Networks of motifs from sequences of symbols

We introduce a method to convert an ensemble of sequences of symbols into a weighted directed network whose nodes are motifs, while the directed links and their weights are defined from statistically significant co-occurences of two motifs in the same sequence. The analysis of communities of networks of motifs is shown to be able to correlate sequences with functions in the human proteome database, to detect hot topics from online social dialogs, to characterize trajectories of dynamical systems, and it might find other useful applications to process large amounts of data in various fields.     

Modeling online social networks based on preferential linking

We study the phenomena of preferential linking in a large-scale evolving online social network and find that the linear preference holds for preferential creation,preferential acceptance,and preferential attachment.Based on the linear preference,we propose an analyzable model,which illustrates the mechanism of network growth and reproduces the process of network evolution.Our simulations demonstrate that the degree distribution of the network produced by the model is in good agreement with that of the real network.This work provides a possible bridge between the micro-mechanisms of network growth and the macrostructures of online social networks.     

Reconstructing phase dynamics of oscillator networks

We generalize our recent approach to the reconstruction of phase dynamics of coupled oscillators from data [B. Kralemann et al., Phys. Rev. E 77, 066205 (2008)] to cover the case of small networks of coupled periodic units. Starting from a multivariate time series, we first reconstruct genuine phases and then obtain the coupling functions in terms of these phases. Partial norms of these coupling functions quantify directed coupling between oscillators. We illustrate the method by different network motifs for three coupled oscillators and for random networks of five and nine units. We also discuss nonlinear effects in coupling.     

Motifs in co-authorship networks and their relation to the impact of scientific publications

Co-authorship networks, where the nodes are authors and a link indicates joint publications, are very helpful representations for studying the processes that shape the scientific community. At the same time, they are social networks with a large amount of data available and can thus serve as vehicles for analyzing social phenomena in general. Previous work on co-authorship networks concentrates on statistical properties on the scale of individual authors and individual publications within the network (e.g., citation distribution, degree distribution), on properties of the network as a whole (e.g., modularity, connectedness), or on the topological function of single authors (e.g., distance, betweenness). Here we show that the success of individual authors or publications depends unexpectedly strongly on an intermediate scale in co-authorship networks. For two large-scale data sets, CiteSeerX and DBLP, we analyze the correlation of (three- and four-node) network motifs with citation frequencies. We find that the average citation frequency of a group of authors depends on the motifs these authors form. In particular, a box motif (four authors forming a closed chain) has the highest average citation frequency per link. This result is robust across the two databases, across different ways of mapping the citation frequencies of publications onto the (uni-partite) co-authorship graph, and over time. We also relate this topological observation to the underlying social and socio-scientific processes that have been shaping the networks. We argue that the box motif may be an interesting category in a broad range of social and technical networks.     

Dynamics of network motifs in genetic regulatory networks

Network motifs hold a very important status in genetic regulatory networks. This paper aims to analyse the dynamical property of the network motifs in genetic regulatory networks. The main result we obtained is that the dynamical property of a single motif is very simple with only an asymptotically stable equilibrium point, but the combination of several motifs can make more complicated dynamical properties emerge such as limit cycles. The above-mentioned result shows that network motif is a stable substructure in genetic regulatory networks while their combinations make the genetic regulatory network more complicated.     

Topological origin of global attractors in gene regulatory networks

Fixed-point attractors with global stability manifest themselves in a number of gene regulatory networks. This property indicates the stability of regulatory networks against small state perturbations and is closely related to other complex dynamics. In this paper, we aim to reveal the core modules in regulatory networks that determine their global attractors and the relationship between these core modules and other motifs. This work has been done via three steps. Firstly, inspired by the signal transmission in the regulation process, we extract the model of chain-like network from regulation networks. We propose a module of “ideal transmission chain(ITC)”, which is proved sufficient and necessary(under certain condition) to form a global fixed-point in the context of chain-like network. Secondly, by examining two well-studied regulatory networks(i.e., the cell-cycle regulatory networks of Budding yeast and Fission yeast), we identify the ideal modules in true regulation networks and demonstrate that the modules have a superior contribution to network stability(quantified by the relative size of the biggest attraction basin). Thirdly, in these two regulation networks, we find that the double negative feedback loops, which are the key motifs of forming bistability in regulation, are connected to these core modules with high network stability. These results have shed new light on the connection between the topological feature and the dynamic property of regulatory networks.     

Adaptive bridge control strategy for opinion evolution on social networks

In this paper, we present an efficient opinion control strategy for complex networks, in particular, for social networks. The proposed adaptive bridge control (ABC) strategy calls for controlling a special kind of nodes named bridge and requires no knowledge of the node degrees or any other global or local knowledge, which are necessary for some other immunization strategies including targeted immunization and acquaintance immunization. We study the efficiency of the proposed ABC strategy on random networks, small-world networks, scale-free networks, and the random networks adjusted by the edge exchanging method. Our results show that the proposed ABC strategy is efficient for all of these four kinds of networks. Through an adjusting clustering coefficient by the edge exchanging method, it is found out that the efficiency of our ABC strategy is closely related with the clustering coefficient. The main contributions of this paper can be listed as follows: (1) A new high-order social network is proposed to describe opinion dynamic. (2) An algorithm, which does not require the knowledge of the nodes' degree and other global∕local network structure information, is proposed to control the "bridges" more accurately and further control the opinion dynamics of the social networks. The efficiency of our ABC strategy is illustrated by numerical examples. (3) The numerical results indicate that our ABC strategy is more efficient for networks with higher clustering coefficient.     

社交网络中基于贝叶斯和半环代数模型的节点影响力计算机理

本文综合考虑网络结构及节点间的互动等关键因素, 提出了一种节点影响力分布式计算机理. 首先根据节点交互行为在时域上的自相似特性, 运用带折扣因子的贝叶斯模型计算节点间的直接影响力; 然后运用半环模型来分析节点间接影响力的聚合; 最后根据社交网络的小世界性质及传播门限, 综上计算出节点的综合影响力. 仿真结果表明, 本文给出的模型能有效抑制虚假粉丝导致的节点影响力波动, 消除了虚假粉丝的出现对节点影响力计算带来的干扰, 从中选择影响力高的若干节点作为传播源节点, 可以将信息传播到更多数目的节点, 促进了信息在社交网络中的传播. 关键词： 社交网络 影响力 贝叶斯 半环代数     

Online social networks—Paradise of computer viruses

Online social network services have attracted more and more users in recent years. So the security of social networks becomes a critical problem. In this paper, we propose a virus propagation model based on the application network of Facebook, which is the most popular among these social network service providers. We also study the virus propagation with an email virus model and compare the behaviors of a virus spreading on Facebook with the original email network. It is found that Facebook provides the same chance for a virus spreading while it gives a platform for application developers. And a virus will spread faster in the Facebook network if users of Facebook spend more time on it.     

Motif structure and cooperation in real-world complex networks

Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.     

Neural networks and chaos: construction, evaluation of chaotic networks, and prediction of chaos with multilayer feedforward networks

Many research works deal with chaotic neural networks for various fields of application. Unfortunately, up to now, these networks are usually claimed to be chaotic without any mathematical proof. The purpose of this paper is to establish, based on a rigorous theoretical framework, an equivalence between chaotic iterations according to Devaney and a particular class of neural networks. On the one hand, we show how to build such a network, on the other hand, we provide a method to check if a neural network is a chaotic one. Finally, the ability of classical feedforward multilayer perceptrons to learn sets of data obtained from a dynamical system is regarded. Various boolean functions are iterated on finite states. Iterations of some of them are proven to be chaotic as it is defined by Devaney. In that context, important differences occur in the training process, establishing with various neural networks that chaotic behaviors are far more difficult to learn.     

Symmetry-based structure entropy of complex networks

Precisely quantifying the heterogeneity or disorder of network systems is important and desired in studies of behaviors and functions of network systems. Although various degree-based entropies have been available to measure the heterogeneity of real networks, heterogeneity implicated in the structures of networks can not be precisely quantified yet. Hence, we propose a new structure entropy based on automorphism partition. Analysis of extreme cases shows that entropy based on automorphism partition can quantify the structural heterogeneity of networks more precisely than degree-based entropies. We also summarized symmetry and heterogeneity statistics of many real networks, finding that real networks are more heterogeneous in the view of automorphism partition than what have been depicted under the measurement of degree-based entropies; and that structural heterogeneity is strongly negatively correlated to symmetry of real networks.     

利用邻域“结构洞”寻找社会网络中最具影响力节点

识别复杂网络中的关键节点对网络结构优化和鲁棒性增强具有十分重要的意义. 经典的关键节点测量方法在一定程度上能够辨识网络中影响力节点, 但存在一定局限性: 局部中心性测量方法仅考虑节点邻居的数目, 忽略了邻居间的拓扑关系, 不能在计算中反映邻居节点间的相互作用; 全局测量方法则由于算法本身的复杂性而不能应用于大规模社会网络的分析, 另外, 经典的关键节点测量方法也没有考虑社会网络特有的社区特征. 为高效、准确地辨识具有社区结构的社会网络中最具影响力节点, 提出了一种基于节点及其邻域结构洞的局部中心性测量方法, 该方法综合考虑了节点的邻居数量及其与邻居间的拓扑结构, 在节点约束系数的计算中同时体现了节点的度属性和“桥接”属性. 利用SIR(易感-感染-免疫)模型在真实社会网络数据上对节点传播能力进行评价后发现, 所提方法可以准确地评价节点的传播能力且具有强的鲁棒性.     

基于Kendall改进的同步算法癫痫脑网络分析

提出了一种基于Kendall等级相关改进的同步算法IRC(inverse rank correlation).Kendall等级相关是非线性动力学分析的一般化算法,可有效地度量变量间的非线性相关性.复杂网络的研究已逐渐深入到社会科学的各个领域,脑网络的研究已经成为当今脑功能研究的热点.利用改进的IRC算法,基于脑电EEG(electroencephalogram)数据来构建大脑功能性网络.对构建的脑功能网络的度指标进行了分析,以调查癫痫脑功能网络是否异于正常人.结果显示:使用该改进的算法能够对癫痫和正常脑功能网络显著区分,且只需要记录很短的脑电数据.实验结果数据表明,该方法适用于区分癫痫和正常脑组织网络度指标,它可有助于进一步地加深对大脑的神经动力学行为的研究,并为临床诊断提供有效工具.     

Diversity of social ties in scientific collaboration networks

Diversity is one of the important perspectives to characterize behaviors of individuals in social networks. It is intuitively believed that diversity of social ties accounts for competition advantage and idea innovation. However, quantitative evidences in a real large social network can be rarely found in the previous research. Thanks to the availability of scientific publication records on WWW; now we can construct a large scientific collaboration network, which provides us a chance to gain insight into the diversity of relationships in a real social network through statistical analysis. In this article, we dedicate our efforts to perform empirical analysis on a scientific collaboration network extracted from DBLP, an online bibliographic database in computer science, in a systematical way, finding the following: distributions of diversity indices tend to decay in an exponential or Gaussian way; diversity indices are not trivially correlated to existing vertex importance measures; authors of diverse social ties tend to connect to each other and these authors are generally more competitive than others.     

Classes of complex networks defined by role-to-role connectivity profiles

In physical, biological, technological and social systems, interactions between units give rise to intricate networks. These-typically non-trivial-structures, in turn, critically affect the dynamics and properties of the system. The focus of most current research on complex networks is, still, on global network properties. A caveat of this approach is that the relevance of global properties hinges on the premise that networks are homogeneous, whereas most real-world networks have a markedly modular structure. Here, we report that networks with different functions, including the Internet, metabolic, air transportation and protein interaction networks, have distinct patterns of connections among nodes with different roles, and that, as a consequence, complex networks can be classified into two distinct functional classes on the basis of their link type frequency. Importantly, we demonstrate that these structural features cannot be captured by means of often studied global properties.     

手机短信息传播过程和短信息寿命研究

比较了短信息在无标度网络、小世界网络和实际的短信息网络三种网络中的传播过程,寻找影响短信息传播的因素.研究发现,网络拓扑结构和手机用户的转发短信行为均会影响短信息传播过程.在无标度网络中短信息传播速率快于小世界网络和实际的短信息网络,而无标度网络的短信息寿命较小世界网络和实际的短信息网络短;网络中手机用户的转发短信息行为明显影响短信息的传播过程.同时还发现短信息寿命与网络直径有关. 关键词： 复杂网络 短信息 信息传播 人类行为     

Robustness measurement of scale-free networks based on motif entropy

As a classical complex network model, scale-free network is widely used and studied. And motifs, as a high-order subgraph structure, frequently appear in scale-free networks, and have a great influence on the structural integrity, functional integrity and dynamics of the networks. In order to overcome the shortcomings in the existing work on the robustness of complex networks, only nodes or edges are considered, while the defects of high-order structure in the network are ignored. From the perspective of network motif, we propose an entropy of node degree distribution based on motif to measure the robustness of scale-free networks under random attacks. The effectiveness and superiority of our method are verified and analyzed in the BA scale-free networks.     

Dominant phase-advanced driving analysis of self-sustained oscillations in biological networks

Oscillatory behaviors can be ubiquitously observed in various systems. Biological rhythms are significant in governing living activities of all units. The emergence of biological rhythms is the consequence of large numbers of units. In this paper we discuss several important examples of sustained oscillations in biological media, where the unit composed in the system does not possess the oscillation behavior. The dominant phase-advanced driving method is applied to study the skeletons and oscillatory organizing motifs in excitable networks and gene regulatory networks.     

On the motif distribution in random block-hierarchical networks

The distribution of motifs in random hierarchical topological networks defined by nonsymmetric random block-hierarchical adjacency matrices, is constructed for the first time. According to the classification of U. Alon et al. of network superfamilies (Milo et al., 2004 [11]) by their motifs distributions, our artificial directed random hierarchical networks fall into the superfamily of natural networks to which the neuron networks belong. This is the first example of a class of “handmade” topological networks with the motifs distribution as in a special class of natural networks of essential biological importance.