Genes associated with similar diseases are often functionally related.This principle is largely supported by many biological data sources,such as disease phenotype similarities,protein complexes,protein-protein intera...Genes associated with similar diseases are often functionally related.This principle is largely supported by many biological data sources,such as disease phenotype similarities,protein complexes,protein-protein interactions,pathways and gene expression profiles.Integrating multiple types of biological data is an effective method to identify disease genes for many genetic diseases.To capture the gene-disease associations based on biological networks,a kernel-based Markov random field(MRF)method is proposed by combining graph kernels and the MRF method.In the proposed method,three kinds of kernels are employed to describe the overall relationships of vertices in five biological networks,respectively,and a novel weighted MRF method is developed to integrate those data.In addition,an improved Gibbs sampling procedure and a novel parameter estimation method are proposed to generate predictions from the kernel-based MRF method.Numerical experiments are carried out by integrating known gene-disease associations,protein complexes,protein-protein interactions,pathways and gene expression profiles.The proposed kernel-based MRF method is evaluated by the leave-one-out cross validation paradigm,achieving an AUC score of 0.771 when integrating all those biological data in our experiments,which indicates that our proposed method is very promising compared with many existing methods.展开更多
In this paper, we investigate a blow-up phenomenon for a semilinear parabolic system on locally finite graphs. Under some appropriate assumptions on the curvature condition CDE’(n,0), the polynomial volume growth of ...In this paper, we investigate a blow-up phenomenon for a semilinear parabolic system on locally finite graphs. Under some appropriate assumptions on the curvature condition CDE’(n,0), the polynomial volume growth of degree m, the initial values, and the exponents in absorption terms, we prove that every non-negative solution of the semilinear parabolic system blows up in a finite time. Our current work extends the results achieved by Lin and Wu (Calc Var Partial Differ Equ, 2017, 56: Art 102) and Wu (Rev R Acad Cien Serie A Mat, 2021, 115: Art 133).展开更多
Using the linear space over the binary field that related to a graph G, a sufficient and necessary condition for the chromatic number of G is obtained.
网络遥测是一种新型的网络测量技术,具有实时性强、准确性高、开销低的特点。现有网络遥测技术存在无法收集多粒度网络数据、无法有效存储大量原始网络数据、无法快速提取及生成网络遥测信息、无法利用内核态及用户态特性设计网络遥测...网络遥测是一种新型的网络测量技术,具有实时性强、准确性高、开销低的特点。现有网络遥测技术存在无法收集多粒度网络数据、无法有效存储大量原始网络数据、无法快速提取及生成网络遥测信息、无法利用内核态及用户态特性设计网络遥测方案等问题。为此,提出了一种融合内核态及用户态的、基于遥测数据图和同步控制块的多粒度、可扩展、覆盖全网的网络遥测机制(a nEtwork telemetry mechAnism based on telemetry data Graph in kerneL and usEr mode,EAGLE)。EAGLE设计了一种能够收集多粒度数据且数据平面上灵活可控的网络遥测数据包结构,用于获取上层应用所需的数据。此外,为快速存储、查询、统计、聚合网络状态数据,实现网络遥测数据包所需遥测数据的快速提取与生成,EAGLE提出了一种基于遥测数据图及同步控制块的网络遥测信息生成方法。在此基础上,为了最大化网络遥测机制中网络遥测数据包的处理效率,EAGLE提出了融合内核态及用户态特性的网络遥测信息嵌入架构。在Open vSwitch上实现了EAGLE方案并进行了测试,测试结果表明,EAGLE能够收集多粒度数据并快速提取与生成遥测数据,且仅增加极少量的处理时延及资源占用率。展开更多
目的采用图注意力网络(graph attention network,GAT)预测人类微生物与药物之间的潜在关联。方法选取三个常用的微生物-药物关联(microbe-drug associations,MDA)数据集(MDAD、aBiofilm和Drug Virus),基于数据集中丰富的生物信息构建一...目的采用图注意力网络(graph attention network,GAT)预测人类微生物与药物之间的潜在关联。方法选取三个常用的微生物-药物关联(microbe-drug associations,MDA)数据集(MDAD、aBiofilm和Drug Virus),基于数据集中丰富的生物信息构建一个异构网络,并提出一种基于GAT框架预测MDA的模型——GATMDA模型,用于预测微生物与药物间的关联。结果与现有的8种预测方法相比,GATMDA通过三种交叉验证方法在三个数据集上具有较好的预测效果。在5折交叉验证的性能评估中,在三个数据集上的受试者工作特征曲线下的面积(area under the curve,AUC)分别为0.9886、0.9941和0.9836,精确率-召回率曲线下的面积(area under the precision-recall curve,AUPR)分别为0.9667、0.9869和0.8795。通过病例研究进一步验证了GATMDA在预测MDA方面的有效性。结论基于GAT,GATMDA模型可以通过构建的异构网络对微生物-药物进行有效的关联预测。展开更多
将压缩映射和同构映射引入核化图嵌入框架(kernel extension of graph embedding,简称KGE),从理论上证明了KGE框架内的各种核算法其实质是KPCA(kernel principal component analysis)+LGE(linear extension of graph embedding,简称LGE...将压缩映射和同构映射引入核化图嵌入框架(kernel extension of graph embedding,简称KGE),从理论上证明了KGE框架内的各种核算法其实质是KPCA(kernel principal component analysis)+LGE(linear extension of graph embedding,简称LGE)框架内的线性降维算法,并且基于所给出的理论框架提出了一种综合利用零空间和非零空间鉴别信息的组合方法.任何一种可以用核化图嵌入框架描述的核算法,都可以有相应的组合方法.在ORL,Yale,FERET和PIE人脸数据库上验证了所提出的理论和方法的有效性.展开更多
基金supported by the Natural Sciences and Engineering Research Council of CanadaNational Natural Science Foundation of China(61428209,61232001)
文摘Genes associated with similar diseases are often functionally related.This principle is largely supported by many biological data sources,such as disease phenotype similarities,protein complexes,protein-protein interactions,pathways and gene expression profiles.Integrating multiple types of biological data is an effective method to identify disease genes for many genetic diseases.To capture the gene-disease associations based on biological networks,a kernel-based Markov random field(MRF)method is proposed by combining graph kernels and the MRF method.In the proposed method,three kinds of kernels are employed to describe the overall relationships of vertices in five biological networks,respectively,and a novel weighted MRF method is developed to integrate those data.In addition,an improved Gibbs sampling procedure and a novel parameter estimation method are proposed to generate predictions from the kernel-based MRF method.Numerical experiments are carried out by integrating known gene-disease associations,protein complexes,protein-protein interactions,pathways and gene expression profiles.The proposed kernel-based MRF method is evaluated by the leave-one-out cross validation paradigm,achieving an AUC score of 0.771 when integrating all those biological data in our experiments,which indicates that our proposed method is very promising compared with many existing methods.
基金supported by the Zhejiang Provincial Natural Science Foundation of China(LY21A010016)the National Natural Science Foundation of China(11901550).
文摘In this paper, we investigate a blow-up phenomenon for a semilinear parabolic system on locally finite graphs. Under some appropriate assumptions on the curvature condition CDE’(n,0), the polynomial volume growth of degree m, the initial values, and the exponents in absorption terms, we prove that every non-negative solution of the semilinear parabolic system blows up in a finite time. Our current work extends the results achieved by Lin and Wu (Calc Var Partial Differ Equ, 2017, 56: Art 102) and Wu (Rev R Acad Cien Serie A Mat, 2021, 115: Art 133).
文摘Using the linear space over the binary field that related to a graph G, a sufficient and necessary condition for the chromatic number of G is obtained.
文摘网络遥测是一种新型的网络测量技术,具有实时性强、准确性高、开销低的特点。现有网络遥测技术存在无法收集多粒度网络数据、无法有效存储大量原始网络数据、无法快速提取及生成网络遥测信息、无法利用内核态及用户态特性设计网络遥测方案等问题。为此,提出了一种融合内核态及用户态的、基于遥测数据图和同步控制块的多粒度、可扩展、覆盖全网的网络遥测机制(a nEtwork telemetry mechAnism based on telemetry data Graph in kerneL and usEr mode,EAGLE)。EAGLE设计了一种能够收集多粒度数据且数据平面上灵活可控的网络遥测数据包结构,用于获取上层应用所需的数据。此外,为快速存储、查询、统计、聚合网络状态数据,实现网络遥测数据包所需遥测数据的快速提取与生成,EAGLE提出了一种基于遥测数据图及同步控制块的网络遥测信息生成方法。在此基础上,为了最大化网络遥测机制中网络遥测数据包的处理效率,EAGLE提出了融合内核态及用户态特性的网络遥测信息嵌入架构。在Open vSwitch上实现了EAGLE方案并进行了测试,测试结果表明,EAGLE能够收集多粒度数据并快速提取与生成遥测数据,且仅增加极少量的处理时延及资源占用率。
文摘目的采用图注意力网络(graph attention network,GAT)预测人类微生物与药物之间的潜在关联。方法选取三个常用的微生物-药物关联(microbe-drug associations,MDA)数据集(MDAD、aBiofilm和Drug Virus),基于数据集中丰富的生物信息构建一个异构网络,并提出一种基于GAT框架预测MDA的模型——GATMDA模型,用于预测微生物与药物间的关联。结果与现有的8种预测方法相比,GATMDA通过三种交叉验证方法在三个数据集上具有较好的预测效果。在5折交叉验证的性能评估中,在三个数据集上的受试者工作特征曲线下的面积(area under the curve,AUC)分别为0.9886、0.9941和0.9836,精确率-召回率曲线下的面积(area under the precision-recall curve,AUPR)分别为0.9667、0.9869和0.8795。通过病例研究进一步验证了GATMDA在预测MDA方面的有效性。结论基于GAT,GATMDA模型可以通过构建的异构网络对微生物-药物进行有效的关联预测。
文摘将压缩映射和同构映射引入核化图嵌入框架(kernel extension of graph embedding,简称KGE),从理论上证明了KGE框架内的各种核算法其实质是KPCA(kernel principal component analysis)+LGE(linear extension of graph embedding,简称LGE)框架内的线性降维算法,并且基于所给出的理论框架提出了一种综合利用零空间和非零空间鉴别信息的组合方法.任何一种可以用核化图嵌入框架描述的核算法,都可以有相应的组合方法.在ORL,Yale,FERET和PIE人脸数据库上验证了所提出的理论和方法的有效性.
