Network Topological Similarity Research Articles

On the current failure-but bright future-of topology-driven biological network alignment.

Since the function of a protein is defined by its interaction partners, and since we expect similar interaction patterns across species, the alignment of protein-protein interaction (PPI) networks between species, based on network topology alone, should uncover functionally related proteins across species. Surprisingly, despite the publication of more than fifty algorithms aimed at performing PPI network alignment, few have demonstrated a statistically significant link between network topology and functional similarity, and none have demonstrated that orthologs can be recovered using network topology alone. We find that the major contributing factors to this surprising failure are: (i) edge densities in most currently available experimental PPI networks are demonstrably too low to expect topological network alignment to succeed; (ii) in the few cases where the edge densities are high enough, some measures of topological similarity easily uncover functionally similar proteins while others do not; and (iii) most network alignment algorithms to date perform poorly at optimizing even their own topological objective functions, hampering their ability to use topology effectively. We demonstrate that SANA-the Simulated Annealing Network Aligner-significantly outperforms existing aligners at optimizing their own objective functions, even achieving near-optimal solutions when the optimal solution is known. We offer the first demonstration of global network alignments based on topology alone that align functionally similar proteins with p-values in some cases below 10-300. We predict that topological network alignment has a bright future as edge densities increase toward the value where good alignments become possible. We demonstrate that when enough common topology is present at high enough edge densities-for example in the recent, partly synthetic networks of the Integrated Interaction Database-topological network alignment easily recovers most orthologs, paving the way toward high-throughput functional prediction based on topology-driven network alignment.

INTS-MFS: A novel method to predict microRNA-disease associations by integrating network topology similarity and microRNA function similarity

Identifying associations between microRNAs (miRNAs) and diseases is very important to understand the occurrence and development of human diseases. However, these existing methods suffer from the following limitation: first, some disease-related miRNAs are obtained from the miRNA functional similarity networks consisting of heterogeneous data sources, i.e., disease similarity, protein interaction network, gene expression. Second, little approaches infer disease-related miRNAs depending on the network topological features without the functional similarity of miRNAs. In this paper, we develop a novel model of Integrating Network Topology Similarity and MicroRNA Function Similarity (INTS-MFS). The integrated miRNA similarities are calculated based on miRNA functional similarity and network topological characteristics. INTS-MFS obtained AUC of 0.872 based on five-fold cross-validation and was applied to three common human diseases in case studies. As a results, 30 out of top 30 predicted Prostatic Neoplasm-related miRNAs were included in the two databases of dbDEMC and PhenomiR2.0. 29 out of top 30 predicted Lung Neoplasm-related miRNAs and Breast Neoplasm-related miRNAs were included in dbDEMC, PhenomiR2.0 and experimental reports. Moreover, INTS-MFS found unknown association with hsa-mir-371a in breast cancer and lung cancer, which have not been reported. It provides biologists new clues for diagnosing breast and lung cancer.

ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks

BackgroundThe current computational methods on identifying conserved protein complexes across multiple Protein-Protein Interaction (PPI) networks suffer from the lack of explicit modeling of the desired topological properties within conserved protein complexes as well as their scalability.ResultsTo overcome those issues, we propose a scalable algorithm—ClusterM—for identifying conserved protein complexes across multiple PPI networks through the integration of network topology and protein sequence similarity information. ClusterM overcomes the computational barrier that existed in previous methods, where the complexity escalates exponentially when handling an increasing number of PPI networks; and it is able to detect conserved protein complexes with both topological separability and cohesive protein sequence conservation. On two independent compendiums of PPI networks from Saccharomyces cerevisiae (Sce, yeast), Drosophila melanogaster (Dme, fruit fly), Caenorhabditis elegans (Cel, worm), and Homo sapiens (Hsa, human), we demonstrate that ClusterM outperforms other state-of-the-art algorithms by a significant margin and is able to identify de novo conserved protein complexes across four species that are missed by existing algorithms.ConclusionsClusterM can better capture the desired topological property of a typical conserved protein complex, which is densely connected within the complex while being well-separated from the rest of the networks. Furthermore, our experiments have shown that ClusterM is highly scalable and efficient when analyzing multiple PPI networks.

Predicting lncRNA-disease associations using network topological similarity based on deep mining heterogeneous networks

A kind of noncoding RNA with length more than 200 nucleotides named long noncoding RNA (lncRNA) has gained considerable attention in recent decades. Many studies have confirmed that human genome contains many thousands of lncRNAs. LncRNAs play significant roles in many important biological processes, including complex disease diagnosis, prognosis, prevention and treatment. For some important diseases such as cancer, lncRNAs have been novel candidate biomarkers. However, the role of lncRNAs in human diseases is still in its infancy, and only a small part of lncRNA-disease associations have been experimentally verified. Predicting lncRNA-disease association is an important way to understand the mechanism and function of lncRNA involved in diseases to enrich the annotations of lncRNA. Therefore, it is urgent to prioritize lncRNAs potentially associated with diseases. Biological system is a highly complex heterogenous network involved different molecules. Therefore, the algorithms based on network methods have been extensively applied in information fields which can provide a quantifiable characterization for the networks characterizing multifarious biological systems. A heterogeneous network topology possessing abundant interactions between biomedical entities is rarely utilized in similarity-based methods for predicting lncRNA-disease associations based on the array of varying features of lncRNAs and diseases. DeepWalk, encoding the relations of nodes in a continuous vector space, is an extension of language model and unsupervised learning from sequence-based word to network. In this article, we present a novel lncRNA-disease association prediction method based on DeepWalk, which enhances the existing association discovery methods through a topology-based similarity measure. We integrate the heterogeneous data to construct a Linked Tripartite Network which is a heterogeneous network containing three types od nodes which generated from bioinformatics linked datasets and use DeepWalk method to extract topological structure features of the nodes in the linked tripartite network for calculating similarities. Our proposed method can be separated into the following steps: Firstly, we integrate heterogeneous data to construct a Linked Tripartite Network: containing the topological interactions of known lncRNA-disease, lncRNA-microRNA and microRNA-disease. Secondly, the topological structure features of the nodes are extracted based on DeepWalk. Thirdly, similarity scores of disease-disease pairs and lncRNA-lncRNA pairs are computed based on the topology of this network. Finally, new lncRNA and disease associations are discovered by rule-based inference method with lncRNA-lncRNA similarities. Our proposed method shows superior predictive performance for prediction of lncRNA-disease associations based on topological similarity from heterogenous network. The AUC value is used to show the performance of our method. The similarity measurement using network topology based on DeepWalk provide a novel perspective which is different from the similarity derived from sequence or structure information.Availability: All the data and codes are freely availability at: https://github.com/Pengeace/lncRNA-disease-link.

Prediction of Epitope-Associated TCR by Using Network Topological Similarity Based on Deepwalk

Currently, there are many tools available online for T-cell epitope prediction. They usually focus on the binding of peptides to major histocompatibility complex (MHC) molecules on the surface of antigen-presenting cells (APCs). However, the binding of peptides and MHC complexes to the T-cell receptor (TCR) is also critical for the immune process. Identifying the binding of human epitopes to TCRs will be useful for developing vaccines. It also has great prospects in medical issues such as cancer and autoimmune diseases. We propose a similarity-based TCR-epitope prediction method using a similarity measure. This paper introduces the Deepwalk method to calculate the topological similarity between TCR-TCRs, constructs a TCR similarity network topology, and predicts the correlation between TCRs and epitopes based on known TCR-epitope associations. We selected data from 22 types of epitopes from the VDJDB database and trained models to implement TCR-epitope prediction. We trained a model on the data from the 22 types of epitopes, predicting which epitope each TCR belongs to. To compare with other methods, we also generated a second method involving training a model for each type of epitope so that we can predict which TCR is bound to the epitope from a large pool of TCRs. We used the ROC curve, PR curve and other evaluation indicators to evaluate our model in 10-fold cross-validation. In the first model, the AUC value of our method is 0.926, and that of the support vector machine (SVM) method is 0.924. Considering that no one has ever used the first prediction model, we used the second method for the predictions. The results show better predictive performance compared to the SVM method, TCRGP method and random forest method. Our AUC values range from 0.660 to 0.950. The experimental results show that our method outperforms other methods in TCR-epitope prediction, which can help predict the TCR-epitope.

Domain Knowledge-Based Link Prediction in Customer-Product Bipartite Graph for Product Recommendation

In this paper, we propose domain knowledge-based link prediction algorithm in customer-product bipartite network to improve effectiveness of product recommendation in retail. The domain knowledge is classified into product domain knowledge and time context knowledge, which play an important part in link prediction. We take both of them into consideration in recommendation and form a unified domain knowledge-based link prediction framework. We capture product semantic similarity by ontology-based analysis and time attenuation factor from time context knowledge, then incorporate them into network topological similarity to form a new linkage measure. To evaluate the algorithm, we use a real retail transaction dataset from Food Mart. Experimental results demonstrate that the usage of domain knowledge in link prediction achieved significantly better performance.

Variational Approach for Learning Community Structures

Discovering and modeling community structure exist to be a fundamentally challenging task. In domains such as biology, chemistry, and physics, researchers often rely on community detection algorithms to uncover community structures from complex systems yet no unified definition of community structure exists. Furthermore, existing models tend to be oversimplified leading to a neglect of richer information such as nodal features. Coupled with the surge of user generated information on social networks, a demand for newer techniques beyond traditional approaches is inevitable. Deep learning techniques such as network representation learning have shown tremendous promise. More specifically, supervised and semisupervised learning tasks such as link prediction and node classification have achieved remarkable results. However, unsupervised learning tasks such as community detection remain widely unexplored. In this paper, a novel deep generative model for community detection is proposed. Extensive experiments show that the proposed model, empowered with Bayesian deep learning, can provide insights in terms of uncertainty and exploit nonlinearities which result in better performance in comparison to state-of-the-art community detection methods. Additionally, unlike traditional methods, the proposed model is community structure definition agnostic. Leveraging on low-dimensional embeddings of both network topology and feature similarity, it automatically learns the best model configuration for describing similarities in a community.

P04.56 Brain tumor patients with impaired cognitive flexibility do not efficiently update functional connectivity within the fronto-parietal network

Background The majority of brain tumor patients suffers from cognitive deficits. These deficits can be very disruptive for a person’s daily functioning, quality of life and treatment compliance. Examining functional connectivity patterns during the performance of a cognitive task may enhance our understanding of the relationship between functional brain networks and cognitive performance. Despite the similarity in network topology across rest and task states, there are also meaningful differences in functional connectivity that are likely to be linked to cognitive performance. Currently, it is largely unknown how differences between rest and task functional connectivity patterns are related to cognitive functioning in brain tumor patients. The goal of this study was therefore to explore this relationship, whereby we focussed on cognitive flexibility. We expected less intense task-evoked network reconfiguration in patients with worse cognitive flexibility abilities. Material and Methods Resting state and functional MRI data (while performing several working memory tasks) were acquired in 50 brain tumor patients (23 meningioma, 13 low grade and 14 high grade glioma patients) before tumor resection. Performance on the “Shifting Attention Test” (SAT; part of CNS-VS) was used as an independent measure of a patient’s cognitive flexibility. Task-evoked network reconfiguration was investigated at the whole-brain and at the network level (fronto-parietal (FPN), cingulo-opercular (CON), and default mode (DMN) network). Whole-brain and network-specific connectivity matrices were created for each patient. We used the Pearson correlation value as a measure of similarity between rest and task functional connectivity patterns. For each network and for the whole brain, a linear regression (4 in total) using demographic and clinical factors, tumor characteristics and the reconfiguration measure was performed to test the relationship between the reconfiguration measure and cognitive flexibility performance while correcting for the other variables. Results We found that, across patients, SAT performance was negatively associated with the similarity of the FPN connectivity pattern between task and rest (β= -75.84, t(42)=-3.63, p<0.001). No association was found between SAT scores and degree of reconfiguration at the whole brain level or for the CON or DMN. Conclusion Our results show that cognitive flexibility problems in brain tumor patients are associated with a higher rest-task similarity in the fronto-parietal network topology. Possibly, the problems with cognitive flexibility are related to reduced capacity to update the fronto-parietal connections to changing cognitive demands. Our findings provide an important step towards individually-tailored treatment of cognitive deficits.

Propagating annotations of molecular networks using in silico fragmentation.

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

NTSHMDA: Prediction of Human Microbe-Disease Association Based on Random Walk by Integrating Network Topological Similarity.

Accumulating clinic evidences have demonstrated that the microbes residing in human bodies play a significantly important role in the formation, development, and progression of various complex human diseases. Identifying latent related microbes for disease could provide insight into human disease mechanisms and promote disease prevention, diagnosis, and treatment. In this paper, we first construct a heterogeneous network by connecting the disease similarity network and the microbe similarity network through known microbe-disease association network, and then develop a novel computational model to predict human microbe-disease associations based on random walk by integrating network topological similarity (NTSHMDA). Specifically, each microbe-disease association pair is regarded as a distinct relationship level and, thus, assigned different weights based on network topological similarity. The experimental results show that NTSHMDA outperforms some state-of-the-art methods with average AUCs of 0.9070, 0.8896 ± 0.0038 in the frameworks of Leave-one-out cross validation and 5-fold cross validation, respectively. In case studies, 9, 18, 38 and 9, 18, 45 out of top-10, 20, 50 candidate microbes are verified by recently published literatures for asthma and inflammatory bowel disease, respectively. In conclusion, NTSHMDA has potential ability to identify novel disease-microbe associations and can also provide valuable information for drug discovery and biological researches.

Dynamic community detection based on network structural perturbation and topological similarity

Community detection in dynamic networks has been extensively studied since it sheds light on the structure-function relation of the overall complex systems. Recently, it has been demonstrated that the structural perturbation in static networks is excellent in characterizing the topology. In order to investigate the perturbation structural theory in dynamic networks, we extend the theory by considering the dynamic variation information between networks of consecutive time. Then a novel similarity is proposed by combing structural perturbation and topological features. Finally, we present an evolutionary clustering algorithm to detect dynamic communities under the temporal smoothness framework. Experimental results on both artificial and real dynamic networks demonstrate that the proposed similarity is promising in dynamic community detection since it improves the clustering accuracy compared with state-of-the-art methods, indicating the superiority of the presented similarity measure.

Predicting MicroRNA-Disease Associations Using Network Topological Similarity Based on DeepWalk

Recently, increasing experimental studies have shown that microRNAs (miRNAs) involved in multiple physiological processes are connected with several complex human diseases. Identifying human disease-related miRNAs will be useful in uncovering novel prognostic markers for cancer. Currently, several computational approaches have been developed for miRNA-disease association prediction based on the integration of additional biological information of diseases and miRNAs, such as disease semantic similarity and miRNA functional similarity. However, these methods do not work well when this information is unavailable. In this paper, we present a similarity-based miRNA-disease prediction method that enhances the existing association discovery methods through a topology-based similarity measure. DeepWalk, a deep learning method, is utilized in this paper to calculate similarities within a miRNA-disease association network. It shows superior predictive performance for 22 complex diseases, with area under the ROC curve scores ranging from 0.805 to 0.937 by using five-fold cross-validation. In addition, case studies on breast cancer, lung cancer, and prostatic cancer further justify the use of our method to discover latent miRNA-disease pairs.

Uncovering fuzzy communities in networks with structural similarity

Community detection is an important task for uncovering underlying structures and analyzing group behavior in complex networks. A fuzzy community detection method is proposed in this paper to detect fuzzy community structures without any prior knowledge. Compared with previous studies, we introduce a structural similarity to measure fuzzy relation between vertices based on local interactions between neighboring vertices. In our method, we take the fuzzy similarity between vertices and fuzzy transitivity of the similarity in network topology into consideration. Moreover, multiresolution community structures can be detected by varying the fuzzy threshold. Experimental results and comparisons with some state-of-the-art methods are presented on a variety of benchmark graphs. It shows that the method is efficient in detecting communities on both real-world and synthetic networks.

Protein-fold recognition using an improved single-source K diverse shortest paths algorithm.

Protein structure prediction, when construed as a fold recognition problem, is one of the most important applications of similarity search in bioinformatics. A new protein-fold recognition method is reported which combines a single-source K diverse shortest path (SSKDSP) algorithm with Enrichment of Network Topological Similarity (ENTS) algorithm to search a graphic feature space generated using sequence similarity and structural similarity metrics. A modified, more efficient SSKDSP algorithm is developed to improve the performance of graph searching. The new implementation of the SSKDSP algorithm empirically requires 82% less memory and 61% less time than the current implementation, allowing for the analysis of larger, denser graphs. Furthermore, the statistical significance of fold ranking generated from SSKDSP is assessed using ENTS. The reported ENTS-SSKDSP algorithm outperforms original ENTS that uses random walk with restart for the graph search as well as other state-of-the-art protein structure prediction algorithms HHSearch and Sparks-X, as evaluated by a benchmark of 600 query proteins. The reported methods may easily be extended to other similarity search problems in bioinformatics and chemoinformatics. The SSKDSP software is available at http://compsci.hunter.cuny.edu/~leixie/sskdsp.html.

NTSMDA: prediction of miRNA-disease associations by integrating network topological similarity.

Recently, accumulating studies have indicated that microRNAs (miRNAs) play an important role in exploring the pathogenesis of various human diseases at the molecular level and may result in the design of specific tools for diagnosis, treatment evaluation and prevention. Experimental identification of disease-related miRNAs is time-consuming and labour-intensive. Hence, there is a stressing need to propose efficient computational methods to detect more potential miRNA-disease associations. Currently, several computational approaches for identifying disease-related miRNAs on the miRNA-disease network have gained much attention by means of integrating miRNA functional similarities and disease semantic similarities. However, these methods rarely consider the network topological similarity of the miRNA-disease association network. Here, in this paper we develop an improved computational method named NTSMDA that is based on known miRNA-disease network topological similarity to exploit more potential disease-related miRNAs. We achieve an AUC of 89.4% by using the leave-one-out cross-validation experiment, demonstrating the excellent predictive performance of NTSMDA. Furthermore, predicted highly ranked miRNA-disease associations of breast neoplasms, lung neoplasms and prostatic neoplasms are manually confirmed by different related databases and literature, providing evidence for the good performance and potential value of the NTSMDA method in inferring miRNA-disease associations. The R code and readme file of NTSMDA can be downloaded from .

A new method to improve network topological similarity search: applied to fold recognition.

Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework-Enrichment of Network Topological Similarity (ENTS)-to improve the performance of large scale similarity searches in bioinformatics. We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network. Source code freely available upon request : lxie@iscb.org.

An integrative approach for a network based meta-analysis of viral RNAi screens

BackgroundBig data is becoming ubiquitous in biology, and poses significant challenges in data analysis and interpretation. RNAi screening has become a workhorse of functional genomics, and has been applied, for example, to identify host factors involved in infection for a panel of different viruses. However, the analysis of data resulting from such screens is difficult, with often low overlap between hit lists, even when comparing screens targeting the same virus. This makes it a major challenge to select interesting candidates for further detailed, mechanistic experimental characterization.ResultsTo address this problem we propose an integrative bioinformatics pipeline that allows for a network based meta-analysis of viral high-throughput RNAi screens. Initially, we collate a human protein interaction network from various public repositories, which is then subjected to unsupervised clustering to determine functional modules. Modules that are significantly enriched with host dependency factors (HDFs) and/or host restriction factors (HRFs) are then filtered based on network topology and semantic similarity measures. Modules passing all these criteria are finally interpreted for their biological significance using enrichment analysis, and interesting candidate genes can be selected from the modules.ConclusionsWe apply our approach to seven screens targeting three different viruses, and compare results with other published meta-analyses of viral RNAi screens. We recover key hit genes, and identify additional candidates from the screens. While we demonstrate the application of the approach using viral RNAi data, the method is generally applicable to identify underlying mechanisms from hit lists derived from high-throughput experimental data, and to select a small number of most promising genes for further mechanistic studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13015-015-0035-7) contains supplementary material, which is available to authorized users.

Prioritization of candidate disease genes by enlarging the seed set and fusing information of the network topology and gene expression

The identification of disease genes is very important not only to provide greater understanding of gene function and cellular mechanisms which drive human disease, but also to enhance human disease diagnosis and treatment. Recently, high-throughput techniques have been applied to detect dozens or even hundreds of candidate genes. However, experimental approaches to validate the many candidates are usually time-consuming, tedious and expensive, and sometimes lack reproducibility. Therefore, numerous theoretical and computational methods (e.g. network-based approaches) have been developed to prioritize candidate disease genes. Many network-based approaches implicitly utilize the observation that genes causing the same or similar diseases tend to correlate with each other in gene-protein relationship networks. Of these network approaches, the random walk with restart algorithm (RWR) is considered to be a state-of-the-art approach. To further improve the performance of RWR, we propose a novel method named ESFSC to identify disease-related genes, by enlarging the seed set according to the centrality of disease genes in a network and fusing information of the protein-protein interaction (PPI) network topological similarity and the gene expression correlation. The ESFSC algorithm restarts at all of the nodes in the seed set consisting of the known disease genes and their k-nearest neighbor nodes, then walks in the global network separately guided by the similarity transition matrix constructed with PPI network topological similarity properties and the correlational transition matrix constructed with the gene expression profiles. As a result, all the genes in the network are ranked by weighted fusing the above results of the RWR guided by two types of transition matrices. Comprehensive simulation results of the 10 diseases with 97 known disease genes collected from the Online Mendelian Inheritance in Man (OMIM) database show that ESFSC outperforms existing methods for prioritizing candidate disease genes. The top prediction results of Alzheimer's disease are consistent with previous literature reports.

Analyzing and Visualizing Web Opinion Development and Social Interactions With Density-Based Clustering

Due to the advancement of Web 2.0 technologies, a large volume of Web opinions is available on social media sites such as Web forums and Weblogs. These technologies provide a platform for Internet users around the world to communicate with each other and express their opinions. Analysis of developing Web opinions is potentially valuable for discovering ongoing topics of interests of the public like terrorist and crime detection, understanding how topics evolve together with the underlying social interaction between participants, and identifying important participants who have great influence in various topics of discussions. Nonetheless, the work of analyzing and clustering Web opinions is extremely challenging. Unlike regular documents, Web opinions are short and sparse text messages with noisy content. Typical document clustering techniques with the goal of clustering all documents applied to Web opinions produce unsatisfactory performance. In this paper, we investigated the density-based clustering algorithm and proposed the scalable distance-based clustering technique for Web opinion clustering. We conducted experiments and benchmarked with the density-based algorithm to show that the new algorithm obtains higher microaccuracy and macroaccuracy. This Web opinion clustering technique enables the identification of themes within discussions in Web social networks and their development, as well as the interactions of active participants. We also developed interactive visualization tools, which make use of the identified topic clusters to display social network development, the network topology similarity between topics, and the similarity values between participants.

Identification of overlapping and non-overlapping community structure by fuzzy clustering in complex networks

This paper proposes a novel method based on fuzzy clustering to detect community structure in complex networks. In contrast to previous studies, our method does not focus on a graph model, but rather on a fuzzy relation model, which uses the operations of fuzzy relation to replace a traversal search of the graph for identifying community structure. In our method, we first use a fuzzy relation to describe the relation between vertices as well as the similarity in network topology to determine the membership grade of the relation. Then, we transform this fuzzy relation into a fuzzy equivalence relation. Finally, we map the non-overlapping communities as equivalence classes that satisfy a certain equivalence relation. Because most real-world networks are made of overlapping communities (e.g., in social networks, people may belong to multiple communities), we can consider the equivalence classes above as the skeletons of overlapping communities and extend our method by adding vertices to the skeletons to identify overlapping communities. We evaluated our method on artificial networks with built-in communities and real-world networks with known and unknown communities. The experimental results show that our method works well for detecting these communities and gives a new understanding of network division and community formation.