Weighted networks in immune system shape space

In this paper we present a model of immune system development when subjected to repeated infection events. The emergence of a complex network in shape space is outlined, the edges of which are characterised by both direction and weight. Such a network model supports a more comprehensive classification of immune function than was previously available in that the efficacy of infection elimination is directly dependent on both connectivity and weight distributions. The network model which emerges possesses both small-world characteristics, as well as a truncated scale-free degree and weight distribution commonly observed in social network models.     

Effects of accelerating growth on the evolution of weighted complex networks

Many real systems possess accelerating statistics where the total number of edges grows faster than the network size. In this paper, we propose a simple weighted network model with accelerating growth. We derive analytical expressions for the evolutions and distributions for strength, degree, and weight, which are relevant to accelerating growth. We also find that accelerating growth determines the clustering coefficient of the networks. Interestingly, the distributions for strength, degree, and weight display a transition from scale-free to exponential form when the parameter with respect to accelerating growth increases from a small to large value. All the theoretical predictions are successfully contrasted with numerical simulations.     

Complex network structure of musical compositions: Algorithmic generation of appealing music

In this paper we construct networks for music and attempt to compose music artificially. Networks are constructed with nodes and edges corresponding to musical notes and their co-occurring connections. We analyze classical music from Bach, Mozart, Chopin, as well as other types of music such as Chinese pop music. We observe remarkably similar properties in all networks constructed from the selected compositions. We conjecture that preserving the universal network properties is a necessary step in artificial composition of music. Power-law exponents of node degree, node strength and/or edge weight distributions, mean degrees, clustering coefficients, mean geodesic distances, etc. are reported. With the network constructed, music can be composed artificially using a controlled random walk algorithm, which begins with a randomly chosen note and selects the subsequent notes according to a simple set of rules that compares the weights of the edges, weights of the nodes, and/or the degrees of nodes. By generating a large number of compositions, we find that this algorithm generates music which has the necessary qualities to be subjectively judged as appealing.     

Mapping Nuclear Decay to a Complex Network

Nuclear decay is investigated by the view of network science and the relationship of nuclear decay among different radionuclide can be mapped to a network topology directly.The network includes 1410 nodes and 1275 edges.The average degree of the network of nuclear decay is about 1.8,the cumulative degree distribution still meets the typical power-law distribution,and the corresponding exponent is about 4.1.Not considering their dynamic behavior,the fitting parameters of the nuclear decay network are obtained according to the LUHNM theory proposed by our group before.Their cumulated degree distributions of the nuclear decay network match well.The idea and method may provide a new way to study some other problems of nuclear physics.     

一类权重网络的加速演化模型

采用动态形成权重网络的方法，研究了在演化过程中新增边具有加速连接情况下权重网络的拓扑特性和强度分布，给出了节点强度与度的解析表达式.分析表明，加速演化的权重模型具有明显的无标度特性.再者，只要权重网络的边权重服从某一概率分布，则在演化过程中强度择优连接与度择优连接对于网络的度分布没有影响，且与具体的概率分布无关.     

供应链型网络中双幂律分布模型

考察了供应链网络的基本特征，提出了节点到达过程是更新过程、新增入边和出边数是具有Bernoulli分布随机变量的供应链型有向网络.研究了这类网络节点的瞬态度分布和稳态平均度分布.利用更新过程理论对这类网络进行了分析，获得了网络节点瞬态度分布和网络稳态平均度分布的解析表达式.分析表明, 虽然这类网络节点的稳态度分布不存在，但是网络的稳态平均度分布具有双向幂律性. 关键词： 复杂网络 入度 出度 度分布     

The hierarchical backbone of complex networks

Given any complex directed network, a set of acyclic subgraphs can be extracted that will provide valuable information about its hierarchical structure. This Letter presents how the interpretation of the network weight matrix as a transition matrix allows the hierarchical backbone to be identified and characterized in terms of the concepts of hierarchical degree, which expresses the total weights of virtual edges established along successive transitions. The potential of the proposed approach is illustrated with respect to simulated random and preferential-attachment networks as well as real data related to word associations and gene sequencing.     

Weighted and unweighted network of amino acids within protein

The information regarding the structure of a single protein is encoded in the network of interacting amino acids considered as nodes. If any two atoms from two different amino acids (nodes) are within higher cut-off distance of London-van der Waals forces, the amino acids are considered to be linked or connected. Several atoms of any amino acids in a protein may be within the above prescribed distance of several atoms of another amino acid resulting in possible multiple links between them. These multiple links are the basis of the weight of the connectivity in a protein network. Each protein has been considered as a weighted and an unweighted network of amino acids. A total of forty nine protein structures that covers the three branches of life on earth has been analyzed and several network properties have been studied. The probability degree and strength distributions of network connectivity have been obtained. It has been observed that the average strength of amino acid node depends on its degree. The results show that the average clustering coefficient of weighted network is less than that of unweighted network. It implies that the topological clustering is generated by edges with low weights. The power-law behavior of clustering coefficients of weighted and unweighted networks as a function of degree indicates that they have signatures of hierarchy. It has also been observed that the network is of assortative type.     

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.     

Damage spreading on networks: Clustering effects

The damage spreading of the Ising model on three kinds of networks is studied with Glauber dynamics. One of the networks is generated by evolving the hexagonal lattice with the star-triangle transformation. Another kind of network is constructed by connecting the midpoints of the edges of the topological hexagonal lattice. With the evolution of these structures, damage spreading transition temperature increases and a general explanation for this phenomenon is presented from the view of the network. The relationship between the transition temperature and the network measure-clustering coefficient is set up and it is shown that the increase of damage spreading transition temperature is the result of more and more clustering of the network. We construct the third kind of network-random graphs with Poisson degree distributions by changing the average degree of the network. We show that the increase in the average degree is equivalent to the clustering of nodes and this leads to the increase in damage spreading transition temperature.      

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.     

Weighted evolving networks: coupling topology and weight dynamics

We propose a model for the growth of weighted networks that couples the establishment of new edges and vertices and the weights' dynamical evolution. The model is based on a simple weight-driven dynamics and generates networks exhibiting the statistical properties observed in several real-world systems. In particular, the model yields a nontrivial time evolution of vertices' properties and scale-free behavior for the weight, strength, and degree distributions.     

Exploring evolutionary features of directed weighted hazard network in the subway construction

A better understanding of previous accidents is an effective way to reduce the occurrence of similar accidents in the future. In this paper, a complex network approach is adopted to construct a directed weighted hazard network(DWHN) to analyze topological features and evolution of accidents in the subway construction. The nodes are hazards and accidents, the edges are multiple relationships of these nodes and the weight of edges are occurrence times of repetitive relationships. The results indicate that the DWHN possesses the property of small-world with small average path length and large clustering coefficient, indicating that hazards have better connectivity and will spread widely and quickly in the network. Moreover,the DWHN has the property of scale-free network for the cumulative degree distribution follows a power-law distribution.It makes DWHN more vulnerable to target attacks. Controlling key nodes with higher degree, strength and betweenness centrality will destroy the connectivity of DWHN and mitigate the spreading of accidents in the network. This study is helpful for discovering inner relationships and evolutionary features of hazards and accidents in the subway construction.     

Weighted scale-free networks with variable power-law exponents

We present a weighted scale-free network model, in which the power-law exponents can be controlled by the model parameters. The network is generated through the weight-driven preferential attachment of new nodes to existing nodes and the growth of the weights of existing links. The simplicity of the model enables us to derive analytically the various statistical properties, such as the distributions of degree, strength, and weight, the degree-strength and degree-weight relationship, and the dependencies of these power-law exponents on the model parameters. Finally, we demonstrate that networks of words, coauthorship of researchers, and collaboration of actor/actresses are quantitatively well described by this model.     

Characteristics of the network of scientific journals pertaining to Chinese patents

We present the network of scientific journals pertaining to Chinese patent data in the period of 1995-2002, in which two journals are considered linked if they have been cited by a common patent. We study a variety of statistical properties of the network of scientific journals of China (NSJC), including degree distribution, local clustering and average degree of the nearest neighbors in the one-mode projected network. Besides this, we generate a weighted network for the NSJC in which the number of common patents citing two particular journals is mapped to line weights. For such a weighted network, distributions of weight, vertex strength, weight per degree, and the relationship between the vertex strength and degree have been analyzed. The above findings show that for the NSJC, small-world behavior is not distinct, while properties of random networks are observed.     

Modified DM Models for Aging Networks Based on Neighborhood Connectivity

Two modified Dorogovtsev-Mendes （DM） models of aging networks based on the dynamics of connecting nearest-neighbors are introduced. One edge of the new site is connected to the old site with probability - kt^-α as in the DM＇s model, where the degree and age of the old site are k and t, respectively. We consider two cases, i.e. the other edges of the new site attaching to the nearest-neighbors of the old site with uniform and degree connectivity probability, respectively. The network structure changes with an increase of aging exponent α It is found that the networks can produce scale-free degree distributions with small-world properties. And the different connectivity probabilities lead to the different properties of the networks.     

Empirical investigation of topological and weighted properties of a bus transport network from China

Many bus transport networks(BTNs) have evolved into directed networks. A new representation model for BTNs is proposed, called directed-space P. The bus transport network of Harbin(BTN-H) is described as a directed and weighted complex network by the proposed representation model and by giving each node weights. The topological and weighted properties are revealed in detail. In-degree and out-degree distributions, in-weight and out-weight distributions are presented as an exponential law, respectively. There is a strong relation between in-weight and in-degree(also between out-weight and out-degree), which can be fitted by a power function. Degree–degree and weight–weight correlations are investigated to reveal that BTN-H has a disassortative behavior as the nodes have relatively high degree(or weight). The disparity distributions of out-degree and in-degree follow an approximate power-law. Besides, the node degree shows a near linear increase with the number of routes that connect to the corresponding station. These properties revealed in this paper can help public transport planners to analyze the status quo of the BTN in nature.     

On the degree distribution of projected networks mapped from bipartite networks

Many real-world systems can be represented by bipartite networks. In a bipartite network, the nodes are divided into two disjoint sets, and the edges connect nodes that belong to different sets. Given a bipartite network (i.e. two-mode network) it is possible to construct two projected networks (i.e. one-mode networks) where each one is composed of only one set of nodes. While network analyses have focused on unipartite networks, considerably less attention has been paid to the analytical study of bipartite networks. Here, we analytically derive simple mathematical relationships that predict degree distributions of the projected networks by only knowing the structure of the original bipartite network. These analytical results are confirmed by computational simulations using artificial and real-world bipartite networks from a variety of biological and social systems. These findings offer in our view new insights into the structure of real-world bipartite networks.     

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.     

Order or chaos in Boolean gene networks depends on the mean fraction of canalizing functions

We explore the connection between order/chaos in Boolean networks and the naturally occurring fraction of canalizing functions in such systems. This fraction turns out to give a very clear indication of whether the system possesses ordered or chaotic dynamics, as measured by Derrida plots, and also the degree of order when we compare different networks with the same number of vertices and edges. By studying also a wide distribution of indegrees in a network, we show that the mean probability of canalizing functions is a more reliable indicator of the type of dynamics for a finite network than the classical result on stability relating the bias to the mean indegree. Finally, we compare by direct simulations two biologically derived networks with networks of similar sizes but with power-law and Poisson distributions of indegrees, respectively. The biologically motivated networks are not more ordered than the latter, and in one case the biological network is even chaotic while the others are not.