Communication on the structure of biological networks

Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from different domains may vary quite significantly. As there is an interplay between network architecture and dynamics, structure plays an important role in communication and spreading of information in a network. Here we investigate the underlying undirected topology of different biological networks which support faster spreading of information and are better in communication. We analyse the good expansion property by using the spectral gap and communicability between nodes. Different epidemic models are also used to study the transmission of information in terms of spreading of disease through individuals (nodes) in those networks. Moreover, we explore the structural conformation and properties which may be responsible for better communication. Among all biological networks studied here, the undirected structure of neuronal networks not only possesses the small-world property but the same is also expressed remarkably to a higher degree compared to any randomly generated network which possesses the same degree sequence. A relatively high percentage of nodes, in neuronal networks, form a higher core in their structure. Our study shows that the underlying undirected topology in neuronal networks, in a significant way, is qualitatively different from the same in other biological networks and that they may have evolved in such a way that they inherit a (undirected) structure which is excellent and robust in communication.     

Weighted Networks Model Based on Traffic Dynamics with Local Perturbation

In the study of weighted complex networks, the interplay between traffic and topology have been paid much attention. However, the variation of topology and weight brought by new added vertices or edges should also be considered. In this paper, an evolution model of weighted networks driven by traffic dynamics with local perturbation is proposed. The model gives power-law distribution of degree, weight and strength, as confirmed by empirical measurements. By choosing appropriate parameters W and δ, the exponents of various power law distributions can be adjusted to meet real world networks. Nontrivial clustering coefficient C, degree assortativity coefficient r, and strength-degree correlation are also considered. What should be emphasized is that, with the consideration of local perturbation, one can adjust the exponent of strength-degree correlation more effectively. It makes our model more general than previous ones and may help reproducing real world networks more appropriately. PACS numbers： 87.23.Kg, 89.75.Da, 89.75.Fb, 89.75.Hc.     

虚拟社区网络的演化过程研究

模拟了虚拟社区网络的演化过程并研究其拓扑结构.发现虚拟社区网络在演化过程中,节点的加入、边的加入、网络中度分布、节点的度与其加入网络时间的关系、平均度随时间的变化等方面与传统的无标度网络有所不符.根据国内某论坛的实际网络数据统计与分析,提出了虚拟社区网络的演化机理——虚拟社区网络构造算法.仿真结果表明,模拟以互联网论坛为代表的虚拟社区网络时,该模型能够得到与真实网络相符的特性. 关键词： 复杂网络 虚拟社区 无标度网络     

基于Web 2.0的边与节点同时增长网络模型

模拟了Web2.0网络的发展过程并研究其拓扑结构,分析某门户网站实际博客数据的度分布、节点度时间变化,发现与先前的无标度网络模型有所差别.根据真实网络的生长特点,提出了边与节点同时增长的网络模型,包括随机连接及近邻互联的网络构造规则.仿真研究表明,模拟的网络更接近实际,在没有优先连接过程时,模型能得到幂率的度分布;并且网络有更大的聚类系数以及正的度相关性。     

Constructing refined null models for statistical analysis of signed networks

The establishment of effective null models can provide reference networks to accurately describe statistical properties of real-life signed networks.At present,two classical null models of signed networks(i.e.,sign and full-edge randomized models)shuffle both positive and negative topologies at the same time,so it is difficult to distinguish the effect on network topology of positive edges,negative edges,and the correlation between them.In this study,we construct three re-fined edge-randomized null models by only randomizing link relationships without changing positive and negative degree distributions.The results of nontrivial statistical indicators of signed networks,such as average degree connectivity and clustering coefficient,show that the position of positive edges has a stronger effect on positive-edge topology,while the signs of negative edges have a greater influence on negative-edge topology.For some specific statistics(e.g.,embeddedness),the results indicate that the proposed null models can more accurately describe real-life networks compared with the two existing ones,which can be selected to facilitate a better understanding of complex structures,functions,and dynamical behaviors on signed networks.     

Fault-tolerant topology in the wireless sensor networks for energy depletion and random failure

Nodes in the wireless sensor networks(WSNs) are prone to failure due to energy depletion and poor environment,which could have a negative impact on the normal operation of the network. In order to solve this problem, in this paper, we build a fault-tolerant topology which can effectively tolerate energy depletion and random failure. Firstly, a comprehensive failure model about energy depletion and random failure is established. Then an improved evolution model is presented to generate a fault-tolerant topology, and the degree distribution of the topology can be adjusted. Finally, the relation between the degree distribution and the topological fault tolerance is analyzed, and the optimal value of evolution model parameter is obtained. Then the target fault-tolerant topology which can effectively tolerate energy depletion and random failure is obtained. The performances of the new fault tolerant topology are verified by simulation experiments. The results show that the new fault tolerant topology effectively prolongs the network lifetime and has strong fault tolerance.     

Emergence of fractal scale-free networks from stochastic evolution on the Cayley tree

An unexpected recognition of fractal topology in some real-world scale-free networks has evoked again an interest in the mechanisms stimulating their evolution. To explain this phenomenon a few models of a deterministic construction as well as a probabilistic growth controlled by a tunable parameter have been proposed so far. A quite different approach based on the fully stochastic evolution of the fractal scale-free networks presented in this Letter counterpoises these former ideas. It is argued that the diffusive evolution of the network on the Cayley tree shapes its fractality, self-similarity and the branching number criticality without any control parameter. The last attribute of the scale-free network is an intrinsic property of the skeleton, a special type of spanning tree which determines its fractality.     

Kinetic models for wealth exchange on directed networks

We propose some kinetic models of wealth exchange and investigate their behavior on directed networks though numerical simulations. We observe that network topology and directedness yields a variety of interesting features in these models. The nature of asset distribution in such directed networks show varied results, the degree of asset inequality increased with the degree of disorder in the graphs.     

一种基于文本互信息的金融复杂网络模型

复杂网络能够解决许多金融问题,能够发现金融市场的拓扑结构特征,反映不同金融主体之间的相互依赖关系.相关性度量在金融复杂网络构建中至关重要.通过将多元金融时间序列符号化,借鉴文本特征提取以及信息论的方法,定义了一种基于文本互信息的相关系数.为检验方法的有效性,分别构建了基于不同相关系数(Pearson和文本互信息)和不同网络缩减方法(阈值和最小生成树)的4个金融复杂网络模型.在阈值网络中提出了使用分位数来确定阈值的方法,将相关系数6等分,取第4部分的中点作为阈值,此时基于Pearson和文本互信息的阈值模型将会有相近的边数,有利于这两种模型的对比.数据使用了沪深两地证券市场地区指数收盘价,时间从2006年1月4日至2016年12月30日,共计2673个交易日.从网络节点相关性看,基于文本互信息的方法能够体现出大约20%的非线性相关关系;在网络整体拓扑指标上,本文计算了4种指标,结果显示能够使所保留的节点联系更为紧密,有效提高保留节点的重要性以及挖掘出更好的社区结构;最后,计算了阈值网络的动态指标,将数据按年分别构建网络,缩减方法只用了阈值方法,结果显示本文提出的方法在小世界动态和网络度中心性等指标上能够成功捕捉到样本区间内存在的两次异常波动.此外,本文构建的地区金融网络具有服从幂律分布、动态稳定性、一些经济欠发达地区在金融地区网络中占据重要地位等特性.     

一类高聚类系数的加权无标度网络及其同步能力分析

针对真实世界中大规模网络都具有明显聚类效应的特点, 提出一类具有高聚类系数的加权无标度网络演化模型, 该模型同时考虑了优先连接、三角结构、随机连接和社团结构等四种演化机制. 在模型演化规则中, 以概率p增加单个节点, 以概率1–p增加一个社团. 与以往研究的不同在于新边的建立, 以概率φ在旧节点之间进行三角连接, 以概率1–φ进行随机连接. 仿真分析表明, 所提出的网络度、强度和权值分布都是服从幂律分布的形式, 且具有高聚类系数的特性, 聚类系数的提高与社团结构和随机连接机制有直接的关系. 最后通过数值仿真分析了网络演化机制对同步动态特性的影响, 数值仿真结果表明, 网络的平均聚类系数越小, 网络的同步能力越强. 关键词： 无标度网络 加权网络 聚类系数 同步能力     

General dynamics of topology and traffic on weighted technological networks

For most technical networks, the interplay of dynamics, traffic, and topology is assumed crucial to their evolution. In this Letter, we propose a traffic-driven evolution model of weighted technological networks. By introducing a general strength-coupling mechanism under which the traffic and topology mutually interact, the model gives power-law distributions of degree, weight, and strength, as confirmed in many real networks. Particularly, depending on a parameter W that controls the total weight growth of the system, the nontrivial clustering coefficient C, degree assortativity coefficient r, and degree-strength correlation are all consistent with empirical evidence.     

Modeling complex networks with accelerating growth and aging effect

Numerous empirical studies have revealed that a large number of real networks exhibit the property of accelerating growth, i.e. network size (nodes) increases superlinearly with time. Examples include the size of social networks, the output of scientists, the population of cities, and so on. In the literature, these real systems are widely represented by complex networks for analysis, and many network models have been proposed to explain the observed properties in these systems such as power-law degree distribution. However, most of these models (e.g. the well-known BA model) are based on linear growth of these systems. In this paper, we propose a network model with accelerating growth and aging effect, resulting in an emergence of super hubs which is consistent with the empirical observation in citation networks.     

Modeling network growth with assortative mixing

We propose a model of an underlying mechanism responsible for the formation of assortative mixing in networks between “similar” nodes or vertices based on generic vertex properties. Existing models focus on a particular type of assortative mixing, such as mixing by vertex degree, or present methods of generating a network with certain properties, rather than modeling a mechanism driving assortative mixing during network growth. The motivation is to model assortative mixing by non-topological vertex properties, and the influence of these non-topological properties on network topology. The model is studied in detail for discrete and hierarchical vertex properties, and we use simulations to study the topology of resulting networks. We show that assortative mixing by generic properties directly drives the formation of community structure beyond a threshold assortativity of r ∼0.5, which in turn influences other topological properties. This direct relationship is demonstrated by introducing a new measure to characterise the correlation between assortative mixing and community structure in a network. Additionally, we introduce a novel type of assortative mixing in systems with hierarchical vertex properties, from which a hierarchical community structure is found to result. Electronic supplementary material Supplementary Online Material     

手机短信网络的生长过程研究

模拟了短信网络的生长过程并研究其拓扑结构.发现短信网络在生长过程中，度分布、节点的度与其加入网络时间的关系、平均度随时间的变化等方面与先前的模型有所不符.根据短信网络的数据分析，提出了短信网络的生长机制——局部优先连接机制.结果表明，模拟以短信网络为代表的实际网络时，局部优先连接模型优于其他网络模型. 关键词： 复杂网络 短信网络 局部优先连接     

中国城市航空网络的实证研究与分析

以城市为节点，城市间直航线路为边，实证地研究了中国城市航空网络的拓扑性质.研究表明，中国城市航空网络是一个小世界网络，具有短的平均路径长度和大的簇系数，且其度分布服从双段幂律分布.它的度度相关性质与世界航空网络和北美航空网络都不相同.当度较小时，世界航空网络和北美航空网络都是正相关的，但中国城市航空网络未表现出度度相关性；而对于度较大的节点，世界航空网络中其邻点平均度几乎是一个常值，但中国城市航空网络却呈现出负相关性.以往的实证研究暗示，节点具有明确几何位置的网络，如计算机互联网、电力网络等，不表现层次性.但是中国城市航空网络展现出明显的层次性，表明地理因素对其结构演化的影响并不强烈.进一步地，以城市间直航计划每周提供的座位数为边权，研究了网络的含权性质，发现该网络节点度权之间是幂律相关的，相关指数为1.37.     

有倾向性重连产生的反匹配网络

在具有网络结构的系统中度关联属性对于动力学行为具有重要的影响, 所以产生适当度关联网络的方法对于大量网络系统的研究具有重要的作用. 尽管产生正匹配网络的方法已经得到很好的验证, 但是产生反匹配网络的方法还没有被系统的讨论过. 重新连接网络中的边是产生度关联网络的一个常用方法. 这里我们研究使用重连方法产生反匹配无标度网络的有效性. 我们的研究表明, 有倾向的重连可以增强网络的反匹配属性. 但是有倾向重连不能使皮尔森度相关系数下降到-1, 而是存在一个依赖于网络参数的最小值. 我们研究了网络的主要参数对于网络度相关系数的影响, 包括网络尺寸, 网络的连接密度和网络节点的度差异程度. 研究表明在网络尺寸大的情况下和节点度差异性强的情况下, 重连的效果较差. 我们研究了真实Internet网络, 发现模型产生的网络经过重连不能达到真实网络的度关联系数.     

Extractive summarization using complex networks and syntactic dependency

The realization that statistical physics methods can be applied to analyze written texts represented as complex networks has led to several developments in natural language processing, including automatic summarization and evaluation of machine translation. Most importantly, so far only a few metrics of complex networks have been used and therefore there is ample opportunity to enhance the statistics-based methods as new measures of network topology and dynamics are created. In this paper, we employ for the first time the metrics betweenness, vulnerability and diversity to analyze written texts in Brazilian Portuguese. Using strategies based on diversity metrics, a better performance in automatic summarization is achieved in comparison to previous work employing complex networks. With an optimized method the Rouge score (an automatic evaluation method used in summarization) was 0.5089, which is the best value ever achieved for an extractive summarizer with statistical methods based on complex networks for Brazilian Portuguese. Furthermore, the diversity metric can detect keywords with high precision, which is why we believe it is suitable to produce good summaries. It is also shown that incorporating linguistic knowledge through a syntactic parser does enhance the performance of the automatic summarizers, as expected, but the increase in the Rouge score is only minor. These results reinforce the suitability of complex network methods for improving automatic summarizers in particular, and treating text in general.     

Epidemic dynamics on an adaptive network

Many real-world networks are characterized by adaptive changes in their topology depending on the state of their nodes. Here we study epidemic dynamics on an adaptive network, where the susceptibles are able to avoid contact with the infected by rewiring their network connections. This gives rise to assortative degree correlation, oscillations, hysteresis, and first order transitions. We propose a low-dimensional model to describe the system and present a full local bifurcation analysis. Our results indicate that the interplay between dynamics and topology can have important consequences for the spreading of infectious diseases and related applications.     

A Collaboration Network Model with Multiple Evolving Factors

To describe the empirical data of collaboration networks,several evolving mechanisms have been proposed,which usually introduce different dynamics factors controlling the network growth.These models can reasonably reproduce the empirical degree distributions for a number of well-studied real-world collaboration networks.On the basis of the previous studies,in this work we propose a collaboration network model in which the network growth is simultaneously controlled by three factors,including partial preferential attachment,partial random attachment and network growth speed.By using a rate equation method,we obtain an analytical formula for the act degree distribution.We discuss the dependence of the act degree distribution on these different dynamics factors.By fitting to the empirical data of two typical collaboration networks,we can extract the respective contributions of these dynamics factors to the evolution of each networks.     

Investigating the topology of interacting networks

Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems of interest should be treated, more appropriately, as interacting networks or networks of networks. Here we introduce a novel graph-theoretical framework for studying the interaction structure between subnetworks embedded within a complex network of networks. This framework allows us to quantify the structural role of single vertices or whole subnetworks with respect to the interaction of a pair of subnetworks on local, mesoscopic and global topological scales. Climate networks have recently been shown to be a powerful tool for the analysis of climatological data. Applying the general framework for studying interacting networks, we introduce coupled climate subnetworks to represent and investigate the topology of statistical relationships between the fields of distinct climatological variables. Using coupled climate subnetworks to investigate the terrestrial atmosphere’s three-dimensional geopotential height field uncovers known as well as interesting novel features of the atmosphere’s vertical stratification and general circulation. Specifically, the new measure “cross-betweenness” identifies regions which are particularly important for mediating vertical wind field interactions. The promising results obtained by following the coupled climate subnetwork approach present a first step towards an improved understanding of the Earth system and its complex interacting components from a network perspective.