Null Model and Community Structure in Heterogeneous Networks

Heterogeneous information networks have drawn much attention in recent years due to their significant applications, such as text mining, e-commerce, social networks, and bioinformatics. Clustering different types of objects simultaneously based upon not only their relations of the same type, but also the relations between different types of objects can improve the clustering quality mutually. In this paper, we propose a general model, in which both the homogeneous and heterogeneous relations are considered simultaneously, to describe the structure of the heterogeneous information networks and devise a novel parametric free multi-type overlapped clustering approach. In this model, different types of relations between different types of objects are represented by a group of matrices. In this way, we transfer the multi-type clustering problem into the information compression problem. Subsequently, greedy search approaches, which aim at describing the group of relational matrices with least bits, are proposed. Moreover, by discovering the discriminative clusters among different types of objects, we devise effective parameter-free strategies to discover either overlapping or non-overlapping structure among different types of clusters. Extensive experiments on real-world and synthetic data sets demonstrate our methods are effective and efficient.

Networks have become a widely used tool for modeling complex systems in many different fields. This approach is extremely useful for representing interactions among genes, social relationships, Internet communications or correlations of prices within a stock market, to name just a few examples. By analyzing the structure of these networks and understanding how their different elements interact, we could improve our knowledge of the whole system. Usually, nodes that compose these networks tend to create tightly knit groups. This property, of high interest in many scientific fields, is called community structure and improving its detection and characterization is what this thesis is all about. The first objective of this work is the generation of efficient methods able to characterize the communities of a network and to understand its structure. Second, we will try to create a set of tests where such methods can be studied. Finally, we will suggest a statistical measure in order to be able to properly assess the quality of the community structure of a network. To accomplish these objectives, first, we generate a set of algorithms that can transform a network into a hierarchical tree and, from there, to determine their most relevant communities. Furthermore, we have developed a new type of benchmarks for effectively testing these and other community detection algorithms. Finally, and as the most important contribution of this work, it is shown that the community structure of a network can be accurately evaluated using a hypergeometric distribution-based index. Thus, the maximization of this measure, called Surprise, appears as the best proposed strategy for detecting the optimal partition into communities of a network. Surprise exhibits an excellent behavior in all networks analyzed, qualitatively outperforming any previous method. Thus, it appears as the best measure proposed to this end and the data suggests that it could be an optimal strategy to determine the quality of the community structure of complex networks.

In reality many complex networks present modules or community structures obviously. Modularity is a benefit function used in quantifying the quality of a division of a network into communities. And it usually can be used as a basis for optimization methods of detecting community structure in networks. But the most popular modularity which is proposed by M. E. J. Newman and M. Girvan has the resolution limit in community detection. Multi-resolution modularity cannot overcome the misclassifications caused by merging and splitting the communities either. In this paper, we propose a multi-resolution density modularity based on the network density. The proposed function is tested on the artificial networks. Computational results show that it can reduce the rate of misclassification considerably. And the systematicness of the community structures can be demonstrated by the multi-resolution density modularity.

The Taihu Lake plain is a highly urbanized region in China with many water-related environmental problems. Although point-source pollution has been effectively controlled by government legislation, urban surface runoff pollution is still a major issue. Different types of urban communities were selected for rainfall runoff experiments. According to the monitoring data of rainfall events, multiple methods were used to analyze the characteristics of surface runoff pollution and estimate the pollution load for different types of communities. The results indicated that surface runoff from urban communities reduced the river water quality. Certain degrees of the 'first flush' effect occurred in different types of urban communities. The surface runoff pollution in the commercial residential community was weaker than that in commercial and private residential communities; however, the first flush occurred more frequently in the commercial residential community. Holding back 30% of the surface runoff could effectively improve the runoff water quality in commercial and private residential communities as well as the commercial residential community with restaurants. In the commercial residential community, 25% of surface runoff should be held to improve runoff water quality effectively. The loads of pollutants, especially nitrogen and phosphorus, in urban communities in the Taihu Lake basin were higher than those in other regions in China. This research can assist with the reduction of surface runoff pollution in highly urbanized communities.

Complex networks have in generally communities. These communities are very important. Network’s communities represent sets of nodes, which are very connected. In this research, we developed a new method to find the community structure in networks. Our method is based on flower pollination algorithm (FPA) witch is used in the splitting process. The splitting of networks in our method maximizes a function of quality called modularity. We provide a general framework for implementing our new method to find community structure in networks. We present the effectiveness of our method by comparison with some known methods on computer-generated and real-world networks.

Mining different types of communities from web data have attracted a lot of research efforts in recent years. However, none of the existing community mining techniques has taken into account both the dynamic as well as heterogeneous nature of web data. In this paper, we propose to characterize and predict community members from the evolution of heterogeneous web data. We first propose a general framework for analyzing the evolution of heterogeneous networks. Then, the academic network, which is extracted from 1 million computer science papers, is used as an example to illustrate the framework. Finally, two example applications of the academic network are presented. Experimental results with a real and very large heterogeneous academic network show that our proposed framework can produce good results in terms of community member recommendation. Also, novel knowledge and insights can be gained by analyzing the community evolution pattern.

Identifying and evaluating community structure in complex networks

Heterogeneous networks have multiple types of nodes and edges. Single-layer stochastic block model (SBM), bipartite SBM, and multiplex SBM have been proposed as a tool for detecting community structure in networks and generating synthetic networks for use as benchmarks. Yet, any SBM has not been introduced specifically for detecting community in heterogeneous networks. In this paper, we introduce heterogeneous multilayer SBMs for detecting communities in heterogeneous networks. According to these models, we look at heterogeneous networks as multilayer networks, which means each edge type shows one layer. We can categorize these models into two broad groups, those based on the independent degree principle and other based on the shared degree principle. According to our results, in general, the independent degree model has better performance in networks that have less common communities between nodes types. In contrast, the shared degree model has better performance in networks which have more common communities between nodes types. Also, we show that our models outperform in real-world networks. If we put aside the exception case, simulation results and real data applications show the effectiveness of these proposed models compared to single-layer models that are applied to heterogeneous networks.

Nowadays, the wide use of the Internet around the world allows people to socialize and connect together. This results of the explosion of the Web 2.0 giving rise to a growing demand for Social Recommendation Systems. Social recommendation systems are introduced to rescue users from searching and choosing by predicting users’ preferences. In this paper, we will focus on recommendation via link prediction across heterogeneous social network. The main objective is to recommend items by predicting the missing or unobserved interactions between actors within a social network while pinpointing different types of objects and links. Probabilistic relational models will be used for prediction of new interactions in a citation network.

When studying dynamic networks, it is often of interest to understand how the community structure of the network changes. However, before studying the community structure of dynamic social networks, one must first collect appropriate network data. In this paper we present a network sampling technique to crawl the community structure of dynamic networks when there is a limitation on the number of nodes that can be queried. The process begins by obtaining a sample for the first time step. In subsequent time steps, the crawling process is guided by community structure discoveries made in the past. Experiments conducted on the proposed approach and certain baseline techniques reveal the proposed approach has at least 35% performance increase in cases when the total query budget is fixed over the entire period and at least 8% increase in cases when the query budget is fixed per time step.

Heterogeneous networks are useful for modeling complex systems that consist of different types of objects. However, there are limited statistical models to deal with heterogeneous networks. In this paper, we propose a statistical model for community detection in heterogeneous networks. We formulate a heterogeneous version of the mixed membership stochastic blockmodel to accommodate heterogeneity in the data and the content dependent property of the pairwise relationship. We also apply a variational algorithm for posterior inference. The proposed procedure is shown to be consistent for community detection under mixed membership stochastic blockmodels for heterogeneous networks. We demonstrate the advantage of the proposed method in modeling overlapping communities and multiple memberships through simulation studies and applications to a real data set.

Identifying meaningful cancer driver genes in a cohort of tumors is a challenging task in cancer genomics. Although existing studies have identified known cancer drivers, most of them focus on detecting coding drivers with mutations. It is acknowledged that non-coding drivers can regulate driver mutations to promote cancer growth. In this work, we propose a novel node importance-based network analysis (NIBNA) framework to detect coding and non-coding cancer drivers. We hypothesize that cancer drivers are crucial to the formation of community structures in cancer network, and removing them from the network greatly perturbs the network structure thereby critically affecting the functioning of the network. NIBNA detects cancer drivers using a three-step process: first, a condition-specific network is built by incorporating gene expression data and gene networks; second, the community structures in the network are estimated; and third, a centrality-based metric is applied to compute node importance. We apply NIBNA to the BRCA dataset, and it outperforms existing state-of-art methods in detecting coding cancer drivers. NIBNA also predicts 265 miRNA drivers, and majority of these drivers have been validated in literature. Further we apply NIBNA to detect cancer subtype-specific drivers, and several predicted drivers have been validated to be associated with cancer subtypes. Lastly, we evaluate NIBNA's performance in detecting epithelial-mesenchymal transition drivers, and we confirmed 8 coding and 13 miRNA drivers in the list of known genes. The source code can be accessed at https://github.com/mandarsc/NIBNA. Supplementary data are available at Bioinformatics online.

A similarity-based community detection method with multiple prototype representation

Currently, many of the processing techniques for the location-based queries provide information of a single type of spatial objects, based on their spatial closeness to the query object. However, in real-life applications the user may be interested in obtaining information about different types of objects, in terms of their quality, cost, and neighboring relationship. We term the different types of objects with better quality and closer to each other the Neighboring skyline set (or NS set). Three new types of location-based queries, the Distance-based neighboring skyline query (Dist-NS query), the Cost-based neighboring skyline query (Cost-NS query), and the Budget-based neighboring skyline query (BGT-NS query), are presented to determine the NS sets according to user’s specific requirement. A R-tree-based index, the $$R^{a,c}$$-tree, is first designed to manage each type of objects with their locations, attributes, and costs. Then, a simultaneous traversal of the $$R^{a,c}$$-trees built on different types of objects is employed with several pruning criteria to prune the non-qualifying object sets as early as possible, so as to improve the query performance. Extensive experiments using the synthetic dataset demonstrate the efficiency and the effectiveness of the proposed algorithms.

Community detection via closure extension