Near linear time algorithm to detect community structures in large-scale networks

Joint Detection of Community and Structural Hole Spanner of Networks in Hyperbolic Space

Community detection and structural hole spanner (the node bridging different communities) identification, revealing the mesoscopic and microscopic structural properties of complex networks, have drawn much attention in recent years. As the determinant of mesoscopic structure, communities and structural hole spanners discover the clustering and hierarchy of networks, which has a key impact on transmission phenomena such as epidemic transmission, information diffusion, etc. However, most existing studies address the two tasks independently, which ignores the structural correlation between mesoscale and microscale and suffers from high computational costs. In this article, we propose an algorithm for simultaneously detecting communities and structural hole spanners via hyperbolic embedding (SDHE). Specifically, we first embed networks into a hyperbolic plane, in which, the angular distribution of the nodes reveals community structures of the embedded network. Then, we analyze the critical gap to detect communities and the angular region where structural hole spanners may exist. Finally, we identify structural hole spanners via two-step connectivity. Experimental results on synthetic networks and real networks demonstrate the effectiveness of our proposed algorithm compared with several state-of-the-art methods.

Network Representation Learning With Community Awareness and Its Applications in Brain Networks

Previously network representation learning methods mainly focus on exploring the microscopic structure, i.e., the pairwise relationship or similarity between nodes. However, the mesoscopic structure, i.e., community structure, an essential property in real networks, has not been thoroughly studied in the network representation learning. We here propose a deep attributed network representation learning with community awareness (DANRL-CA) framework. Specifically, we design a neighborhood enhancement autoencoder module to capture the 2-step relations between node pairs. To explore the multi-step relations, we construct a community-aware skip-gram module based on the encoder. We introduce two variants of DANRL-CA, namely, DANRL-CA-AM and DANRL-CA-CSM, which incorporate the community information and attribute semantics into node neighbors with different methods. We compare two variant models with the state-of-the-art methods on four datasets for node classification and link prediction. Especially, we apply our models on a brain network. The superiority indicates the scalability and effectiveness of our method on various networks. Compared with DANRL-CA-AM, DANRL-CA-CSM can more flexibly coordinate the role of node attributes and community information in the process of network representation learning, and shows superiority in the networks with sparse topological structure and node attributes.

Network approaches for modeling the effect of drugs and diseases

The network approach is quickly becoming a fundamental building block of computational methods aiming at elucidating the mechanism of action (MoA) and therapeutic effect of drugs. By modeling the effect of drugs and diseases on different biological networks, it is possible to better explain the interplay between disease perturbations and drug targets as well as how drug compounds induce favorable biological responses and/or adverse effects. Omics technologies have been extensively used to generate the data needed to study the mechanisms of action of drugs and diseases. These data are often exploited to define condition-specific networks and to study whether drugs can reverse disease perturbations. In this review, we describe network data mining algorithms that are commonly used to study drug’s MoA and to improve our understanding of the basis of chronic diseases. These methods can support fundamental stages of the drug development process, including the identification of putative drug targets, the in silico screening of drug compounds and drug combinations for the treatment of diseases. We also discuss recent studies using biological and omics-driven networks to search for possible repurposed FDA-approved drug treatments for SARS-CoV-2 infections (COVID-19).

Multilevel Coarsening for Interactive Visualization of Large Bipartite Networks

Bipartite networks are pervasive in modeling real-world phenomena and play a fundamental role in graph theory. Interactive exploratory visualization of such networks is an important problem, and particularly challenging when handling large networks. In this paper we present results from an investigation on using a general multilevel method for this purpose. Multilevel methods on networks have been introduced as a general approach to increase scalability of community detection and other complex optimization algorithms. They employ graph coarsening algorithms to create a hierarchy of increasingly coarser (reduced) approximations of an original network. Multilevel coarsening has been applied, e.g., to the problem of drawing simple (“unipartite”) networks. We build on previous work that extended multilevel coarsening to bipartite graphs to propose a visualization interface that uses multilevel coarsening to compute a multi-resolution hierarchical representation of an input bipartite network. From this hierarchy, interactive node-link drawings are displayed following a genuine route of the “overview first, zoom and filter, details on demand” visual information seeking mantra. Analysts may depart from the coarsest representation and select nodes or sub-graphs to be expanded and shown at greater detail. Besides intuitive navigation of large-scale networks, this solution affords great flexibility, as users are free to select different coarsening strategies in different scenarios. We illustrate its potential with case studies involving real networks on distinct domains. The experimental analysis shows our strategy is effective to reveal topological structures, such as communities and holes, that may remain hidden in a conventional node-link layout. It is also useful to highlight connectivity patterns across the bipartite layers, as illustrated in an example that emphasizes the correlation between diseases and genes in genetic disorders, and in a study of a scientific collaboration network of authors and papers.

Social Network Analysis: A Survey on Measure, Structure, Language Information Analysis, Privacy, and Applications

The rapid growth in popularity of online social networks provides new opportunities in computer science, sociology, math, information studies, biology, business, and more. Social network analysis (SNA) is a paramount technique supporting understanding social relationships and networks. Accordingly, certain studies and reviews have been presented focusing on information dissemination, influence analysis, link prediction, and more. However, the ultimate aim is for social network background knowledge and analysis to solve real-world social network problems. SNA still has several research challenges in this context, including users’ privacy in online social networks. Inspired by these facts, we have presented a survey on social network analysis techniques, visualization, structure, privacy, and applications. This detailed study has started with the basics of network representation, structure, and measures. Our primary focus is on SNA applications with state-of-the-art techniques. We further provide a comparative analysis of recent developments on SNA problems in the sequel. The privacy preservation with SNA is also surveyed. In the end, research challenges and future directions are discussed to suggest researchers a starting point for their research.

NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization

The Network Makeup Artist (NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g., Gene Ontology, Pathway enrichment, community detection, or clustering results) can be uploaded and visualized in a network, either as colored pie-chart nodes or as color-filled areas in a 2D/3D Venn-diagram-like style. In the case where no annotation exists, algorithms for automated community detection are offered. Users can adjust the network views using standard layout algorithms or allow NORMA to slightly modify them for visually better group separation. Once a network view is set, users can interactively select and highlight any group of interest in order to generate publication-ready figures. Briefly, with NORMA, users can encode three types of information simultaneously. These are 1) the network, 2) the communities or annotations of interest, and 3) node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at http://norma.pavlopouloslab.info, whereas the code is available at https://github.com/PavlopoulosLab/NORMA.

Identification of Two Exosomal miRNAs in Circulating Blood of Cancer Patients by Using Integrative Transcriptome and Network Analysis

Exosomes carry molecules of great biological and clinical interest, such as miRNAs. The contents of exosomes vary between healthy controls and cancer patients. Therefore, miRNAs and other molecules transported in exosomes are considered a potential source of diagnostic and prognostic biomarkers in cancer. Many miRNAs have been detected in recent years. Consequently, a substantial amount of miRNA-related data comparing patients and healthy individuals is available, which contributes to a better understanding of the initiation, development, malignancy, and metastasis of cancer using non-invasive sampling procedures. However, a re-analysis of available ncRNA data is rare. This study used available data about miRNAs in exosomes comparing healthy individuals and cancer patients to identify possible global changes related to the presence of cancer. A robust transcriptomic analysis identified two common miRNAs (miR-495-3p and miR-543) deregulated in five cancer datasets. They had already been implicated in different cancers but not reported in exosomes circulating in blood. The study also examined their target genes and the implications of these genes for functional processes.

Multiscale and Extended Retrieval of Associative Memory Structures in a Cortical Model of Local-Global Inhibition Balance

Inhibitory neurons take on many forms and functions. How this diversity contributes to memory function is not completely known. Previous formal studies indicate inhibition differentiated by local and global connectivity in associative memory networks functions to rescale the level of retrieval of excitatory assemblies. However, such studies lack biological details such as a distinction between types of neurons (excitatory and inhibitory), unrealistic connection schemas, and nonsparse assemblies. In this study, we present a rate-based cortical model where neurons are distinguished (as excitatory, local inhibitory, or global inhibitory), connected more realistically, and where memory items correspond to sparse excitatory assemblies. We use this model to study how local-global inhibition balance can alter memory retrieval in associative memory structures, including naturalistic and artificial structures. Experimental studies have reported inhibitory neurons and their subtypes uniquely respond to specific stimuli and can form sophisticated, joint excitatory-inhibitory assemblies. Our model suggests such joint assemblies, as well as a distribution and rebalancing of overall inhibition between two inhibitory subpopulations, one connected to excitatory assemblies locally and the other connected globally, can quadruple the range of retrieval across related memories. We identify a possible functional role for local-global inhibitory balance to, in the context of choice or preference of relationships, permit and maintain a broader range of memory items when local inhibition is dominant and conversely consolidate and strengthen a smaller range of memory items when global inhibition is dominant. This model, while still theoretical, therefore highlights a potentially biologically-plausible and behaviorally-useful function of inhibitory diversity in memory.

A Robust Algorithm Based on Link Label Propagation for Identifying Functional Modules From Protein-Protein Interaction Networks

Identifying functional modules in protein-protein interaction (PPI) networks elucidates cellular organization and mechanism. Various methods have been proposed to identify the functional modules in PPI networks, but most of these methods do not consider the noisy links in PPI networks. They achieve a competitive performance on the PPI networks without noisy links, but the performance of these methods considerably deteriorates in the noisy PPI networks. Furthermore, the noisy links are inevitable in the PPI networks. In this paper, we propose a novel link-driven label propagation algorithm (LLPA) to identify functional modules in PPI networks. The LLPA first find link clusters in PPI networks, and then the functional modules are identified from the link clusters. Two strategies aimed to ensure the robustness of LLPA are proposed. One strategy involves the proposed LLPA updating the link labels in accordance with the designed weight of the link, which can reduce the incidence of noisy links. The other strategy involves the filtration of some noisy labels from the link clusters to further reduce the influence of noisy links. The performance evaluation on three real PPI networks shows that LLPA outperforms other eight state-of-the-art detection algorithms in terms of accuracy and robustness.

Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a leading cause of death in adults that may have origins in early lung development. It is a complex disease, influenced by multiple factors including genetic variants and environmental factors. Maternal smoking during pregnancy may influence the risk for diseases during adulthood, potentially through epigenetic modifications including methylation.

METHODS

In this work, we explore the fetal origins of COPD by utilizing lung DNA methylation marks associated with in utero smoke (IUS) exposure, and evaluate the network relationships between methylomic and transcriptomic signatures associated with adult lung tissue from former smokers with and without COPD. To identify potential pathobiological mechanisms that may link fetal lung, smoke exposure and adult lung disease, we study the interactions (physical and functional) of identified genes using protein-protein interaction networks.

RESULTS

We build IUS-exposure and COPD modules, which identify connected subnetworks linking fetal lung smoke exposure to adult COPD. Studying the relationships and connectivity among the different modules for fetal smoke exposure and adult COPD, we identify enriched pathways, including the AGE-RAGE and focal adhesion pathways.

CONCLUSIONS

The modules identified in our analysis add new and potentially important insights to understanding the early life molecular perturbations related to the pathogenesis of COPD. We identify AGE-RAGE and focal adhesion as two biologically plausible pathways that may reveal lung developmental contributions to COPD. We were not only able to identify meaningful modules but were also able to study interconnections between smoke exposure and lung disease, augmenting our knowledge about the fetal origins of COPD.

Brexit and bots: characterizing the behaviour of automated accounts on Twitter during the UK election

Online Social Networks (OSNs) offer new means for political communications that have quickly begun to play crucial roles in political campaigns, due to their pervasiveness and communication speed. However, the OSN environment is quite slippery and hides potential risks: many studies presented evidence about the presence of d/misinformation campaigns and malicious activities by genuine or automated users, putting at severe risk the efficiency of online and offline political campaigns. This phenomenon is particularly evident during crucial political events, as political elections. In the present paper, we provide a comprehensive description of the networks of interactions among users and bots during the UK elections of 2019. In particular, we focus on the polarised discussion about Brexit on Twitter, analysing a data set made of more than 10 millions tweets posted for over a month. We found that the presence of automated accounts infected the debate particularly in the days before the UK national elections, in which we find a steep increase of bots in the discussion; in the days after the election day, their incidence returned to values similar to the ones observed few weeks before the elections. On the other hand, we found that the number of suspended users (i.e. accounts that were removed by the platform for some violation of the Twitter policy) remained constant until the election day, after which it reached significantly higher values. Remarkably, after the TV debate between Boris Johnson and Jeremy Corbyn, we observed the injection of a large number of novel bots whose behaviour is markedly different from that of pre-existing ones. Finally, we explored the bots' political orientation, finding that their activity is spread across the whole political spectrum, although in different proportions, and we studied the different usage of hashtags and URLs by automated accounts and suspended users, targeting the formation of common narratives in different sides of the debate.

Community Detection Based on Node Influence and Similarity of Nodes

Community detection is a fundamental topic in network science, with a variety of applications. However, there are still fundamental questions about how to detect more realistic network community structures. To address this problem and considering the structure of a network, we propose an agglomerative community detection algorithm, which is based on node influence and the similarity of nodes. The proposed algorithm consists of three essential steps: identifying the central node based on node influence, selecting a candidate neighbor to expand the community based on the similarity of nodes, and merging the small community based on the similarity of communities. The performance and effectiveness of the proposed algorithm were tested on real and synthetic networks, and they were further evaluated through modularity and NMI anlaysis. The experimental results show that the proposed algorithm is effective in community detection and it is quite comparable to existing classic methods.

Assessing the impact of the density and sparsity of the network on community detection using a Gaussian mixture random partition graph generator

Identification of sub-networks within a network is essential to understand the functionality of a network. This process is called as ’Community detection’. There are various existing community detection algorithms, and the performance of these algorithms can be varied based on the network structure. In this paper, we introduce a novel random graph generator using a mixture of Gaussian distributions. The community sizes of the generated network depend on the given Gaussian distributions. We then develop simulation studies to understand the impact of density and sparsity of the network on community detection. We use Infomap, Label propagation, Spinglass, and Louvain algorithms to detect communities. The similarity between true communities and detected communities is evaluated using Adjusted Rand Index, Adjusted Mutual Information, and Normalized Mutual Information similarity scores. We also develop a method to generate heatmaps to compare those similarity score values. The results indicate that the Louvain algorithm has the highest capacity to detect perfect communities while Label Propagation has the lowest capacity

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the HiCzin normalization method and the Leiden clustering algorithm and includes the spurious contact detection into binning pipelines for the first time. HiCBin is validated on one synthetic and two real metagenomic samples and is shown to outperform the existing Hi-C-based binning methods. HiCBin is available at https://github.com/dyxstat/HiCBin .

Selecting Graph Metrics with Ecological Significance for Deepening Landscape Characterization: Review and Applications

The usual approaches to describing and understanding ecological processes in a landscape use patch-mosaic models based on traditional landscape metrics. However, they do not consider that many of these processes cannot be observed without considering the multiple interactions between different land-use patches in the landscape. The objective of this research was to provide a synthetic overview of graph metrics that characterize landscapes based on patch-mosaic models and to analyze the ecological meaning of the metrics to propose a relevant selection explaining biodiversity patterns and ecological processes. First, we conducted a literature review of graph metrics applied in ecology. Second, a case study was used to explore the behavior of a group of selected graph metrics in actual differentiated landscapes located in a long-term socioecological research site in Brittany, France. Thirteen landscape-scale metrics and 10 local-scale metrics with ecological significance were analyzed. Metrics were grouped for landscape-scale and local-scale analysis. Many of the metrics were able to identify differences between the landscapes studied. Lastly, we discuss how graph metrics offer a new perspective for landscape analysis, describe the main characteristics related to their calculation and the type of information provided, and discuss their potential applications in different ecological contexts.

Geographical network model for COVID-19 spread among dynamic epidemic regions

Pandemic due to SARS-CoV-2 (COVID-19) has affected to world in several aspects: high number of confirmed cases, high number of deaths, low economic growth, among others. Understanding of spatio-temporal dynamics of the virus is helpful and necessary for decision making, for instance to decide where, whether and how, non-pharmaceutical intervention policies are to be applied. This point has not been properly addressed in literature since typical strategies do not consider marked differences on the epidemic spread across country or large territory. Those strategies assume similarities and apply similar interventions instead. This work is focused on posing a methodology where spatio-temporal epidemic dynamics is captured by means of dividing a territory in time-varying epidemic regions, according to geographical closeness and infection level. In addition, a novel Lagrangian-SEIR-based model is posed for describing the dynamic within and between those regions. The capabilities of this methodology for identifying local outbreaks and reproducing the epidemic curve are discussed for the case of COVID-19 epidemic in Jalisco state (Mexico). The contagions from July 31, 2020 to March 31, 2021 are analyzed, with monthly adjustments, and the estimates obtained at the level of the epidemic regions present satisfactory results since Relative Root Mean Squared Error RRMSE is below 15% in most of regions, and at the level of the whole state outstanding with RRMSE below 5%.

Gap-com: general model selection criterion for sparse undirected gene networks with nontrivial community structure

We introduce a new model selection criterion for sparse complex gene network modeling where gene co-expression relationships are estimated from data. This is a novel formulation of the gap statistic and it can be used for the optimal choice of a regularization parameter in graphical models. Our criterion favors gene network structure which differs from a trivial gene interaction structure obtained totally at random. We call the criterion the gap-com statistic (gap community statistic). The idea of the gap-com statistic is to examine the difference between the observed and the expected counts of communities (clusters) where the expected counts are evaluated using either data permutations or reference graph (the Erdős-Rényi graph) resampling. The latter represents a trivial gene network structure determined by chance. We put emphasis on complex network inference because the structure of gene networks is usually nontrivial. For example, some of the genes can be clustered together or some genes can be hub genes. We evaluate the performance of the gap-com statistic in graphical model selection and compare its performance to some existing methods using simulated and real biological data examples.

#fridaysforfuture – What does Instagram tell us about a social movement?

Understanding social movement structures is important for political decision-makers to enable them to recognise the various motivating factors behind these movements. The Fridays for Future movement characterises a political group that has a majority of young people, frequently using social media to organise actions. By conducting a social network analysis on hashtags, this study contributes to the understanding of the global Fridays for Future movement. Particularly, we focus on the use and connection of hashtags on Instagram. We collected 59,112 posts tagged with #fridaysforfuture and analysed 91,172 hashtags used therein. Subsequently, the 140 most used hashtags were divided into 11 clusters, which provide not only information about the organisation of the social movement via social media, but also insights into lifestyle-related aspects. The clusters include the topics: climate; nutrition, lifestyle and health; memes; cycling; art; sustainable consumption and the Earth Day. The article shows that the motives of the Fridays for Future movement are broad. We can demonstrate that Fridays for Future is connected to other social movements and gain insights into the everyday life of the Fridays for Future stakeholders.

Semi-Local Integration Measure of Node Importance

Numerous centrality measures have been introduced as tools to determine the importance of nodes in complex networks, reflecting various network properties, including connectivity, survivability, and robustness. In this paper, we introduce Semi-Local Integration (SLI), a node centrality measure for undirected and weighted graphs that takes into account the coherence of the locally connected subnetwork and evaluates the integration of nodes within their neighbourhood. We illustrate SLI node importance differentiation among nodes in lexical networks and demonstrate its potential in natural language processing (NLP). In the NLP task of sense identification and sense structure analysis, the SLI centrality measure evaluates node integration and provides the necessary local resolution by differentiating the importance of nodes to a greater extent than standard centrality measures. This provides the relevant topological information about different subnetworks based on relatively local information, revealing the more complex sense structure. In addition, we show how the SLI measure can improve the results of sentiment analysis. The SLI measure has the potential to be used in various types of complex networks in different research areas.

Generalised popularity-similarity optimisation model for growing hyperbolic networks beyond two dimensions

Hyperbolic network models have gained considerable attention in recent years, mainly due to their capability of explaining many peculiar features of real-world networks. One of the most widely known models of this type is the popularity-similarity optimisation (PSO) model, working in the native disk representation of the two-dimensional hyperbolic space and generating networks with small-world property, scale-free degree distribution, high clustering and strong community structure at the same time. With the motivation of better understanding hyperbolic random graphs, we hereby introduce the dPSO model, a generalisation of the PSO model to any arbitrary integer dimension [Formula: see text]. The analysis of the obtained networks shows that their major structural properties can be affected by the dimension of the underlying hyperbolic space in a non-trivial way. Our extended framework is not only interesting from a theoretical point of view but can also serve as a starting point for the generalisation of already existing two-dimensional hyperbolic embedding techniques.

Synwalk: community detection via random walk modelling

Complex systems, abstractly represented as networks, are ubiquitous in everyday life. Analyzing and understanding these systems requires, among others, tools for community detection. As no single best community detection algorithm can exist, robustness across a wide variety of problem settings is desirable. In this work, we present Synwalk, a random walk-based community detection method. Synwalk builds upon a solid theoretical basis and detects communities by synthesizing the random walk induced by the given network from a class of candidate random walks. We thoroughly validate the effectiveness of our approach on synthetic and empirical networks, respectively, and compare Synwalk’s performance with the performance of Infomap and Walktrap (also random walk-based), Louvain (based on modularity maximization) and stochastic block model inference. Our results indicate that Synwalk performs robustly on networks with varying mixing parameters and degree distributions. We outperform Infomap on networks with high mixing parameter, and Infomap and Walktrap on networks with many small communities and low average degree. Our work has a potential to inspire further development of community detection via synthesis of random walks and we provide concrete ideas for future research.

Protein complexes detection based on node local properties and gene expression in PPI weighted networks

BACKGROUND

Identifying protein complexes from protein-protein interaction (PPI) networks is a crucial task, and many related algorithms have been developed. Most algorithms usually employ direct neighbors of nodes and ignore resource allocation and second-order neighbors. The effective use of such information is crucial to protein complex detection.

RESULT

Based on this observation, we propose a new way by combining node resource allocation and gene expression information to weight protein network (NRAGE-WPN), in which protein complexes are detected based on core-attachment and second-order neighbors.

CONCLUSIONS

Through comparison with eleven methods in Yeast and Human PPI network, the experimental results demonstrate that this algorithm not only performs better than other methods on 75% in terms of f-measure+, but also can achieve an ideal overall performance in terms of a composite score consisting of five performance measures. This identification method is simple and can accurately identify more complexes.

Network Analysis of Microarray Data

DNA microarrays are widely used to investigate gene expression. Even though the classical analysis of microarray data is based on the study of differentially expressed genes, it is well known that genes do not act individually. Network analysis can be applied to study association patterns of the genes in a biological system. Moreover, it finds wide application in differential coexpression analysis between different systems. Network based coexpression studies have for example been used in (complex) disease gene prioritization, disease subtyping, and patient stratification.In this chapter we provide an overview of the methods and tools used to create networks from microarray data and describe multiple methods on how to analyze a single network or a group of networks. The described methods range from topological metrics, functional group identification to data integration strategies, topological pathway analysis as well as graphical models.

Spatial compartmentalization: A nonlethal predator mechanism to reduce parasite transmission between prey species

Predators can modulate disease transmission within prey populations by influencing prey demography and behavior. Predator-prey dynamics can involve multiple species in heterogeneous landscapes; however, studies of predation on disease transmission rarely consider the role of landscapes or the transmission among diverse prey species (i.e., spillover). We used high-resolution habitat and movement data to model spillover risk of the brainworm parasite (Parelaphostrongylus tenuis) between two prey species [white-tailed deer (Odocoileus virginianus) and moose (Alces alces)], accounting for predator [gray wolf (Canis lupus)] presence and landscape configuration. Results revealed that spring migratory movements of cervid hosts increased parasite spillover risk from deer to moose, an effect tempered by changes in elevation, land cover, and wolf presence. Wolves induced host-species segregation, a nonlethal mechanism that modulated disease emergence by reducing spatiotemporal overlap between infected and susceptible prey, showing that wildlife disease dynamics may change with landscape disturbance and the loss of large carnivores.

Community detection in complex network by network embedding and density clustering

 In a complex network system, the structure of the network is an extremely important element for the analysis of the system, and the study of community detection algorithms is key to exploring the structure of the complex network. Traditional community detection algorithms would represent the network using an adjacency matrix based on observations, which may contain redundant information or noise that interferes with the detection results. In this paper, we propose a community detection algorithm based on density clustering. In order to improve the performance of density clustering, we consider an algorithmic framework for learning the continuous representation of network nodes in a low-dimensional space. The network structure is effectively preserved through network embedding, and density clustering is applied in the embedded low-dimensional space to compute the similarity of nodes in the network, which in turn reveals the implied structure in a given network. Experiments show that the algorithm has superior performance compared to other advanced community detection algorithms for real-world networks in multiple domains as well as synthetic networks, especially when the network data chaos is high.

Finding Central Vertices and Community Structure via Extended Density Peaks-Based Clustering

Community detection is a significant research field of social networks, and modularity is a common method to measure the division of communities in social networks. Many classical algorithms obtain community partition by improving the modularity of the whole network. However, there is still a challenge in community division, which is that the traditional modularity optimization is difficult to avoid resolution limits. To a certain extent, the simple pursuit of improving modularity will cause the division to deviate from the real community structure. To overcome these defects, with the help of clustering ideas, we proposed a method to filter community centers by the relative connection coefficient between vertices, and we analyzed the community structure accordingly. We discuss how to define the relative connection coefficient between vertices, how to select the community centers, and how to divide the remaining vertices. Experiments on both real and synthetic networks demonstrated that our algorithm is effective compared with the state-of-the-art methods.

From heterogeneous morphogenetic fields to homogeneous regions as a step towards understanding complex tissue dynamics

Within developing tissues, cell proliferation, cell motility and other cell behaviors vary spatially, and this variability gives a complexity to the morphogenesis. Recently, novel formalisms have been developed to quantify tissue deformation and underlying cellular processes. A major challenge for the study of morphogenesis now is to objectively define tissue sub-regions exhibiting different dynamics. Here, we propose a method to automatically divide a tissue into regions where the local deformation rate is homogeneous. This was achieved by several steps including image segmentation, clustering and region boundary smoothing. We illustrate the use of the pipeline using a large dataset obtained during the metamorphosis of the Drosophila pupal notum. We also adapt it to determine regions in which the time evolution of the local deformation rate is homogeneous. Finally, we generalize its use to find homogeneous regions for cellular processes such as cell division, cell rearrangement, or cell size and shape changes. We also illustrate it on wing blade morphogenesis. This pipeline will contribute substantially to the analysis of complex tissue shaping, and the biochemical and biomechanical regulations driving tissue morphogenesis.

Revealing the component structure of the world air transportation network

Air transportation plays an essential role in the global economy. Therefore, there is a great deal of work to understand better the complex network formed by the links between the origins and destinations of flights. Some investigations show that the world air transportation network exhibits a community and a core-periphery structure. Although precious, these representations do not distinguish the inter-regional (global) web of connections from the regional (local) one. Therefore, we propose a new mesoscopic model called the component structure that decomposes the network into local and global components. Local components are the dense areas of the network, and global components are the nodes and links bridging the local components. As a case study, we consider the unweighted and undirected world air transportation network. Experiments show that it contains seven large local components and multiple small ones spatially well-defined. Moreover, it has a main global component covering the world. We perform an extensive comparative analysis of the structure of the components. Results demonstrate the non-homogeneous nature of the world air transportation network. The local components structure highlights regional differences, and the global component organization captures the efficiency of inter-regional travel. Centrality analysis of the components allows distinguishing airports centered on regional destinations from those focused on inter-regional exchanges. Core analysis is more accurate in the components than in the whole network where Europe dominates, blurring the rest of the world. Besides the world air transportation network, this paper demonstrates the potential of the component decomposition for modeling and analyzing the mesoscale structure of networks.

Detection of Hidden Communities in Twitter Discussions of Varying Volumes

The community-based structure of communication on social networking sites has long been a focus of scholarly attention. However, the problem of discovery and description of hidden communities, including defining the proper level of user aggregation, remains an important problem not yet resolved. Studies of online communities have clear social implications, as they allow for assessment of preference-based user grouping and the detection of socially hazardous groups. The aim of this study is to comparatively assess the algorithms that effectively analyze large user networks and extract hidden user communities from them. The results we have obtained show the most suitable algorithms for Twitter datasets of different volumes (dozen thousands, hundred thousands, and millions of tweets). We show that the Infomap and Leiden algorithms provide for the best results overall, and we advise testing a combination of these algorithms for detecting discursive communities based on user traits or views. We also show that the generalized K-means algorithm does not apply to big datasets, while a range of other algorithms tend to prioritize the detection of just one big community instead of many that would mirror the reality better. For isolating overlapping communities, the GANXiS algorithm should be used, while OSLOM is not advised.