近年来,生成图模型在复杂网络研究中的作用越来越重要。图的生成过程对于研究疾病的蔓延和信息的传播具有重大意义,同时图模型的生成也有助于更深入地研究复杂网络的特性。为了能够生成既符合真实网络特征又具有结构多样性的复杂网络,...近年来,生成图模型在复杂网络研究中的作用越来越重要。图的生成过程对于研究疾病的蔓延和信息的传播具有重大意义,同时图模型的生成也有助于更深入地研究复杂网络的特性。为了能够生成既符合真实网络特征又具有结构多样性的复杂网络,提出了一种具有社区结构的可调节聚集系数和模块性的无标度网络生成算法——TCMSN(Scale Free Network with Tunable Clustering Coefficient and Modularity)。通过调节混合参数可以调节生成网络的模块性,通过调节社区内连边的概率和混合参数可以对网络聚集系数进行调节。TCMSN采用了合理的连边策略,在不破坏网络结构多样性的情况下,能尽可能维持网络的无标度特性。人工构造数据和真实网络数据的对比实验结果表明,TCMSN算法能够生成可调节聚集系数和模块性的无标度网络模型,且能够生成最接近真实网络社区结构特征的网络模型。展开更多
The protecting requirements and functional connectivity of species in isolated habitat patches are crucial factors of eco-network planning.This study aimed to improve the method of eco-network planning for species con...The protecting requirements and functional connectivity of species in isolated habitat patches are crucial factors of eco-network planning.This study aimed to improve the method of eco-network planning for species conservation.Ecoprofiling was used to group the species by similar behavior types,namely,choice of ecosystem,area requirement,and short distance dispersal abilities.A least-cost model was used to simulate the optimal corridor location to maintain functional connectivity.A combination of ecoprofile and least-cost model was hired to develop an eco-network that promoted species conservation.A case study was also conducted in Beijing,China.In addition to the required ecosystem,habitat area is an important parameter for habitat extraction.Habitat area can remove noise habitat patches because of lacking area.Short-distance dispersal can be used to identify corridor requirements and avoid unnecessary building requirements.Species with various dispersal abilities exhibit significant differences in terms of corridor length and location requirement.Habitat isolation is the main threat for weakly mobile species,and habitat loss is the major risk of mobile species protection.Different species groups also exhibit distinct landscape pattern demands for an eco-network,and the eco-network planning based on specific species can not protect other species.We proposed that a combination of ecoprofile and least-cost model improved the efficiency of species conservation by eco-network planning.展开更多
Informative proteins are the proteins that play critical functional roles inside cells.They are the fundamental knowledge of translating bioinformatics into clinical practices.Many methods of identifying informative b...Informative proteins are the proteins that play critical functional roles inside cells.They are the fundamental knowledge of translating bioinformatics into clinical practices.Many methods of identifying informative biomarkers have been developed which are heuristic and arbitrary,without considering the dynamics characteristics of biological processes.In this paper,we present a generative model of identifying the informative proteins by systematically analyzing the topological variety of dynamic protein-protein interaction networks(PPINs).In this model,the common representation of multiple PPINs is learned using a deep feature generation model,based on which the original PPINs are rebuilt and the reconstruction errors are analyzed to locate the informative proteins.Experiments were implemented on data of yeast cell cycles and different prostate cancer stages.We analyze the effectiveness of reconstruction by comparing different methods,and the ranking results of informative proteins were also compared with the results from the baseline methods.Our method is able to reveal the critical members in the dynamic progresses which can be further studied to testify the possibilities for biomarker research.展开更多
Most previous studies have mainly focused on the analyses of one entire network(graph) or the giant connected components of networks. In this paper, we investigate the disconnected components(non-giant connected compo...Most previous studies have mainly focused on the analyses of one entire network(graph) or the giant connected components of networks. In this paper, we investigate the disconnected components(non-giant connected component) of some real social networks, and report some interesting discoveries about structural properties of disconnected components. We study three diverse, real networks and compute the significance profile of each component. We discover some similarities in the local structure between the giant connected component and disconnected components in diverse social networks. Then we discuss how to detect network attacks based on the local structure properties of networks. Furthermore, we propose an empirical generative model called i Friends to generate networks that follow our observed patterns.展开更多
文摘近年来,生成图模型在复杂网络研究中的作用越来越重要。图的生成过程对于研究疾病的蔓延和信息的传播具有重大意义,同时图模型的生成也有助于更深入地研究复杂网络的特性。为了能够生成既符合真实网络特征又具有结构多样性的复杂网络,提出了一种具有社区结构的可调节聚集系数和模块性的无标度网络生成算法——TCMSN(Scale Free Network with Tunable Clustering Coefficient and Modularity)。通过调节混合参数可以调节生成网络的模块性,通过调节社区内连边的概率和混合参数可以对网络聚集系数进行调节。TCMSN采用了合理的连边策略,在不破坏网络结构多样性的情况下,能尽可能维持网络的无标度特性。人工构造数据和真实网络数据的对比实验结果表明,TCMSN算法能够生成可调节聚集系数和模块性的无标度网络模型,且能够生成最接近真实网络社区结构特征的网络模型。
基金Under the auspices of National Natural Science Foundation of China(No.41271198)
文摘The protecting requirements and functional connectivity of species in isolated habitat patches are crucial factors of eco-network planning.This study aimed to improve the method of eco-network planning for species conservation.Ecoprofiling was used to group the species by similar behavior types,namely,choice of ecosystem,area requirement,and short distance dispersal abilities.A least-cost model was used to simulate the optimal corridor location to maintain functional connectivity.A combination of ecoprofile and least-cost model was hired to develop an eco-network that promoted species conservation.A case study was also conducted in Beijing,China.In addition to the required ecosystem,habitat area is an important parameter for habitat extraction.Habitat area can remove noise habitat patches because of lacking area.Short-distance dispersal can be used to identify corridor requirements and avoid unnecessary building requirements.Species with various dispersal abilities exhibit significant differences in terms of corridor length and location requirement.Habitat isolation is the main threat for weakly mobile species,and habitat loss is the major risk of mobile species protection.Different species groups also exhibit distinct landscape pattern demands for an eco-network,and the eco-network planning based on specific species can not protect other species.We proposed that a combination of ecoprofile and least-cost model improved the efficiency of species conservation by eco-network planning.
基金supported by National Natural Science Foundation of China(30970780)Ph.D.Programs Foundation of Ministry of Education of China(20091103110005)+4 种基金the Project for the Innovation Team of Beijing,National Natural Science Foundation of China(81370038)the Beijing Natural Science Foundation(7142012)the Science and Technology Project of Beijing Municipal Education Commission(km201410005003)the Rixin Fund of Beijing University of Technology(2013-RX-L04)the Basic Research Fund of Beijing University of Technology
文摘Informative proteins are the proteins that play critical functional roles inside cells.They are the fundamental knowledge of translating bioinformatics into clinical practices.Many methods of identifying informative biomarkers have been developed which are heuristic and arbitrary,without considering the dynamics characteristics of biological processes.In this paper,we present a generative model of identifying the informative proteins by systematically analyzing the topological variety of dynamic protein-protein interaction networks(PPINs).In this model,the common representation of multiple PPINs is learned using a deep feature generation model,based on which the original PPINs are rebuilt and the reconstruction errors are analyzed to locate the informative proteins.Experiments were implemented on data of yeast cell cycles and different prostate cancer stages.We analyze the effectiveness of reconstruction by comparing different methods,and the ranking results of informative proteins were also compared with the results from the baseline methods.Our method is able to reveal the critical members in the dynamic progresses which can be further studied to testify the possibilities for biomarker research.
基金supported by the National Natural Science Foundation of China (Grant Nos. 61572060, 61190125, 61472024)CERNET Innovation Project 2015 (Grant No. NGII20151004)
文摘Most previous studies have mainly focused on the analyses of one entire network(graph) or the giant connected components of networks. In this paper, we investigate the disconnected components(non-giant connected component) of some real social networks, and report some interesting discoveries about structural properties of disconnected components. We study three diverse, real networks and compute the significance profile of each component. We discover some similarities in the local structure between the giant connected component and disconnected components in diverse social networks. Then we discuss how to detect network attacks based on the local structure properties of networks. Furthermore, we propose an empirical generative model called i Friends to generate networks that follow our observed patterns.