory for Micro-Nano Energy Materials and Devices School of Physics and Optoelectronic Xiangtan University Hunan 411105 China. ylmao@***. Hunan Key Laboratory for Micro-Nano Energy Materials and Devices School of Physics and Optoelectronic Xiangtan University Hunan 411105 China. Chongqing institute of Green and Intelligent Technology Chinese Academy of Sciences Chongqing 401120 China. hqzhao@***. Chongqing institute of Green and Intelligent Technology Chinese Academy of Sciences Chongqing 401120 China. Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Hunan 411105 China.

The effect of thermal treatment and annealing under different temperatures from 100 °C to 250 °C on the photoluminescence spectroscopy of the GeSe ultrathin slab is reported. After the thermal treatment and annealing under 200 °C, we found that the photoluminescence intensity of A exciton and B exciton in GeSe ultrathin slab is increased to twice as much as that in untreated case, while is increased by ~84% in the photoluminescence intensity of C exciton. Combined by our experimental work and theoretical simulations, our study confirms the significant role of thermal treatments and annealing in reducing surface roughness and removing the Se vacancy to form more compact and smoother regions in GeSe ultrathin slab. Our findings imply that the improved quality of GeSe surface after thermal treatments is an important factor for the photoluminescence enhancement.

关键词： Thermal Treatment First-principles Molecular Dynamics simulations Smoother Regions Reduced Surface Roughness GeSi Samples

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Numerical homogenization of elastoplastic deformations of composite material with small proportion of inclusions

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Journal of Physics: Conference Series 2019年第1期1392卷

作者： Petr V. Sivtsev Aleksandr E. Kolesov Petr E. Zakharov Ying Yang Research Laboratory 'Multiscale Matheatical Modeling and Computing' Ammosov North-Eastern Federal University 58 Belinskogo 677000 Yakutsk Russia Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Xiangtan 411105 Hunan China

Numerical simulation of the stress-strain state of a composite material may be difficult due to large computational complexity associated with a grid resolution of a large number of inclusions. To overcome the problem one may use the homogenization method. But for material with plastic properties, proper modeling of yield stress and hardening may be overcomplicated. In this work we use some simplification associated with a small proportion of inclusions and restriction of stress values by matrix material strength. As model problem, we use deformation of concrete deep beam reinforced with steel or basalt fiber inclusions. For the numerical solution, the finite element method was applied using the FEniCS computing platform.

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Convergence Analysis for the Chebyshev Collocation Methods to Volterra Integral Equations with a Weakly Singular Kernel

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Advances in Applied Mathematics and Mechanics 2017年第6期9卷 1506-1524页

作者： Xiong Liu Yanping Chen Hunan Key Laboratory for Computation and Simulation in Science and Engineering Department of MathematicsXiangtan UniversityXiangtanHunan 411105China School of Mathematical Sciences South China Normal UniversityGuangzhouGuangdong 510631China School of Mathematics and Statistics Lingnan Normal UniversityZhanjiangGuangdong 524048China

In this paper,a Chebyshev-collocation spectral method is developed for Volterra integral equations(VIEs)of second kind with weakly singular *** first change the equation into an equivalent VIE so that the solution of the new equation possesses better *** integral term in the resulting VIE is approximated by Gauss quadrature formulas using the Chebyshev collocation *** convergence analysis of this method is based on the Lebesgue constant for the Lagrange interpolation polynomials,approximation theory for orthogonal polynomials,and the operator *** spectral rate of convergence for the proposed method is established in the L^(∞)-norm and weighted L^(2)-*** results are presented to demonstrate the effectiveness of the proposed method.

关键词： Chebyshev collocation method Volterra integral equations spectral rate of convergence H¨older continuity

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A decoupling two-grid method for the time-dependent poisson-nernst-planck equations

arXiv

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arXiv 2018年

作者： Shen, Ruigang Shu, Shi Yang, Ying Lu, Benzhuo School of Mathematics and Computational Science Xiangtan University Xiangtan Hunan411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan411105 China School of Mathematics and Computational Science Guangxi Colleges Universities Key Laboratory of Data Analysis and Computation Guangxi Key Laboratory of Cryptography and information Security Guilin University of Electronic Technology Guilin Guangxi541004 China Institute of Computational Mathematics and Scientific/Engineering Computing National Center for Mathematics and Interdisciplinary Sciences Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China

We study a two-grid strategy for decoupling the time-dependent Poisson-Nernst-Planck equations describing the mass concentration of ions and the electrostatic potential. The computational system is decoupled to smaller systems by using coarse space solutions at each time level, which can speed up the solution process compared with the finite element method combined with the Gummel iteration. We derive the optimal error estimates in L2 norm for both semi- and fully discrete finite element approximations. Based on the a priori error estimates, the error estimates in H1 norm are presented for the two-grid algorithm. The theoretical results indicate this decoupling method can retain the same accuracy as the finite element method. Numerical experiments including the Poisson-Nernst-Planck equations for an ion channel show the efficiency and effectiveness of the decoupling two-grid method. Copyright © 2018, The Authors. All rights reserved.

关键词： Finite element method

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Long-time behavior of numerical solutions to nonlinear fractional odes

arXiv

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arXiv 2018年

作者： WANG, DONGLING XIAO, AIGUO ZOU, JUN Department of Mathematics and Center for Nonlinear Studies Northwest University Xi'an Shaanxi710075 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan411105 China Deptartment of Mathematics Chinese University of Hong Kong Shatin N.T. Hong Kong

In this work, we study the long time behaviors, including asymptotic contractivity and dissipativity, of the solutions to several numerical methods for fractional ordinary differential equations (F-ODEs). The existing algebraic contractivity and dissipativity rates of the solutions to the scalar F-ODEs are first improved. In order to study the long time behavior of numerical solutions to fractional backward differential formulas (F-BDFs), two crucial analytical techniques are developed, with the first one for the discrete version of the fractional generalization of the traditional Leibniz rule, and the other for the algebraic decay rate of the solution to a linear Volterra difference equation. By mens of these auxiliary tools and some natural conditions, the solutions to F-BDFs are shown to be contractive and dissipative, and also preserve the exact contractivity rate of the continuous solutions. Two typical F-BDFs, based on the Grünwald-Letnikov formula and L1 method respectively, are studied. For high order F-BDFs, including some second order F-BDFs and 3-α order method, their numerical contractivity and dissipativity are also developed under some slightly stronger conditions. Numerical experiments are presented to validate the long time qualitative characteristics of the solutions to F-BDFs, revealing very different decay rates of the numerical solutions in terms of the the initial values between F-ODEs and integer ODEs and demonstrating the superiority of the structure-preserving numerical methods. Copyright © 2018, The Authors. All rights reserved.

关键词： Ordinary differential equations

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Superconvergence and asymptotic expansions for bilinear finite volume element approximation on non-uniform grids

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Journal of Computational and Applied Mathematics 2017年 321卷 323-335页

作者： Cunyun Nie Shi Shu Haiyuan Yu Wenhua Xia The School of Science Hunan Institute of Engineering 411104 China Hunan Key Laboratory for Computation & Simulation in Science and Engineering Xiangtan University Hunan 411105 China Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education Xiangtan University Hunan 411105 China

We initially derive an asymptotic expansion and a high accuracy combination formula of the derivatives in the sense of pointwise for the isoparametric bilinear finite volume element scheme by employing the energy-embedded method on some non-uniform grids. Furthermore, we prove that the approximate derivatives are convergent of order two. Numerical examples confirm theoretical results.

关键词： Isoparametric bilinear finite volume element scheme Non-uniform grids Asymptotic expansion Superconvergence

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Evolution of the electronic and magnetic properties of zigzag silicene nanoribbon used for hydrogen storage material

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International Journal of Hydrogen Energy 2017年第44期42卷 27184-27205页

作者： Yuliang Mao Chan Tang Gang Guo Jianmei Yuan Jianxin Zhong Hunan Key Laboratory for Micro–Nano Energy Materials and Devices School of Physics and Optoelectronic Engineering Xiangtan University Hunan 411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Hunan 411105 China

Using first-principles calculations, we investigate the evolution of electronic and magnetic properties of zigzag silicene nanoribbon (ZSiNR) along with the concentration of edge adsorbed hydrogen adatoms. Our study shows that the significant covalent bonding helps to stabilize the configurations of hydrogen adsorbed ZSiNRs. The ferro-metallic electronic property of ZSiNR originated from the σ-π mixing effect is suppressed by mono-hydrogenation at the adsorption sites due to the sp 2 bonding. However, bi-hydrogenation at the adsorbed sites will lead to the typical sp 3 bonding, which dominates the electronic property with the increasing of hydrogen adatoms. Under the coexisting situation with mono-hydrogenation and bi-hydrogenation, we find that both the number of adsorption sites and the bonding type of sp 2 or sp 3 have impact on the electronic property of ZSiNR. It is found that symmetry adsorption at the edges changes the stable magnetic state of ZSiNR from ferromagnetic to antiferromagnetic. In contrast, unsymmetrical adsorption along the two edges of ZSiNR keeps its ferromagnetic property.

关键词： Silicene nanoribbon Hydrogen adatom First-principles Edge-adsorption

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Fully finite element adaptive algebraic multigrid method for time-space caputo-riesz fractional diffusion equations

arXiv

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arXiv 2017年

作者： Yue, Xiaoqiang Bu, Weiping Shu, Shi Liu, Menghuan Wang, Shuai School of Mathematics and Computational Science Xiangtan University Hunan411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan411105 China

The paper aims to establish a fully discrete finite element (FE) scheme and provide cost-effective solutions for one-dimensional time-space Caputo-Riesz fractional diffusion equations on a bounded domain Ω. Firstly, we construct a fully discrete scheme of the linear FE method in both temporal and spatial directions, derive many characterizations on the coefficient matrix and numerically verify that the fully FE approximation possesses the saturation error order under L2(Ω) norm. Secondly, we theoretically prove the estimation 1 + O(ταh−2β) on the condition number of the coefficient matrix, in which τ and h respectively denote time and space step sizes. Finally, on the grounds of the estimation and fast Fourier transform, we develop and analyze an adaptive algebraic multigrid (AMG) method with low algorithmic complexity, reveal a reference formula to measure the strength-of-connection tolerance which severely affect the robustness of AMG methods in handling fractional diffusion equations, and illustrate the well robustness and high efficiency of the proposed algorithm compared with the classical AMG, conjugate gradient and Jacobi iterative methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Computational complexity

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