Kernel-based methods work by embedding the data into a feature space and then searching linear hypothesis among the embedding data points. The performance is mostly affected by which kernel is used. A promising way is...Kernel-based methods work by embedding the data into a feature space and then searching linear hypothesis among the embedding data points. The performance is mostly affected by which kernel is used. A promising way is to learn the kernel from the data automatically. A general regularized risk functional （RRF） criterion for kernel matrix learning is proposed. Compared with the RRF criterion, general RRF criterion takes into account the geometric distributions of the embedding data points. It is proven that the distance between different geometric distdbutions can be estimated by their centroid distance in the reproducing kernel Hilbert space. Using this criterion for kernel matrix learning leads to a convex quadratically constrained quadratic programming （QCQP） problem. For several commonly used loss functions, their mathematical formulations are given. Experiment results on a collection of benchmark data sets demonstrate the effectiveness of the proposed method.展开更多
The kernel energy method(KEM) has been shown to provide fast and accurate molecular energy calculations for molecules at their equilibrium geometries.KEM breaks a molecule into smaller subsets,called kernels,for the p...The kernel energy method(KEM) has been shown to provide fast and accurate molecular energy calculations for molecules at their equilibrium geometries.KEM breaks a molecule into smaller subsets,called kernels,for the purposes of calculation.The results from the kernels are summed according to an expression characteristic of KEM to obtain the full molecule energy.A generalization of the kernel expansion to density matrices provides the full molecule density matrix and orbitals.In this study,the kernel expansion for the density matrix is examined in the context of density functional theory(DFT) Kohn-Sham(KS) calculations.A kernel expansion for the one-body density matrix analogous to the kernel expansion for energy is defined,and is then converted into a normalizedprojector by using the Clinton algorithm.Such normalized projectors are factorizable into linear combination of atomic orbitals(LCAO) matrices that deliver full-molecule Kohn-Sham molecular orbitals in the atomic orbital basis.Both straightforward KEM energies and energies from a normalized,idempotent density matrix obtained from a density matrix kernel expansion to which the Clinton algorithm has been applied are compared to reference energies obtained from calculations on the full system without any kernel expansion.Calculations were performed both for a simple proof-of-concept system consisting of three atoms in a linear configuration and for a water cluster consisting of twelve water molecules.In the case of the proof-of-concept system,calculations were performed using the STO-3 G and6-31 G(d,p) bases over a range of atomic separations,some very far from equilibrium.The water cluster was calculated in the 6-31 G(d,p) basis at an equilibrium geometry.The normalized projector density energies are more accurate than the straightforward KEM energy results in nearly all cases.In the case of the water cluster,the energy of the normalized projector is approximately four times more accurate than the straightforward KEM energy result.The KS density matrices of this study are applicable to quantum crystallography.展开更多
稀疏线性方程组求解等高性能计算应用常常涉及稀疏矩阵向量乘(SpMV)序列Ax,A2x,…,Asx的计算.上述SpMV序列操作又称为稀疏矩阵幂函数(matrix power kernel,MPK).由于MPK执行多次SpMV且稀疏矩阵保持不变,在缓存(cache)中重用稀疏矩阵,可...稀疏线性方程组求解等高性能计算应用常常涉及稀疏矩阵向量乘(SpMV)序列Ax,A2x,…,Asx的计算.上述SpMV序列操作又称为稀疏矩阵幂函数(matrix power kernel,MPK).由于MPK执行多次SpMV且稀疏矩阵保持不变,在缓存(cache)中重用稀疏矩阵,可避免每次执行SpMV均从主存加载A,从而缓解SpMV访存受限问题,提升MPK性能.但缓存数据重用会导致相邻SpMV操作之间的数据依赖,现有MPK优化多针对单次SpMV调用,或在实现数据重用时引入过多额外开销.提出了缓存感知的MPK(cache-awareMPK,Ca-MPK),基于稀疏矩阵的依赖图,设计了体系结构感知的递归划分方法,将依赖图划分为适合缓存大小的子图/子矩阵,通过构建分割子图解耦数据依赖,根据特定顺序在子矩阵上调度执行SpMV,实现缓存数据重用.测试结果表明,Ca-MPK相对于Intel OneMKL库和最新MPK实现,平均性能提升分别多达约1.57倍和1.40倍.展开更多
Driven by the challenge of integrating large amount of experimental data, classification technique emerges as one of the major and popular tools in computational biology and bioinformatics research. Machine learning m...Driven by the challenge of integrating large amount of experimental data, classification technique emerges as one of the major and popular tools in computational biology and bioinformatics research. Machine learning methods, especially kernel methods with Support Vector Machines （SVMs） are very popular and effective tools. In the perspective of kernel matrix, a technique namely Eigen- matrix translation has been introduced for protein data classification. The Eigen-matrix translation strategy has a lot of nice properties which deserve more exploration. This paper investigates the major role of Eigen-matrix translation in classification. The authors propose that its importance lies in the dimension reduction of predictor attributes within the data set. This is very important when the dimension of features is huge. The authors show by numerical experiments on real biological data sets that the proposed framework is crucial and effective in improving classification accuracy. This can therefore serve as a novel perspective for future research in dimension reduction problems.展开更多
基金supported by the National Natural Science Fundation of China (60736021)the Joint Funds of NSFC-Guangdong Province(U0735003)
文摘Kernel-based methods work by embedding the data into a feature space and then searching linear hypothesis among the embedding data points. The performance is mostly affected by which kernel is used. A promising way is to learn the kernel from the data automatically. A general regularized risk functional （RRF） criterion for kernel matrix learning is proposed. Compared with the RRF criterion, general RRF criterion takes into account the geometric distributions of the embedding data points. It is proven that the distance between different geometric distdbutions can be estimated by their centroid distance in the reproducing kernel Hilbert space. Using this criterion for kernel matrix learning leads to a convex quadratically constrained quadratic programming （QCQP） problem. For several commonly used loss functions, their mathematical formulations are given. Experiment results on a collection of benchmark data sets demonstrate the effectiveness of the proposed method.
文摘The kernel energy method(KEM) has been shown to provide fast and accurate molecular energy calculations for molecules at their equilibrium geometries.KEM breaks a molecule into smaller subsets,called kernels,for the purposes of calculation.The results from the kernels are summed according to an expression characteristic of KEM to obtain the full molecule energy.A generalization of the kernel expansion to density matrices provides the full molecule density matrix and orbitals.In this study,the kernel expansion for the density matrix is examined in the context of density functional theory(DFT) Kohn-Sham(KS) calculations.A kernel expansion for the one-body density matrix analogous to the kernel expansion for energy is defined,and is then converted into a normalizedprojector by using the Clinton algorithm.Such normalized projectors are factorizable into linear combination of atomic orbitals(LCAO) matrices that deliver full-molecule Kohn-Sham molecular orbitals in the atomic orbital basis.Both straightforward KEM energies and energies from a normalized,idempotent density matrix obtained from a density matrix kernel expansion to which the Clinton algorithm has been applied are compared to reference energies obtained from calculations on the full system without any kernel expansion.Calculations were performed both for a simple proof-of-concept system consisting of three atoms in a linear configuration and for a water cluster consisting of twelve water molecules.In the case of the proof-of-concept system,calculations were performed using the STO-3 G and6-31 G(d,p) bases over a range of atomic separations,some very far from equilibrium.The water cluster was calculated in the 6-31 G(d,p) basis at an equilibrium geometry.The normalized projector density energies are more accurate than the straightforward KEM energy results in nearly all cases.In the case of the water cluster,the energy of the normalized projector is approximately four times more accurate than the straightforward KEM energy result.The KS density matrices of this study are applicable to quantum crystallography.
文摘稀疏线性方程组求解等高性能计算应用常常涉及稀疏矩阵向量乘(SpMV)序列Ax,A2x,…,Asx的计算.上述SpMV序列操作又称为稀疏矩阵幂函数(matrix power kernel,MPK).由于MPK执行多次SpMV且稀疏矩阵保持不变,在缓存(cache)中重用稀疏矩阵,可避免每次执行SpMV均从主存加载A,从而缓解SpMV访存受限问题,提升MPK性能.但缓存数据重用会导致相邻SpMV操作之间的数据依赖,现有MPK优化多针对单次SpMV调用,或在实现数据重用时引入过多额外开销.提出了缓存感知的MPK(cache-awareMPK,Ca-MPK),基于稀疏矩阵的依赖图,设计了体系结构感知的递归划分方法,将依赖图划分为适合缓存大小的子图/子矩阵,通过构建分割子图解耦数据依赖,根据特定顺序在子矩阵上调度执行SpMV,实现缓存数据重用.测试结果表明,Ca-MPK相对于Intel OneMKL库和最新MPK实现,平均性能提升分别多达约1.57倍和1.40倍.
基金supported by Research Grants Council of Hong Kong under Grant No.17301214HKU CERG Grants,Fundamental Research Funds for the Central Universities+2 种基金the Research Funds of Renmin University of ChinaHung Hing Ying Physical Research Grantthe Natural Science Foundation of China under Grant No.11271144
文摘Driven by the challenge of integrating large amount of experimental data, classification technique emerges as one of the major and popular tools in computational biology and bioinformatics research. Machine learning methods, especially kernel methods with Support Vector Machines （SVMs） are very popular and effective tools. In the perspective of kernel matrix, a technique namely Eigen- matrix translation has been introduced for protein data classification. The Eigen-matrix translation strategy has a lot of nice properties which deserve more exploration. This paper investigates the major role of Eigen-matrix translation in classification. The authors propose that its importance lies in the dimension reduction of predictor attributes within the data set. This is very important when the dimension of features is huge. The authors show by numerical experiments on real biological data sets that the proposed framework is crucial and effective in improving classification accuracy. This can therefore serve as a novel perspective for future research in dimension reduction problems.
