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

Diagnosis of autism spectrum disorder based on functional brain networks and machine learning

Autism is a multifaceted neurodevelopmental condition whose accurate diagnosis may be challenging because the associated symptoms and severity vary considerably. The wrong diagnosis can affect families and the educational system, raising the risk of depression, eating disorders, and self-harm. Recently, many works have proposed new methods for the diagnosis of autism based on machine learning and brain data. However, these works focus on only one pairwise statistical metric, ignoring the brain network organization. In this paper, we propose a method for the automatic diagnosis of autism based on functional brain imaging data recorded from 500 subjects, where 242 present autism spectrum disorder considering the regions of interest throughout Bootstrap Analysis of Stable Cluster map. Our method can distinguish the control group from autism spectrum disorder patients with high accuracy. Indeed the best performance provides an AUC near 1.0, which is higher than that found in the literature. We verify that the left ventral posterior cingulate cortex region is less connected to an area in the cerebellum of patients with this neurodevelopment disorder, which agrees with previous studies. The functional brain networks of autism spectrum disorder patients show more segregation, less distribution of information across the network, and less connectivity compared to the control cases. Our workflow provides medical interpretability and can be used on other fMRI and EEG data, including small data sets.

Detecting local communities in complex network via the optimization of interaction relationship between node and community

The goal of local community detection algorithms is to explore the optimal community with a reference to a given node. Such algorithms typically include two primary processes: seed selection and community expansion. This study develops and tests a novel local community detection algorithm called OIRLCD that is based on the optimization of interaction relationships between nodes and the community. First, we introduce an improved seed selection method to solve the seed deviation problem. Second, this study uses a series of similarity indices to measure the interaction relationship between nodes and community. Third, this study uses a series of algorithms based on different similarity indices, and designs experiments to reveal the role of the similarity index in algorithms based on relationship optimization. The proposed algorithm was compared with five existing local community algorithms in both real-world networks and artificial networks. Experimental results show that the optimization of interaction relationship algorithms based on node similarity can detect communities accurately and efficiently. In addition, a good similarity index can highlight the advantages of the proposed algorithm based on interaction optimization.

LazyFox: fast and parallelized overlapping community detection in large graphs

The detection of communities in graph datasets provides insight about a graph's underlying structure and is an important tool for various domains such as social sciences, marketing, traffic forecast, and drug discovery. While most existing algorithms provide fast approaches for community detection, their results usually contain strictly separated communities. However, most datasets would semantically allow for or even require overlapping communities that can only be determined at much higher computational cost. We build on an efficient algorithm, Fox, that detects such overlapping communities. Fox measures the closeness of a node to a community by approximating the count of triangles which that node forms with that community. We propose LazyFox, a multi-threaded adaptation of the Fox algorithm, which provides even faster detection without an impact on community quality. This allows for the analyses of significantly larger and more complex datasets. LazyFox enables overlapping community detection on complex graph datasets with millions of nodes and billions of edges in days instead of weeks. As part of this work, LazyFox's implementation was published and is available as a tool under an MIT licence at https://github.com/TimGarrels/LazyFox.

clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape

BACKGROUND

Since the initial publication of clusterMaker, the need for tools to analyze large biological datasets has only increased. New datasets are significantly larger than a decade ago, and new experimental techniques such as single-cell transcriptomics continue to drive the need for clustering or classification techniques to focus on portions of datasets of interest. While many libraries and packages exist that implement various algorithms, there remains the need for clustering packages that are easy to use, integrated with visualization of the results, and integrated with other commonly used tools for biological data analysis. clusterMaker2 has added several new algorithms, including two entirely new categories of analyses: node ranking and dimensionality reduction. Furthermore, many of the new algorithms have been implemented using the Cytoscape jobs API, which provides a mechanism for executing remote jobs from within Cytoscape. Together, these advances facilitate meaningful analyses of modern biological datasets despite their ever-increasing size and complexity.

RESULTS

The use of clusterMaker2 is exemplified by reanalyzing the yeast heat shock expression experiment that was included in our original paper; however, here we explored this dataset in significantly more detail. Combining this dataset with the yeast protein-protein interaction network from STRING, we were able to perform a variety of analyses and visualizations from within clusterMaker2, including Leiden clustering to break the entire network into smaller clusters, hierarchical clustering to look at the overall expression dataset, dimensionality reduction using UMAP to find correlations between our hierarchical visualization and the UMAP plot, fuzzy clustering, and cluster ranking. Using these techniques, we were able to explore the highest-ranking cluster and determine that it represents a strong contender for proteins working together in response to heat shock. We found a series of clusters that, when re-explored as fuzzy clusters, provide a better presentation of mitochondrial processes.

CONCLUSIONS

clusterMaker2 represents a significant advance over the previously published version, and most importantly, provides an easy-to-use tool to perform clustering and to visualize clusters within the Cytoscape network context. The new algorithms should be welcome to the large population of Cytoscape users, particularly the new dimensionality reduction and fuzzy clustering techniques.

Semi-supervised sentiment clustering on natural language texts

In this paper, we propose a semi-supervised method to cluster unstructured textual data called semi-supervised sentiment clustering on natural language texts. The aim is to identify clusters homogeneous with respect to the overall sentiment of the texts analyzed. The method combines different techniques and methodologies: Sentiment Analysis, Threshold-based Naïve Bayes classifier, and Network-based Semi-supervised Clustering. It involves different steps. In the first step, the unstructured text is transformed into structured text, and it is categorized into positive or negative classes using a sentiment analysis algorithm. In the second step, the Threshold-based Naïve Bayes classifier is applied to identify the overall sentiment of the texts and to define a specific sentiment value for the topics. In the last step, Network-based Semi-supervised Clustering is applied to partition the instances into disjoint groups. The proposed algorithm is tested on a collection of reviews written by customers on Booking.com. The results have highlighted the capacity of the proposed algorithm to identify clusters that are distinct, non-overlapped, and homogeneous with respect to the overall sentiment. Results are also easily interpretable thanks to the network representation of the instances that helps to understand the relationship between them.

MultiSimNeNc: A network representation learning-based module identification method by network embedding and clustering

Accurate identification of gene modules based on biological networks is an effective approach to understanding gene patterns of cancer from a module-level perspective. However, most graph clustering algorithms just consider low-order topological connectivity, which limits their accuracy in gene module identification. In this study, we propose a novel network-based method, MultiSimNeNc, to identify modules in various types of networks by integrating network representation learning (NRL) and clustering algorithms. In this method, we first obtain the multi-order similarity of the network using graph convolution (GC). Then, we aggregate the multi-order similarity to characterize the network structure and use non-negative matrix factorization (NMF) to achieve low-dimensional node characterization. Finally, we predict the number of modules based on the bayesian information criterion (BIC) and use the gaussian mixture model (GMM) to identify modules. To testify to the efficacy of MultiSimeNc in module identification, we apply this method to two types of biological networks and six benchmark networks, where the biological networks are constructed based on the fusion of multi-omics data from glioblastoma (GBM). The analysis shows that MultiSimNeNc outperforms several state-of-the-art module identification algorithms in identification accuracy, which is an effective method for understanding biomolecular mechanisms of pathogenesis from a module-level perspective.

Stochastic Processes Drive the Assembly and Metabolite Profiles of Keystone Taxa during Chinese Strong-Flavor Baijiu Fermentation

Multispecies communities participate in the fermentation of Chinese strong-flavor Baijiu (CSFB), and the metabolic activity of the dominant and keystone taxa is key to the flavor quality of the final product. However, their roles in metabolic function and assembly processes are still not fully understood. Here, we identified the variations in the metabolic profiles of dominant and keystone taxa and characterized their community assembly using 16S rRNA and internal transcribed spacer (ITS) gene amplicon and metatranscriptome sequencing. We demonstrate that CSFB fermentations with distinct metabolic profiles display distinct microbial community compositions and microbial network complexities and stabilities. We then identified the dominant taxa (Limosilactobacillus fermentum, Kazachstania africana, Saccharomyces cerevisiae, and Pichia kudriavzevii) and the keystone ecological cluster (module 0, affiliated mainly with Thermoascus aurantiacus, Weissella confusa, and Aspergillus amstelodami) that cause changes in metabolic profiles. Moreover, we highlight that the alpha diversity of keystone taxa contributes to changes in metabolic profiles, whereas dominant taxa exert their influence on metabolic profiles by virtue of their relative abundance. Additionally, our results based on the normalized stochasticity ratio (NST) index and the neutral model revealed that stochastic and deterministic processes together shaped CSFB microbial community assemblies. Stochasticity and environmental selection structure the keystone and dominant taxa differently. This study provides new insights into understanding the relationships between microbial communities and their metabolic functions. IMPORTANCE From an ecological perspective, keystone taxa in microbial networks with high connectivity have crucial roles in community assembly and function. We used CSFB fermentation as a model system to study the ecological functions of dominant and keystone taxa at the metabolic level. We show that both dominant taxa (e.g., those taxa that have the highest relative abundances) and keystone taxa (e.g., those taxa with the most cooccurrences) affected the resulting flavor profiles. Moreover, our findings established that stochastic processes were dominant in shaping the communities of keystone taxa during CSFB fermentation. This result is striking as it suggests that although the controlled conditions in the fermentor can determine the dominant taxa, the uncontrolled rare keystone taxa in the microbial community can alter the resulting flavor profiles. This important insight is vital for the development of potential manipulation strategies to improve the quality of CSFB through the regulation of keystone species.

Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.

HNRNPA2B1 as a potential therapeutic target for thymic epithelial tumor recurrence: An integrative network analysis

Thymic epithelial tumors (TETs) are rare malignant tumors, and the molecular mechanisms of both primary and recurrent TETs are poorly understood. Here we established comprehensive proteomic signatures of 15 tumors (5 recurrent and 10 non-recurrent) and 15 pair wised tumor adjacent normal tissues. We then proposed an integrative network approach for studying the proteomics data by constructing protein-protein interaction networks based on differentially expressed proteins and a machine learning-based score, followed by network modular analysis, functional enrichment annotation and shortest path inference analysis. Network modular analysis revealed that primary and recurrent TETs shared certain common molecular mechanisms, including a spliceosome module consisting of RNA splicing and RNA processing, but the recurrent TET was specifically related to the ribosome pathway. Applying the shortest path inference to the collected seed gene module identified that the ribonucleoprotein hnRNPA2B1 probably serves as a potential target for recurrent TET therapy. The drug repositioning combined molecular dynamics simulations suggested that the compound ergotamine could potentially act as a repurposing drug to treat recurrent TETs by targeting hnRNPA2B1. Our study demonstrates the value of integrative network analysis to understand proteotype robustness and its relationships with genotype, and provides hits for further research on cancer therapeutics.

Composition, structure and robustness of Lichen guilds

Symbiosis is a major engine of evolutionary innovation underlying many extant complex organisms. Lichens are a paradigmatic example that offers a unique perspective on the role of symbiosis in ecological success and evolutionary diversification. Lichen studies have produced a wealth of information regarding the importance of symbiosis, but they frequently focus on a few species, limiting our understanding of large-scale phenomena such as guilds. Guilds are groupings of lichens that assist each other's proliferation and are intimately linked by a shared set of photobionts, constituting an extensive network of relationships. To characterize the network of lichen symbionts, we used a large data set ([Formula: see text] publications) of natural photobiont-mycobiont associations. The entire lichen network was found to be modular, but this organization does not directly match taxonomic information in the data set, prompting a reconsideration of lichen guild structure and composition. The multiscale nature of this network reveals that the major lichen guilds are better represented as clusters with several substructures rather than as monolithic communities. Heterogeneous guild structure fosters robustness, with keystone species functioning as bridges between guilds and whose extinction would endanger global stability.

Large network community detection by fast label propagation

Many networks exhibit some community structure. There exists a wide variety of approaches to detect communities in networks, each offering different interpretations and associated algorithms. For large networks, there is the additional requirement of speed. In this context, the so-called label propagation algorithm (LPA) was proposed, which runs in near-linear time. In partitions uncovered by LPA, each node is ensured to have most links to its assigned community. We here propose a fast variant of LPA (FLPA) that is based on processing a queue of nodes whose neighbourhood recently changed. We test FLPA exhaustively on benchmark networks and empirical networks, finding that it can run up to 700 times faster than LPA. In partitions found by FLPA, we prove that each node is again guaranteed to have most links to its assigned community. Our results show that FLPA is generally preferable to LPA.

A Four-Stage Algorithm for Community Detection Based on Label Propagation and Game Theory in Social Networks

Over the years, detecting stable communities in a complex network has been a major challenge in network science. The global and local structures help to detect communities from different perspectives. However, previous methods based on them suffer from high complexity and fall into local optimum, respectively. The Four-Stage Algorithm (FSA) is proposed to reduce these issues and to allocate nodes to stable communities. Balancing global and local information, as well as accuracy and time complexity, while ensuring the allocation of nodes to stable communities, are the fundamental goals of this research. The Four-Stage Algorithm (FSA) is described and demonstrated using four real-world data with ground truth and three real networks without ground truth. In addition, it is evaluated with the results of seven community detection methods: Three-stage algorithm (TS), Louvain, Infomap, Fastgreedy, Walktrap, Eigenvector, and Label propagation (LPA). Experimental results on seven real network data sets show the effectiveness of our proposed approach and confirm that it is sufficiently capable of identifying those communities that are more desirable. The experimental results confirm that the proposed method can detect more stable and assured communities. For future work, deep learning methods can also be used to extract semantic content features that are more beneficial to investigating networks.

Cohesion and segregation in the value migration network: Evidence from network partitioning based on sector classification and clustering

Cluster structure detection of the network is a basic problem of complex network analysis. This study investigates the structure of the value migration network using data from 499 stocks listed in the S&P500 as of the end of 2021. An examination is carried out whether the process of value migration creates a cluster structure in the network of companies according to economic activity. Specifically, the cohesion and segregation of the extracted modules in the network division according to (i) sector classification, (ii) community division, and (iii) network clustering decomposition are assessed. The results of this study show that the sector classification of the value migration network has a non-cohesive structure, which means that the flow of value in the financial market occurs between companies from various industries. Moreover, the divisions of the value migration network based on community detection and clustering algorithm are characterized by intra-cluster similarity between the vertices and have a strong community structure. The structure of the network division into modules corresponding to the classification of economic sectors differs significantly from the partition based on the algorithms applied.

Application of machine learning and complex network measures to an EEG dataset from ayahuasca experiments

Ayahuasca is a blend of Amazonian plants that has been used for traditional medicine by the inhabitants of this region for hundreds of years. Furthermore, this plant has been demonstrated to be a viable therapy for a variety of neurological and mental diseases. EEG experiments have found specific brain regions that changed significantly due to ayahuasca. Here, we used an EEG dataset to investigate the ability to automatically detect changes in brain activity using machine learning and complex networks. Machine learning was applied at three different levels of data abstraction: (A) the raw EEG time series, (B) the correlation of the EEG time series, and (C) the complex network measures calculated from (B). Further, at the abstraction level of (C), we developed new measures of complex networks relating to community detection. As a result, the machine learning method was able to automatically detect changes in brain activity, with case (B) showing the highest accuracy (92%), followed by (A) (88%) and (C) (83%), indicating that connectivity changes between brain regions are more important for the detection of ayahuasca. The most activated areas were the frontal and temporal lobe, which is consistent with the literature. F3 and PO4 were the most important brain connections, a significant new discovery for psychedelic literature. This connection may point to a cognitive process akin to face recognition in individuals during ayahuasca-mediated visual hallucinations. Furthermore, closeness centrality and assortativity were the most important complex network measures. These two measures are also associated with diseases such as Alzheimer's disease, indicating a possible therapeutic mechanism. Moreover, the new measures were crucial to the predictive model and suggested larger brain communities associated with the use of ayahuasca. This suggests that the dissemination of information in functional brain networks is slower when this drug is present. Overall, our methodology was able to automatically detect changes in brain activity during ayahuasca consumption and interpret how these psychedelics alter brain networks, as well as provide insights into their mechanisms of action.

An approach to prevent weight manipulation by minimum adjustment and maximum entropy method in social network group decision making

In social network group decision making (SN-GDM) problem, subgroup weights are mostly unknown, many approaches have been proposed to determine the subgroup weights. However, most of these methods ignore the weight manipulation behavior of subgroups. Some studies indicated that weight manipulation behavior hinders consensus efficiency. To deal with this issue, this paper proposes a theoretical framework to prevent weight manipulation in SN-GDM. Firstly, a community detection based method is used to cluster the large group. The power relations of subgroups are measured by the power index (PI), which depends on the subgroups size and cohesion. Then, a minimum adjustment feedback model with maximum entropy is proposed to prevent subgroups' manipulation behavior. The minimum adjustment rule aims for 'efficiency' while the maximum entropy rule aims for 'justice'. The experimental results show that the proposed model can guarantee the rationality of weight distribution to reach consensus efficiently, which is achieved by maintaining a balance between 'efficiency' and 'justice' in the mechanism of assigning weights. Finally, the detailed numerical and simulation analyses are carried out to verify the validity of the proposed method.

Towards explainable community finding

The detection of communities of nodes is an important task in understanding the structure of networks. Multiple approaches have been developed to tackle this problem, many of which are in common usage in real-world applications, such as in public health networks. However, clear insight into the reasoning behind the community labels produced by these algorithms is rarely provided. Drawing inspiration from the machine learning literature, we aim to provide post-hoc explanations for the outputs of these algorithms using interpretable features of the network. In this paper, we propose a model-agnostic methodology that identifies a set of informative features to help explain the output of a community finding algorithm. We apply it to three well-known algorithms, though the methodology is designed to generalise to new approaches. As well as identifying important features for a post-hoc explanation system, we report on the common features found made by the different algorithms and the differences between the approaches.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s41109-022-00515-6.

Density and node closeness based clustering method for community detection

In a real-world, networked system, the ability to detect communities or clusters has piqued the concern of researchers in a wide range of fields. Many existing methods are simply meant to detect the membership of communities, not the structures of those groups, which is a limitation. We contend that community structures at the local level can also provide valuable insight into their detection. In this study, we developed a simple yet prosperous way of uncovering communities and their cores at the same time while keeping things simple. Essentially, the concept is founded on the theory that the structure of a community may be thought of as a high-density node surrounded by neighbors of minor densities and that community centers are located at a significant distance from one another. We propose a concept termed “community centrality” based on finding motifs to measure the probability of a node becoming the community center in a setting like this and then disseminate multiple, substantial center probabilities all over the network through a node closeness score mechanism. The experimental results show that the proposed method is more efficient than many other already used methods.

Computational systems biology in disease modeling and control, review and perspectives

Omics-based approaches have become increasingly influential in identifying disease mechanisms and drug responses. Considering that diseases and drug responses are co-expressed and regulated in the relevant omics data interactions, the traditional way of grabbing omics data from single isolated layers cannot always obtain valuable inference. Also, drugs have adverse effects that may impair patients, and launching new medicines for diseases is costly. To resolve the above difficulties, systems biology is applied to predict potential molecular interactions by integrating omics data from genomic, proteomic, transcriptional, and metabolic layers. Combined with known drug reactions, the resulting models improve medicines' therapeutical performance by re-purposing the existing drugs and combining drug molecules without off-target effects. Based on the identified computational models, drug administration control laws are designed to balance toxicity and efficacy. This review introduces biomedical applications and analyses of interactions among gene, protein and drug molecules for modeling disease mechanisms and drug responses. The therapeutical performance can be improved by combining the predictive and computational models with drug administration designed by control laws. The challenges are also discussed for its clinical uses in this work.

MHDMF: Prediction of miRNA-disease associations based on Deep Matrix Factorization with Multi-source Graph Convolutional Network

A growing number of works have proved that microRNAs (miRNAs) are a crucial biomarker in diverse bioprocesses affecting various diseases. As a good complement to high-cost wet experiment-based methods, numerous computational prediction methods have sprung up. However, there are still challenges that exist in making effective use of high false-negative associations and multi-source information for finding the potential associations. In this work, we develop an end-to-end computational framework, called MHDMF, which integrates the multi-source information on a heterogeneous network to discover latent disease-miRNA associations. Since high false-negative exist in the miRNA-disease associations, MHDMF utilizes the multi-source Graph Convolutional Network (GCN) to correct the false-negative association by reformulating the miRNA-disease association score matrix. The score matrix reformulation is based on different similarity profiles and known associations between miRNAs, genes, and diseases. Then, MHDMF employs Deep Matrix Factorization (DMF) to predict the miRNA-disease associations based on reformulated miRNA-disease association score matrix. The experimental results show that the proposed framework outperforms highly related comparison methods by a large margin on tasks of miRNA-disease association prediction. Furthermore, case studies suggest that MHDMF could be a convenient and efficient tool and may supply a new way to think about miRNA-disease association prediction.

Community detection in weighted networks using probabilistic generative model

Community detection in networks is a useful tool for detecting the behavioral and inclinations of users to a specific topic or title. Weighted, unweighted, directed, and undirected networks can all be used for detecting communities depending on the network structure and content. The proposed model framework for community detection is based on weighted networks. We use two important and effective concepts in graph analysis. The structural density between nodes is the first concept, and the second is the weight of edges between nodes. The proposed model advantage is using a probabilistic generative model that estimates the latent parameters of the probabilistic model and detecting the community based on the probability of the presence or absence of weighted edge. The output of the proposed model is the intensity of belonging each weighted node to the communities. A relationship between the observation of a pair of nodes in multiple communities and the probability of an edge with a high weight between them, is one of the important outputs that interpret the detected communities by finding relevancy between membership of nodes to communities and edge weight. Experiments are performed on real-world weighted networks and synthetic weighted networks to evaluate the performance and accuracy of the proposed algorithm. The results will show that the proposed algorithm is more density and accurate than other algorithms in weighted community detection.

The Cryptocurrency Market in Transition before and after COVID-19: An Opportunity for Investors?

We analyze the correlation between different assets in the cryptocurrency market throughout different phases, specifically bearish and bullish periods. Taking advantage of a fine-grained dataset comprising 34 historical cryptocurrency price time series collected tick-by-tick on the HitBTC exchange, we observe the changes in interactions among these cryptocurrencies from two aspects: time and level of granularity. Moreover, the investment decisions of investors during turbulent times caused by the COVID-19 pandemic are assessed by looking at the cryptocurrency community structure using various community detection algorithms. We found that finer-grain time series describes clearer the correlations between cryptocurrencies. Notably, a noise and trend removal scheme is applied to the original correlations thanks to the theory of random matrices and the concept of Market Component, which has never been considered in existing studies in quantitative finance. To this end, we recognized that investment decisions of cryptocurrency traders vary between bearish and bullish markets. The results of our work can help scholars, especially investors, better understand the operation of the cryptocurrency market, thereby building up an appropriate investment strategy suitable to the prevailing certain economic situation.

Social media behavior is associated with vaccine hesitancy

Understanding how vaccine hesitancy relates to online behavior is crucial for addressing current and future disease outbreaks. We combined survey data measuring attitudes toward the COVID-19 vaccine with Twitter data in two studies (N 1 = 464 Twitter users, N 2 = 1,600 Twitter users) with preregistered hypotheses to examine how real-world social media behavior is associated with vaccine hesitancy in the United States (US) and the United Kingdom (UK). In Study 1, we found that following the accounts of US Republican politicians or hyper-partisan/low-quality news sites were associated with lower confidence in the COVID-19 vaccine-even when controlling for key demographics such as self-reported political ideology and education. US right-wing influencers (e.g. Candace Owens, Tucker Carlson) had followers with the lowest confidence in the vaccine. Network analysis revealed that participants who were low and high in vaccine confidence separated into two distinct communities (or "echo chambers"), and centrality in the more right-wing community was associated with vaccine hesitancy in the US, but not in the UK. In Study 2, we found that one's likelihood of not getting the vaccine was associated with retweeting and favoriting low-quality news websites on Twitter. Altogether, we show that vaccine hesitancy is associated with following, sharing, and interacting with low-quality information online, as well as centrality within a conservative-leaning online community in the US. These results illustrate the potential challenges of encouraging vaccine uptake in a polarized social media environment.

Application of CCTV Methodology to Analyze COVID-19 Evolution in Italy

Italy was one of the European countries most afflicted by the COVID-19 pandemic. From 2020 to 2022, Italy adopted strong containment measures against the COVID-19 epidemic and then started an important vaccination campaign. Here, we extended previous work by applying the COVID-19 Community Temporal Visualizer (CCTV) methodology to Italian COVID-19 data related to 2020, 2021, and five months of 2022. The aim of this work was to evaluate how Italy reacted to the pandemic in the first two waves of COVID-19, in which only containment measures such as the lockdown had been adopted, in the months following the start of the vaccination campaign, the months with the mildest weather, and the months affected by the new COVID-19 variants. This assessment was conducted by observing the behavior of single regions. CCTV methodology allows us to map the similarities in the behavior of Italian regions on a graph and use a community detection algorithm to visualize and analyze the spatio-temporal evolution of data. The results depict that the communities formed by Italian regions change with respect to the ten data measures and time.

Graph Neural Network Encoding for Community Detection in Attribute Networks

In this article, we first propose a graph neural network encoding method for the multiobjective evolutionary algorithm (MOEA) to handle the community detection problem in complex attribute networks. In the graph neural network encoding method, each edge in an attribute network is associated with a continuous variable. Through nonlinear transformation, a continuous valued vector (i.e., a concatenation of the continuous variables associated with the edges) is transferred to a discrete valued community grouping solution. Further, two objective functions for the single-attribute and multiattribute network are proposed to evaluate the attribute homogeneity of the nodes in communities, respectively. Based on the new encoding method and the two objectives, a MOEA based upon NSGA-II, called continuous encoding MOEA, is developed for the transformed community detection problem with continuous decision variables. Experimental results on single-attribute and multiattribute networks with different types show that the developed algorithm performs significantly better than some well-known evolutionary- and nonevolutionary-based algorithms. The fitness landscape analysis verifies that the transformed community detection problems have smoother landscapes than those of the original problems, which justifies the effectiveness of the proposed graph neural network encoding method.

Contact Tracing Research: A Literature Review Based on Scientific Collaboration Network

Contact tracing is a monitoring process including contact identification, listing, and follow-up, which is a key to slowing down pandemics of infectious diseases, such as COVID-19. In this study, we use the scientific collaboration network technique to explore the evolving history and scientific collaboration patterns of contact tracing. It is observed that the number of articles on the subject remained at a low level before 2020, probably because the practical significance of the contact tracing model was not widely accepted by the academic community. The COVID-19 pandemic has brought an unprecedented research boom to contact tracing, as evidenced by the explosion of the literature after 2020. Tuberculosis, HIV, and other sexually transmitted diseases were common types of diseases studied in contact tracing before 2020. In contrast, research on contact tracing regarding COVID-19 occupies a significantly large proportion after 2000. It is also found from the collaboration networks that academic teams in the field tend to conduct independent research, rather than cross-team collaboration, which is not conducive to knowledge dissemination and information flow.

Bow-tie structures of twitter discursive communities

Bow-tie structures were introduced to describe the World Wide Web (WWW): in the direct network in which the nodes are the websites and the edges are the hyperlinks connecting them, the greatest number of nodes takes part to a bow-tie, i.e. a Weakly Connected Component (WCC) composed of 3 main sectors: IN, OUT and SCC. SCC is the main Strongly Connected Component of WCC, i.e. the greatest subgraph in which each node is reachable by any other one. The IN and OUT sectors are the set of nodes not included in SCC that, respectively, can access and are accessible to nodes in SCC. In the WWW, the greatest part of the websites can be found in the SCC, while the search engines belong to IN and the authorities, as Wikipedia, are in OUT. In the analysis of Twitter debate, the recent literature focused on discursive communities, i.e. clusters of accounts interacting among themselves via retweets. In the present work, we studied discursive communities in 8 different thematic Twitter datasets in various languages. Surprisingly, we observed that almost all discursive communities therein display a bow-tie structure during political or societal debates. Instead, they are absent when the argument of the discussion is different as sport events, as in the case of Euro2020 Turkish and Italian datasets. We furthermore analysed the quality of the content created in the various sectors of the different discursive communities, using the domain annotation from the fact-checking website Newsguard: we observe that, when the discursive community is affected by m/disinformation, the content with the lowest quality is the one produced and shared in SCC and, in particular, a strong incidence of low- or non-reputable messages is present in the flow of retweets between the SCC and the OUT sectors. In this sense, in discursive communities affected by m/disinformation, the greatest part of the accounts has access to a great variety of contents, but whose quality is, in general, quite low; such a situation perfectly describes the phenomenon of infodemic, i.e. the access to "an excessive amount of information about a problem, which makes it difficult to identify a solution", according to WHO.

Emergent entanglement structures and self-similarity in quantum spin chains

We introduce an experimentally accessible network representation for many-body quantum states based on entanglement between all pairs of its constituents. We illustrate the power of this representation by applying it to a paradigmatic spin chain model, the XX model, and showing that it brings to light new phenomena. The analysis of these entanglement networks reveals that the gradual establishment of quasi-long range order is accompanied by a symmetry regarding single-spin concurrence distributions, as well as by instabilities in the network topology. Moreover, we identify the existence of emergent entanglement structures, spatially localized communities enforced by the global symmetry of the system that can be revealed by model-agnostic community detection algorithms. The network representation further unveils the existence of structural classes and a cyclic self-similarity in the state, which we conjecture to be intimately linked to the community structure. Our results demonstrate that the use of tools and concepts from complex network theory enables the discovery, understanding and description of new physical phenomena even in models studied for decades. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Link Pruning for Community Detection in Social Networks

Attempts to discover knowledge through data are gradually becoming diversified to understand complex aspects of social phenomena. Graph data analysis, which models and analyzes complex data as graphs, draws much attention as it combines the latest machine learning techniques. In this paper, we propose a new framework called link pruning for detecting clusters in complex networks, which leverages the cohesiveness of local structures by removing unimportant connections. Link pruning is a flexible framework that reduces the clustering problem in a highly mixed community structure to a simpler problem with a lowly mixed community structure. We analyze which similarities and curvatures defined on the pairs of nodes, which we call the link attributes, allow links inside and outside the community to have a different range of values. Using the link attributes, we design and analyze an algorithm that eliminates links with low attribute values to find a better community structure on the transformed graph with low mixing. Through extensive experiments, we have shown that clustering algorithms with link pruning achieve higher quality than existing algorithms in both synthetic and real-world social networks.

Detecting Community Structure in Financial Markets Using the Bat Optimization Algorithm

A lucid representation of the hidden structure of real-world application has attracted complex network research communities and triggered a vast number of solutions in order to resolve complex network issues. In the same direction, initially, this paper proposes a methodology to act on the financial dataset and construct a stock correlation network of four stock indexes based on the closing stock price. The significance of this research work is to form an effective stock community based on their complex price pattern dependencies (i.e., simultaneous fluctuations in stock prices of companies in a time series data). This paper proposes a community detection approach for stock correlation complex networks using the BAT optimization algorithm aiming to achieve high modularity and better-correlated communities. Theoretical analysis and empirical modularity performance measure results have shown that the usage of BAT algorithm for community detection proves to transcend performance in comparison to standard network community detection algorithms – greedy and label propagation.

Constant community identification in million-scale networks

The inherently stochastic nature of community detection in real-world complex networks poses an important challenge in assessing the accuracy of the results. In order to eliminate the algorithmic and implementation artifacts, it is necessary to identify the groups of vertices that are always clustered together, independent of the community detection algorithm used. Such groups of vertices are called constant communities. Current approaches for finding constant communities are very expensive and do not scale to large networks. In this paper, we use binary edge classification to find constant communities. The key idea is to classify edges based on whether they form a constant community or not. We present two methods for edge classification. The first is a GCN-based semi-supervised approach that we term Line-GCN. The second is an unsupervised approach based on image thresholding methods. Neither of these methods requires explicit detection of communities and can thus scale to very large networks of the order of millions of vertices. Both of our semi-supervised and unsupervised results on real-world graphs demonstrate that the constant communities obtained by our method have higher F1-scores and comparable or higher NMI scores than other state-of-the-art baseline methods for constant community detection. While the training step of Line-GCN can be expensive, the unsupervised algorithm is 10 times faster than the baseline methods. For larger networks, the baseline methods cannot complete, whereas all of our algorithms can find constant communities in a reasonable amount of time. Finally, we also demonstrate that our methods are robust under noisy conditions. We use three different, well-studied noise models to add noise to the networks and show that our results are mostly stable.