Detecting hierarchical and overlapping network communities using locally optimal modularity changes

Agglomerative clustering is a well established strategy for identifying communities in networks. Communities are successively merged into larger communities, coarsening a network of actors into a more manageable network of communities. The order in which merges should occur is not in general clear, necessitating heuristics for selecting pairs of communities to merge. We describe a hierarchical clustering algorithm based on a local optimality property. For each edge in the network, we associate the modularity change for merging the communities it links. For each community vertex, we call the preferred edge that edge for which the modularity change is maximal. When an edge is preferred by both vertices that it links, it appears to be the optimal choice from the local viewpoint. We use the locally optimal edges to define the algorithm: simultaneously merge all pairs of communities that are connected by locally optimal edges that would increase the modularity, redetermining the locally optimal edges after each step and continuing so long as the modularity can be further increased. We apply the algorithm to model and empirical networks, demonstrating that it can efficiently produce high-quality community solutions. We relate the performance and implementation details to the structure of the resulting community hierarchies. We additionally consider a complementary local clustering algorithm, describing how to identify overlapping communities based on the local optimality condition.     

Deterministic modularity optimization

We study community structure of networks. We have developed a scheme for maximizing the modularity Q [Newman and Girvan, Phys. Rev. E 69, 026113 (2004)] based on mean field methods. Further, we have defined a simple family of random networks with community structure; we understand the behavior of these networks analytically. Using these networks, we show how the mean field methods display better performance than previously known deterministic methods for optimization of Q.     

Identifying stochastic basin hopping by partitioning with graph modularity

It has been known that noise in a stochastically perturbed dynamical system can destroy what was the original zero-noise case barriers in the phase space (pseudobarrier). Noise can cause the basin hopping. We use the Frobenius-Perron operator and its finite rank approximation by the Ulam-Galerkin method to study transport mechanism of a noisy map. In order to identify the regions of high transport activity in the phase space and to determine flux across the pseudobarriers, we adapt a new graph theoretical method which was developed to detect active pseudobarriers in the original phase space of the stochastic dynamic. Previous methods to identify basins and basin barriers require a priori knowledge of a mathematical model of the system, and hence cannot be applied to observed time series data of which a mathematical model is not known. Here we describe a novel graph method based on optimization of the modularity measure of a network and introduce its application for determining pseudobarriers in the phase space of a multi-stable system only known through observed data.     

Geometric Kac–Moody modularity

It is shown how the arithmetic structure of algebraic curves encoded in the Hasse–Weil L-function can be related to affine Kac–Moody algebras. This result is useful in relating the arithmetic geometry of Calabi–Yau varieties to the underlying exactly solvable theory. In the case of the genus three Fermat curve we identify the Hasse–Weil L-function with the Mellin transform of the twist of a number theoretic modular form derived from the string function of a non-twisted affine Lie algebra. The twist character is associated to the number field of quantum dimensions of the conformal field theory.     

模块化多路同步快脉冲触发源设计

基于超快速高压大功率半导体开关、脉冲形成电路以及同心等间距传输的关键技术,提出一种模块化多路同步快脉冲触发源技术方案。设计出在负载阻抗为50 时,可同步输出两种快脉冲触发信号：一种幅度大于20 V（4路）、脉冲前沿小于820 ps、脉冲宽度大于100 ns;另一种则是幅度大于100 V（4路）、前沿小于1.4 ns、脉宽大于100 ns;在外触发作用下,触发源系统抖动和脉冲输出同步分散性分别达到2 ns 和36.6 ps。电路结构上充分利用等间距电信号传输的原理,实现了快脉冲触发源模块化的设计。通过实验结果验证了所采用的设计原理及方法的可行性,给出了在外触发脉冲单次和重频（5 kHz）作用下该同步快脉冲触发源输出的实验结果。     

Bayesian approach to network modularity

We present an efficient, principled, and interpretable technique for inferring module assignments and for identifying the optimal number of modules in a given network. We show how several existing methods for finding modules can be described as variant, special, or limiting cases of our work, and how the method overcomes the resolution limit problem, accurately recovering the true number of modules. Our approach is based on Bayesian methods for model selection which have been used with success for almost a century, implemented using a variational technique developed only in the past decade. We apply the technique to synthetic and real networks and outline how the method naturally allows selection among competing models.     

模块化多路同步快脉冲触发源设计

基于超快速高压大功率半导体开关、脉冲形成电路以及同心等间距传输的关键技术,提出一种模块化多路同步快脉冲触发源技术方案。设计出在负载阻抗为50Ω时,可同步输出两种快脉冲触发信号:一种幅度大于20V(4路)、脉冲前沿小于820ps、脉冲宽度大于100ns;另一种则是幅度大于100V(4路)、前沿小于1.4ns、脉宽大于100ns;在外触发作用下,触发源系统抖动和脉冲输出同步分散性分别达到2ns和36.6ps。电路结构上充分利用等间距电信号传输的原理,实现了快脉冲触发源模块化的设计。通过实验结果验证了所采用的设计原理及方法的可行性,给出了在外触发脉冲单次和重频(5kHz)作用下该同步快脉冲触发源输出的实验结果。     

Networks, dynamics, and modularity

The identification of general principles relating structure to dynamics has been a major goal in the study of complex networks. We propose that the special case of linear network dynamics provides a natural framework within which a number of interesting yet tractable problems can be defined. We report the emergence of modularity and hierarchical organization in evolved networks supporting asymptotically stable linear dynamics. Numerical experiments demonstrate that linear stability benefits from the presence of a hierarchy of modules and that this architecture improves the robustness of network stability to random perturbations in network structure. This work illustrates an approach to network science which is simultaneously structural and dynamical in nature.     

Synchronization and modularity in complex networks

We investigate the connection between the dynamics of synchronization and the modularity on complex networks. Simulating the Kuramoto's model in complex networks we determine patterns of meta-stability and calculate the modularity of the partition these patterns provide. The results indicate that the more stable the patterns are, the larger tends to be the modularity of the partition defined by them. This correlation works pretty well in homogeneous networks (all nodes have similar connectivity) but fails when networks contain hubs, mainly because the modularity is never improved where isolated nodes appear, whereas in the synchronization process the characteristic of hubs is to have a large stability when forming its own community.     

Fuzzy modularity and fuzzy community structure in networks

To find the fuzzy community structure in a complex network, in which each node has a certain probability of belonging to a certain community, is a hard problem and not yet satisfactorily solved over the past years. In this paper, an extension of modularity, the fuzzy modularity is proposed, which can provide a measure of goodness for the fuzzy community structure in networks. The simulated annealing strategy is used to maximize the fuzzy modularity function, associating with an alternating iteration based on our previous work. The proposed algorithm can efficiently identify the probabilities of each node belonging to different communities with random initial fuzzy partition during the cooling process. An appropriate number of communities can be automatically determined without any prior knowledge about the community structure. The computational results on several artificial and real-world networks confirm the capability of the algorithm.     

Emergence of modularity and disassortativity in protein-protein interaction networks

In this paper, we present a simple evolution model of protein-protein interaction networks by introducing a rule of small-preference duplication of a node, meaning that the probability of a node chosen to duplicate is inversely proportional to its degree, and subsequent divergence plus nonuniform heterodimerization based on some plausible mechanisms in biology. We show that our model cannot only reproduce scale-free connectivity and small-world pattern, but also exhibit hierarchical modularity and disassortativity. After comparing the features of our model with those of real protein-protein interaction networks, we believe that our model can provide relevant insights into the mechanism underlying the evolution of protein-protein interaction networks.     

Dynamic evolutionary community detection algorithms based on the modularity matrix

Motivated by the relationship of the dynamic behaviors and network structure, in this paper, we present two efficient dynamic community detection algorithms. The phases of the nodes in the network can evolve according to our proposed differential equations. In each iteration, the phases of the nodes are controlled by several parameters. It is found that the phases of the nodes are ultimately clustered into several communities after a short period of evolution. They can be adopted to detect the communities successfully. The second differential equation can dynamically adjust several parameters, so it can obtain satisfactory detection results. Simulations on some test networks have verified the efficiency of the presented algorithms.     

Spontaneous emergence of modularity in a model of evolving individuals

We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of modularity correlates with the rapidity and severity of environmental change. The modularity arises as a synergistic response to the noise in the environment in the presence of horizontal gene transfer. We suggest that the hierarchical structure observed in the natural world may be a broken-symmetry state, which generically results from evolution in a changing environment.     

复杂网络中社团结构发现的多分辨率密度模块度

现实中的许多复杂网络呈现出明显的模块性或社团性.模块度是衡量社团结构划分优劣的效益函数, 它也通常被用作社团结构探测的目标函数,但最为广泛使用的Newman-Girvan模块度却存在着分辨率限制问题,多分辨率模块度也不能克服误合并社团和误分裂社团同时存在的缺陷. 本文在网络密度的基础上提出了多分辨率的密度模块度函数, 通过实验和分析证实了该函数能够使社团结构的误划分率显著降低, 而且能够体现出网络社团结构是一个有机整体,不是各个社团的简单相加.     

Community detection based on modularity and an improved genetic algorithm

Complex networks are widely applied in every aspect of human society, and community detection is a research hotspot in complex networks. Many algorithms use modularity as the objective function, which can simplify the algorithm. In this paper, a community detection method based on modularity and an improved genetic algorithm (MIGA) is put forward. MIGA takes the modularity Q$Q$ as the objective function, which can simplify the algorithm, and uses prior information (the number of community structures), which makes the algorithm more targeted and improves the stability and accuracy of community detection. Meanwhile, MIGA takes the simulated annealing method as the local search method, which can improve the ability of local search by adjusting the parameters. Compared with the state-of-art algorithms, simulation results on computer-generated and four real-world networks reflect the effectiveness of MIGA.     

Community structure and modularity in networks of correlated brain activity

Functional connectivity patterns derived from neuroimaging data may be represented as graphs or networks, with individual image voxels or anatomically-defined structures representing the nodes, and a measure of correlation between the responses in each pair of nodes determining the edges. This explicit network representation allows network-analysis approaches to be applied to the characterization of functional connections within the brain. Much recent research in complex networks has focused on methods to identify community structure, i.e. cohesive clusters of strongly interconnected nodes. One class of such algorithms determines a partition of a network into 'sub-networks' based on the optimization of a modularity parameter, thus also providing a measure of the degree of segregation versus integration in the full network. Here, we demonstrate that a community structure algorithm based on the maximization of modularity, applied to a functional connectivity network calculated from the responses to acute fluoxetine challenge in the rat, can identify communities whose distributions correspond to anatomically meaningful structures and include compelling functional subdivisions in the brain. We also discuss the biological interpretation of the modularity parameter in terms of segregation and integration of brain function.     

Obtaining communities with a fitness growth process

The study of community structure became an important topic of research over the last years. But, while successfully applied in several areas, the concept lacks of a general and precise notion. Facts like the hierarchical structure and heterogeneity of complex networks make it difficult to unify the idea of community and its evaluation. The global functional known as modularity is probably the most used technique in this area. Nevertheless, its limits have been deeply studied. Local techniques as the one by Lancichinetti et al. (2009) [1] arose as an answer to the resolution limit and degeneracies that modularity has.