Based on Arnoldi's method, a version of generalized Arnoldi algorithm has been developed for the reduction of gyroscopic eigenvalue problems. By utilizing the skew symmetry of system matrix, a very simple recurren...Based on Arnoldi's method, a version of generalized Arnoldi algorithm has been developed for the reduction of gyroscopic eigenvalue problems. By utilizing the skew symmetry of system matrix, a very simple recurrence scheme, named gyroscopic Arnoldi reduction algorithm has been obtained, which is even simpler than the Lanczos algorithm for symmetric eigenvalue problems. The complex number computation is completely avoided. A restart technique is used to enable the reduction algorithm to have iterative characteristics. It has been found that the restart technique is not only effective for the convergence of multiple eigenvalues but it also furnishes the reduction algorithm with a technique to check and compute missed eigenvalues. By combining it with the restart technique, the algorithm is made practical for large-scale gyroscopic eigenvalue problems. Numerical examples are given to demonstrate the effectiveness of the method proposed.展开更多
In this paper, we develop an implicitly restarted block Arnoldi algorithm in a vector-wise fashion. The vector-wise construction greatly simplifies both the detection of necessary deflation and the actual deflation it...In this paper, we develop an implicitly restarted block Arnoldi algorithm in a vector-wise fashion. The vector-wise construction greatly simplifies both the detection of necessary deflation and the actual deflation itself, so it is preferable to the block-wise construction. The numerical experiment shows that our algorithm is effective.展开更多
目的 通过重启随机游走(random walk with restart,RWR)算法解析桃红四物汤药味配伍、成分群协同抗血栓作用的生物过程网络与关键成分群,揭示其“多成分-多靶点-多途径”抗血栓作用机制。方法 结合文献和课题组前期研究基础,通过中药系...目的 通过重启随机游走(random walk with restart,RWR)算法解析桃红四物汤药味配伍、成分群协同抗血栓作用的生物过程网络与关键成分群,揭示其“多成分-多靶点-多途径”抗血栓作用机制。方法 结合文献和课题组前期研究基础,通过中药系统药理学数据库与分析平台(TCMSP)、本草组鉴(HERB)等4个数据库,获取桃红四物汤活性成分、成分群及对应靶标基因;在人类基因数据库(Genecards)、人类孟德尔遗传综合数据库(OMIM)等4个数据库收集血栓相关基因;首先将血栓相关基因、中药和成分群靶标基因导入Metascape平台进行生物过程富集,采用Cytoscape 3.9.1软件将血栓生物过程进行聚类,初步分析桃红四物汤中药配伍、成分群协同抗血栓作用;进一步整合RWR算法、Pearson相关性分析与Z得分显著性分析,定量分析复方、单味药与成分群对血栓生物过程网络影响的相关性及显著性,筛选成分群协同抗血栓的关键生物过程、关键成分群;最后构建桃红四物汤抗血栓关键生物过程网络,分子对接筛选核心成分与核心靶点。结果纳入桃红四物汤9类成分群,血栓生物过程聚类为4类,桃红四物汤抗血栓生物过程显著性影响大小依次为氧化应激>炎症反应>细胞内信号传导>细胞活化,氧化应激与炎症反应是其抗血栓的关键生物过程;黄酮类、有机酸类、生物碱类、苯乙醇苷类、萜类、香豆素类、苯酞类是其协同抗血栓的关键成分群;生物网络构建与分子对接筛选出10个核心靶点(TNF、HMGB1、NLRP3、PARP1、PPARA、GAPDH、MMP9、IFNG、IL17A、HRAS)、6个核心成分(川芎哚、儿茶素、绿原酸、毛蕊花糖苷、羟基红花黄色素A、芍药苷)。结论 通过整合生物过程网络和机器学习算法,定量解析桃红四物汤成分群协同抗血栓的关键生物过程和核心成分、靶点,为其临床应用和基础研究提供参考。展开更多
基金This research is supported by The National Science FoundationThe Doctoral Training Foundation
文摘Based on Arnoldi's method, a version of generalized Arnoldi algorithm has been developed for the reduction of gyroscopic eigenvalue problems. By utilizing the skew symmetry of system matrix, a very simple recurrence scheme, named gyroscopic Arnoldi reduction algorithm has been obtained, which is even simpler than the Lanczos algorithm for symmetric eigenvalue problems. The complex number computation is completely avoided. A restart technique is used to enable the reduction algorithm to have iterative characteristics. It has been found that the restart technique is not only effective for the convergence of multiple eigenvalues but it also furnishes the reduction algorithm with a technique to check and compute missed eigenvalues. By combining it with the restart technique, the algorithm is made practical for large-scale gyroscopic eigenvalue problems. Numerical examples are given to demonstrate the effectiveness of the method proposed.
基金This work is supported by National Natural Science Foundation of China No. 10531080.
文摘In this paper, we develop an implicitly restarted block Arnoldi algorithm in a vector-wise fashion. The vector-wise construction greatly simplifies both the detection of necessary deflation and the actual deflation itself, so it is preferable to the block-wise construction. The numerical experiment shows that our algorithm is effective.
文摘目的 通过重启随机游走(random walk with restart,RWR)算法解析桃红四物汤药味配伍、成分群协同抗血栓作用的生物过程网络与关键成分群,揭示其“多成分-多靶点-多途径”抗血栓作用机制。方法 结合文献和课题组前期研究基础,通过中药系统药理学数据库与分析平台(TCMSP)、本草组鉴(HERB)等4个数据库,获取桃红四物汤活性成分、成分群及对应靶标基因;在人类基因数据库(Genecards)、人类孟德尔遗传综合数据库(OMIM)等4个数据库收集血栓相关基因;首先将血栓相关基因、中药和成分群靶标基因导入Metascape平台进行生物过程富集,采用Cytoscape 3.9.1软件将血栓生物过程进行聚类,初步分析桃红四物汤中药配伍、成分群协同抗血栓作用;进一步整合RWR算法、Pearson相关性分析与Z得分显著性分析,定量分析复方、单味药与成分群对血栓生物过程网络影响的相关性及显著性,筛选成分群协同抗血栓的关键生物过程、关键成分群;最后构建桃红四物汤抗血栓关键生物过程网络,分子对接筛选核心成分与核心靶点。结果纳入桃红四物汤9类成分群,血栓生物过程聚类为4类,桃红四物汤抗血栓生物过程显著性影响大小依次为氧化应激>炎症反应>细胞内信号传导>细胞活化,氧化应激与炎症反应是其抗血栓的关键生物过程;黄酮类、有机酸类、生物碱类、苯乙醇苷类、萜类、香豆素类、苯酞类是其协同抗血栓的关键成分群;生物网络构建与分子对接筛选出10个核心靶点(TNF、HMGB1、NLRP3、PARP1、PPARA、GAPDH、MMP9、IFNG、IL17A、HRAS)、6个核心成分(川芎哚、儿茶素、绿原酸、毛蕊花糖苷、羟基红花黄色素A、芍药苷)。结论 通过整合生物过程网络和机器学习算法,定量解析桃红四物汤成分群协同抗血栓的关键生物过程和核心成分、靶点,为其临床应用和基础研究提供参考。
