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

DMFO-CD: A Discrete Moth-Flame Optimization Algorithm for Community Detection

In this paper, a discrete moth–flame optimization algorithm for community detection (DMFO-CD) is proposed. The representation of solution vectors, initialization, and movement strategy of the continuous moth–flame optimization are purposely adapted in DMFO-CD such that it can solve the discrete community detection. In this adaptation, locus-based adjacency representation is used to represent the position of moths and flames, and the initialization process is performed by considering the community structure and the relation between nodes without the need of any knowledge about the number of communities. Solution vectors are updated by the adapted movement strategy using a single-point crossover to distance imitating, a two-point crossover to calculate the movement, and a single-point neighbor-based mutation that can enhance the exploration and balance exploration and exploitation. The fitness function is also defined based on modularity. The performance of DMFO-CD was evaluated on eleven real-world networks, and the obtained results were compared with five well-known algorithms in community detection, including GA-Net, DPSO-PDM, GACD, EGACD, and DECS in terms of modularity, NMI, and the number of detected communities. Additionally, the obtained results were statistically analyzed by the Wilcoxon signed-rank and Friedman tests. In the comparison with other comparative algorithms, the results show that the proposed DMFO-CD is competitive to detect the correct number of communities with high modularity.

Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets

BACKGROUND

The emergence and spread of malaria drug resistance have resulted in the need to understand disease mechanisms and importantly identify essential targets and potential drug candidates. Malaria infection involves the complex interaction between the host and pathogen, thus, functional interactions between human and Plasmodium falciparum is essential to obtain a holistic view of the genetic architecture of malaria. Several functional interaction studies have extended the understanding of malaria disease and integrating such datasets would provide further insights towards understanding drug resistance and/or genetic resistance/susceptibility, disease pathogenesis, and drug discovery.

METHODS

This study curated and analysed data including pathogen and host selective genes, host and pathogen protein sequence data, protein-protein interaction datasets, and drug data from literature and databases to perform human-host and P. falciparum network-based analysis. An integrative computational framework is presented that was developed and found to be reasonably accurate based on various evaluations, applications, and experimental evidence of outputs produced, from data-driven analysis.

RESULTS

This approach revealed 8 hub protein targets essential for parasite and human host-directed malaria drug therapy. In a semantic similarity approach, 26 potential repurposable drugs involved in regulating host immune response to inflammatory-driven disorders and/or inhibiting residual malaria infection that can be appropriated for malaria treatment. Further analysis of host-pathogen network shortest paths enabled the prediction of immune-related biological processes and pathways subverted by P. falciparum to increase its within-host survival.

CONCLUSIONS

Host-pathogen network analysis reveals potential drug targets and biological processes and pathways subverted by P. falciparum to enhance its within malaria host survival. The results presented have implications for drug discovery and will inform experimental studies.

Contextual polarity and influence mining in online social networks

Crowdsourcing is an emerging tool for collaboration and innovation platforms. Recently, crowdsourcing platforms have become a vital tool for firms to generate new ideas, especially large firms such as Dell, Microsoft, and Starbucks, Crowdsourcing provides firms with multiple advantages, notably, rapid solutions, cost savings, and a variety of novel ideas that represent the diversity inherent within a crowd. The literature on crowdsourcing is limited to empirical evidence of the advantage of crowdsourcing for businesses as an innovation strategy. In this study, Starbucks’ crowdsourcing platform, Ideas Starbucks, is examined, with three objectives: first, to determine crowdsourcing participants’ perception of the company by crowdsourcing participants when generating ideas on the platform. The second objective is to map users into a community structure to identify those more likely to produce ideas; the most promising users are grouped into the communities more likely to generate the best ideas. The third is to study the relationship between the users’ ideas’ sentiment scores and the frequency of discussions among crowdsourcing users. The results indicate that sentiment and emotion scores can be used to visualize the social interaction narrative over time. They also suggest that the fast greedy algorithm is the one best suited for community structure with a modularity on agreeable ideas of 0.53 and 8 significant communities using sentiment scores as edge weights. For disagreeable ideas, the modularity is 0.47 with 8 significant communities without edge weights. There is also a statistically significant quadratic relationship between the sentiments scores and the number of conversations between users.

Evaluating the role of community detection in improving influence maximization heuristics

Both community detection and influence maximization are well-researched fields of network science. Here, we investigate how several popular community detection algorithms can be used as part of a heuristic approach to influence maximization. The heuristic is based on the community value, a node-based metric defined on the outputs of overlapping community detection algorithms. This metric is used to select nodes as high influence candidates for expanding the set of influential nodes. Our aim in this paper is twofold. First, we evaluate the performance of eight frequently used overlapping community detection algorithms on this specific task to show how much improvement can be gained compared to the originally proposed method of Kempe et al. Second, selecting the community detection algorithm(s) with the best performance, we propose a variant of the influence maximization heuristic with significantly reduced runtime, at the cost of slightly reduced quality of the output. We use both artificial benchmarks and real-life networks to evaluate the performance of our approach.

Network Analysis Based on Important Node Selection and Community Detection

The stability and robustness of a complex network can be significantly improved by determining important nodes and by analyzing their tendency to group into clusters. Several centrality measures for evaluating the importance of a node in a complex network exist in the literature, each one focusing on a different perspective. Community detection algorithms can be used to determine clusters of nodes based on the network structure. This paper shows by empirical means that node importance can be evaluated by a dual perspective—by combining the traditional centrality measures regarding the whole network as one unit, and by analyzing the node clusters yielded by community detection. Not only do these approaches offer overlapping results but also complementary information regarding the top important nodes. To confirm this mechanism, we performed experiments for synthetic and real-world networks and the results indicate the interesting relation between important nodes on community and network level.

Italian Twitter semantic network during the Covid-19 epidemic

The Covid-19 pandemic has had a deep impact on the lives of the entire world population, inducing a participated societal debate. As in other contexts, the debate has been the subject of several d/misinformation campaigns; in a quite unprecedented fashion, however, the presence of false information has seriously put at risk the public health. In this sense, detecting the presence of malicious narratives and identifying the kinds of users that are more prone to spread them represent the first step to limit the persistence of the former ones. In the present paper we analyse the semantic network observed on Twitter during the first Italian lockdown (induced by the hashtags contained in approximately 1.5 millions tweets published between the 23rd of March 2020 and the 23rd of April 2020) and study the extent to which various discursive communities are exposed to d/misinformation arguments. As observed in other studies, the recovered discursive communities largely overlap with traditional political parties, even if the debated topics concern different facets of the management of the pandemic. Although the themes directly related to d/misinformation are a minority of those discussed within our semantic networks, their popularity is unevenly distributed among the various discursive communities.

Exploring the topology and dynamic growth properties of co-invention networks and technology fields

This study investigates the topology and dynamics of collaboration networks that exist between inventors and their patent co-authors for patents granted by the USPTO from 2007-2019 (2,241,201 patents and 1,879,037 inventors). We study changes in the configurations of different technology fields via the power-law, small-world, preferential attachment, shrinking diameter, densification law, and gelling point hypotheses. Similar to the existing literature, we obtain mixed results. Based on network statistics, we argue that the sudden rise of large networks in six technology sectors can be understood as a phase transition in which small, isolated networks form one giant component. In two other technology sectors, such a transition occurred much later and much less dramatically. The examination of inventor networks over time reveals the increased complexity of all technology sectors, regardless of the individual characteristics of the network. Therefore, we introduce ideas associated with the technological diversification of inventors to complement our analysis, and we find evidence that inventors tend to diversify into new fields that are less mature. This behavior appears to be correlated with the compliance of some of the expected network rules and has implications for the emerging patterns among the different collaboration networks under consideration here.

Analysis of information cascading and propagation barriers across distinctive news events

News reporting, on events that occur in our society, can have different styles and structures, as well as different dynamics of news spreading over time. News publishers have the potential to spread their news and reach out to a large number of readers worldwide. In this paper we would like to understand how well they are doing it and which kind of obstacles the news may encounter when spreading. The news to be spread wider cross multiple barriers such as linguistic (the most evident one, as they get published in other natural languages), economic, geographical, political, time zone, and cultural barriers. Observing potential differences between spreading of news on different events published by multiple publishers can bring insights into what may influence the differences in the spreading patterns. There are multiple reasons, possibly many hidden, influencing the speed and geographical spread of news. This paper studies information cascading and propagation barriers, applying the proposed methodology on three distinctive kinds of events: Global Warming, earthquakes, and FIFA World Cup. Our findings suggest that 1) the scope of a specific event significantly effects the news spreading across languages, 2) geographical size of a news publisher’s country is directly proportional to the number of publishers and articles reporting on the same information, 3) countries with shorter time-zone differences and similar cultures tend to propagate news between each other, 4) news related to Global Warming comes across economic barriers more smoothly than news related to FIFA World Cup and earthquakes and 5) events which may in some way involve political benefits are mostly published by those publishers which are not politically neutral.

Overlapping community detection in networks based on link partitioning and partitioning around medoids

In this paper, we present a new method for detecting overlapping communities in networks with a predefined number of clusters called LPAM (Link Partitioning Around Medoids). The overlapping communities in the graph are obtained by detecting the disjoint communities in the associated line graph employing link partitioning and partitioning around medoids which are done through the use of a distance function defined on the set of nodes. We consider both the commute distance and amplified commute distance as distance functions. The performance of the LPAM method is evaluated with computational experiments on real life instances, as well as synthetic network benchmarks. For small and medium-size networks, the exact solution was found, while for large networks we found solutions with a heuristic version of the LPAM method.

Prognostic targets recognition of rectal adenocarcinoma based on transcriptomics

Colorectal cancer is currently the third most common cancer around the world. In this study, we chose a bioinformatics analysis method based on network analysis to dig out the pathological mechanism and key prognostic targets of rectal adenocarcinoma (READ).In this study, we downloaded the clinical information data and transcriptome data from the Cancer Genome Atlas database. Differentially expressed genes analysis was used to identify the differential expressed genes in READ. Community discovery algorithm analysis and Correlation analysis between gene modules and clinical data were performed to mine the key modules related to tumor proliferation, metastasis, and invasion. Genetic significance (GS) analysis and PageRank algorithm analysis were applied for find key genes in the key module. Finally, the importance of these genes was confirmed by survival analysis.Transcriptome datasets of 165 cancer tissue samples and 9 paracancerous tissue samples were selected. Gene coexpression networks were constructed, multilevel algorithm was used to divide the gene coexpression network into 11 modules. From GO enrichment analysis, module 11 significantly associated with clinical characteristic N, T, and event, mainly involved in 2 types of biological processes which were highly related to tumor metastasis, invasion, and tumor microenvironment regulation: cell development and differentiation; the development of vascular and nervous systems. Based on the results of survival analysis, 7 key genes were found negatively correlated to the survival rate of READ, such as MMP14, SDC2, LAMC1, ELN, ACTA2, ZNF532, and CYBRD1.Our study found that these key genes were predicted playing an important role in tumor invasion and metastasis, and being associated with the prognosis of READ. This may provide some new potential therapeutic targets and thoughts for the prognosis of READ.

The inherent community structure of hyperbolic networks

A remarkable approach for grasping the relevant statistical features of real networks with the help of random graphs is offered by hyperbolic models, centred around the idea of placing nodes in a low-dimensional hyperbolic space, and connecting node pairs with a probability depending on the hyperbolic distance. It is widely appreciated that these models can generate random graphs that are small-world, highly clustered and scale-free at the same time; thus, reproducing the most fundamental common features of real networks. In the present work, we focus on a less well-known property of the popularity-similarity optimisation model and the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbb {S}}^1/{\mathbb {H}}^2$$\end{document}S1/H2 model from this model family, namely that the networks generated by these approaches also contain communities for a wide range of the parameters, which was certainly not an intention at the design of the models. We extracted the communities from the studied networks using well-established community finding methods such as Louvain, Infomap and label propagation. The observed high modularity values indicate that the community structure can become very pronounced under certain conditions. In addition, the modules found by the different algorithms show good consistency, implying that these are indeed relevant and apparent structural units. Since the appearance of communities is rather common in networks representing real systems as well, this feature of hyperbolic models makes them even more suitable for describing real networks than thought before.

A systematic comparison of community detection algorithms for measuring selective exposure in co-exposure networks

The use of community detection techniques for understanding audience fragmentation and selective exposure to information has received substantial scholarly attention in recent years. However, there exists no systematic comparison, that seeks to identify which of the many community detection algorithms are the best suited for studying these dynamics. In this paper, I address this question by proposing a formal mathematical model for audience co-exposure networks by simulating audience behavior in an artificial media environment. I show how a variety of synthetic audience overlap networks can be generated by tuning specific parameters, that control various aspects of the media environment and individual behavior. I then use a variety of community detection algorithms to characterize the level of audience fragmentation in these synthetic networks and compare their performances for different combinations of the model parameters. I demonstrate how changing the manner in which co-exposure networks are constructed significantly improves the performances of some of these algorithms. Finally, I validate these findings using a novel empirical data-set of large-scale browsing behavior. The contributions of this research are two-fold: first, it shows that two specific algorithms, FastGreedy and Multilevel are the best suited for measuring selective exposure patterns in co-exposure networks. Second, it demonstrates the use of formal modeling for informing analytical choices for better capturing complex social phenomena.

A New Method of Identifying Core Designers and Teams Based on the Importance and Similarity of Networks

In the process of product collaborative design, the association between designers can be described by a complex network. Exploring the importance of the nodes and the rules of information dissemination in such networks is of great significance for distinguishing its core designers and potential designer teams, as well as for accurate recommendations of collaborative design tasks. Based on the neighborhood similarity model, combined with the idea of network information propagation, and with the help of the ReLU function, this paper proposes a new method for judging the importance of nodes-LLSR. This method not only reflects the local connection characteristics of nodes but also considers the trust degree of network propagation, and the neighbor nodes' information is used to modify the node value. Next, in order to explore potential teams, an LA-LPA algorithm based on node importance and node similarity was proposed. Before the iterative update, all nodes were randomly sorted to get an update sequence which was replaced by the node importance sequence. When there are multiple largest neighbor labels in the propagation process, the label with the highest similarity is selected for update. The experimental results in the related networks show that the LLSR algorithm can better identify the core nodes in the network, and the LA-LPA algorithm has greatly improved the stability of the original LPA algorithm and has stably mined potential teams in the network.

Quantum inspired community detection for analysis of biodiversity change driven by land-use conversion and climate change

Community detection remains little explored in the analysis of biodiversity change. The challenges linked with global biodiversity change have also multiplied manifold in the past few decades. Moreover, most studies concerning biodiversity change lack the quantitative treatment central to species distribution modeling. Empirical analysis of species distribution and abundance is thus integral to the study of biodiversity loss and biodiversity alterations. Community detection is therefore expected to efficiently model the topological aspect of biodiversity change driven by land-use conversion and climate change; given that it has already proven superior for diverse problems in the domain of social network analysis and subgroup discovery in complex systems. Thus, quantum inspired community detection is proposed as a novel technique to predict biodiversity change considering tiger population in eighteen states of India; leading to benchmarking of two novel datasets. Elements of land-use conversion and climate change are explored to design these datasets viz.-Landscape based distribution and Number of tiger reserves based distribution respectively; for predicting regions expected to maximize Tiger population growth. Furthermore, validation of the proposed framework on the said datasets is performed using standard community detection metrics like-Modularity, Normalized Mutual Information (NMI), Adjusted Rand Index (ARI), Degree distribution, Degree centrality and Edge-betweenness centrality. Quantum inspired community detection has also been successful in demonstrating an association between biodiversity change, land-use conversion and climate change; validated statistically by Pearson's correlation coefficient and p value test. Finally, modularity distribution based on parameter tuning establishes the superiority of the second dataset based on the number of Tiger reserves-in predicting regions maximizing Tiger population growth fostering species distribution and abundance; apart from scripting a stronger correlation of biodiversity change with land-use conversion.

COVID-19 Community Temporal Visualizer: a new methodology for the network-based analysis and visualization of COVID-19 data

Understanding the evolution of the spread of the COVID-19 pandemic requires the analysis of several data at the spatial and temporal levels. Here, we present a new network-based methodology to analyze COVID-19 data measures containing spatial and temporal features and its application on a real dataset. The goal of the methodology is to analyze sets of homogeneous datasets (i.e. COVID-19 data taken in different periods and in several regions) using a statistical test to find similar/dissimilar datasets, mapping such similarity information on a graph and then using a community detection algorithm to visualize and analyze the spatio-temporal evolution of data. We evaluated diverse Italian COVID-19 data made publicly available by the Italian Protezione Civile Department at https://github.com/pcm-dpc/COVID-19/. Furthermore, we considered the climate data related to two periods and we integrated them with COVID-19 data measures to detect new communities related to climate changes. In conclusion, the application of the proposed methodology provides a network-based representation of the COVID-19 measures by highlighting the different behaviour of regions with respect to pandemics data released by Protezione Civile and climate data. The methodology and its implementation as R function are publicly available at https://github.com/mmilano87/analyzeC19D.

Modelling segmental duplications in the human genome

Background

Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copies in a genome. There are several well-studied mechanisms responsible for segmental duplications: non-allelic homologous recombination, non-homologous end joining and replication slippage. Such duplications play an important role in evolution, however, we do not have a full understanding of the dynamic properties of the duplication process.

Results

We study segmental duplications through a graph representation where nodes represent genomic regions and edges represent duplications between them. The resulting network (the SD network) is quite complex and has distinct features which allow us to make inference on the evolution of segmantal duplications. We come up with the network growth model that explains features of the SD network thus giving us insights on dynamics of segmental duplications in the human genome. Based on our analysis of genomes of other species the network growth model seems to be applicable for multiple mammalian genomes.

Conclusions

Our analysis suggests that duplication rates of genomic loci grow linearly with the number of copies of a duplicated region. Several scenarios explaining such a preferential duplication rates were suggested.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-021-07789-7).

Evolutionary Divide-and-Conquer Algorithm for Virus Spreading Control Over Networks

The control of virus spreading over complex networks with a limited budget has attracted much attention but remains challenging. This article aims at addressing the combinatorial, discrete resource allocation problems (RAPs) in virus spreading control. To meet the challenges of increasing network scales and improve the solving efficiency, an evolutionary divide-and-conquer algorithm is proposed, namely, a coevolutionary algorithm with network-community-based decomposition (NCD-CEA). It is characterized by the community-based dividing technique and cooperative coevolution conquering thought. First, to reduce the time complexity, NCD-CEA divides a network into multiple communities by a modified community detection method such that the most relevant variables in the solution space are clustered together. The problem and the global swarm are subsequently decomposed into subproblems and subswarms with low-dimensional embeddings. Second, to obtain high-quality solutions, an alternative evolutionary approach is designed by promoting the evolution of subswarms and the global swarm, in turn, with subsolutions evaluated by local fitness functions and global solutions evaluated by a global fitness function. Extensive experiments on different networks show that NCD-CEA has a competitive performance in solving RAPs. This article advances toward controlling virus spreading over large-scale networks.

A Novel Acceleration Signal Processing Procedure for Cycling Safety Assessment

With the growing rate of urban population and transport congestion, it is important for a city to have bike riding as an attractive travel choice but one of its biggest barriers for people is the perceived lack of safety. To improve the safety of urban cycling, identification of high-risk location and routes are major obstacles for safety countermeasures. Risk assessment is performed by crash data analysis, but the lack of data makes that approach less effective when applied to cyclist safety. Furthermore, the availability of data collected with the modern technologies opens the way to different approaches. This research aim is to analyse data needs and capability to identify critical cycling safety events for urban context where bicyclist behaviour can be recorded with different equipment and bicycle used as a probe vehicle to collect data. More specifically, three different sampling frequencies have been investigated to define the minimum one able to detect and recognize hard breaking. In details, a novel signal processing procedure has been proposed to correctly deal with speed and acceleration signals. Besides common signal filtering approaches, wavelet transformation and Dynamic Time Warping (DTW) techniques have been applied to remove more efficiently the instrument noise and align the signals with respect to the reference. The Euclidean distance of the DTW has been introduced as index to get the best filter parameters configuration. Obtained results, both during the calibration and the investigated real scenario, confirm that at least a GPS signal with a sampling frequency of 1Hz is needed to track the rider’s behaviour to detect events. In conclusion, with a very cheap hardware setup is possible to monitor riders’ speed and acceleration.

Clustering assessment in weighted networks

We provide a systematic approach to validate the results of clustering methods on weighted networks, in particular for the cases where the existence of a community structure is unknown. Our validation of clustering comprises a set of criteria for assessing their significance and stability. To test for cluster significance, we introduce a set of community scoring functions adapted to weighted networks, and systematically compare their values to those of a suitable null model. For this we propose a switching model to produce randomized graphs with weighted edges while maintaining the degree distribution constant. To test for cluster stability, we introduce a non parametric bootstrap method combined with similarity metrics derived from information theory and combinatorics. In order to assess the effectiveness of our clustering quality evaluation methods, we test them on synthetically generated weighted networks with a ground truth community structure of varying strength based on the stochastic block model construction. When applying the proposed methods to these synthetic ground truth networks' clusters, as well as to other weighted networks with known community structure, these correctly identify the best performing algorithms, which suggests their adequacy for cases where the clustering structure is not known. We test our clustering validation methods on a varied collection of well known clustering algorithms applied to the synthetically generated networks and to several real world weighted networks. All our clustering validation methods are implemented in R, and will be released in the upcoming package clustAnalytics.

Political Partisanship and Antiscience Attitudes in Online Discussions About COVID-19: Twitter Content Analysis

BACKGROUND

The novel coronavirus pandemic continues to ravage communities across the United States. Opinion surveys identified the importance of political ideology in shaping perceptions of the pandemic and compliance with preventive measures.

OBJECTIVE

The aim of this study was to measure political partisanship and antiscience attitudes in the discussions about the pandemic on social media, as well as their geographic and temporal distributions.

METHODS

We analyzed a large set of tweets from Twitter related to the pandemic, collected between January and May 2020, and developed methods to classify the ideological alignment of users along the moderacy (hardline vs moderate), political (liberal vs conservative), and science (antiscience vs proscience) dimensions.

RESULTS

We found a significant correlation in polarized views along the science and political dimensions. Moreover, politically moderate users were more aligned with proscience views, while hardline users were more aligned with antiscience views. Contrary to expectations, we did not find that polarization grew over time; instead, we saw increasing activity by moderate proscience users. We also show that antiscience conservatives in the United States tended to tweet from the southern and northwestern states, while antiscience moderates tended to tweet from the western states. The proportion of antiscience conservatives was found to correlate with COVID-19 cases.

CONCLUSIONS

Our findings shed light on the multidimensional nature of polarization and the feasibility of tracking polarized opinions about the pandemic across time and space through social media data.

Global formal live poultry and hatching egg trade network (2004-2016): description and association with poultry disease reporting and presence

As international trade constitutes one of the main spread pathways of diseases, a better understanding of the trade behaviors of countries will help identify strengths and areas for improvement in the approach of national authorities to controlling poultry diseases globally. Using data reported to the United Nations Comtrade and the World Organisation for Animal Health (OIE) between 2004 and 2016 by 193 countries, we used a network analysis on trade data of poultry hatching eggs, live poultry of less than 185 g and live poultry of 185 g or more to determine that: 1) quantities traded between countries are substantial, and tend to increase (average increase of 800,000 poultry heads and 21,000 tons of hatching eggs each year equivalent to an increase by 2-fold in 17 yr); 2) the stability of the networks was low (a quarter to half of trade relationships maintained between 2 consecutive years) and the subnetworks favorable to the spread of diseases were in general consistent with regional clustering, trade exchanges being equally at intracontinental and intercontinental levels; 3) countries with highest number of partners were located in the same world regions for the 3 poultry networks - Americas and Europe for export (up to 107 partners) and Africa, Asia and Europe for import (up to 36 partners); 4) for live poultry, biggest exporting countries shared more poultry disease surveillance data, and reported more disease presence than others, which did not stop them from trading. Biggest importers reported less poultry disease surveillance data and reported more disease presence than others; and 5) the main structural and trend characteristics of the international trade networks were in general similar for the 3 networks. The information derived from this work underlines the importance of applying the preventive measures advocated by the OIE and will support countries to reduce the risk of introduction of pathogens causing poultry diseases.

Comparing Graph Clusterings: Set Partition Measures vs. Graph-Aware Measures

In this paper, we propose a family of graph partition similarity measures that take the topology of the graph into account. These graph-aware measures are alternatives to using set partition similarity measures that are not specifically designed for graphs. The two types of measures, graph-aware and set partition measures, are shown to have opposite behaviors with respect to resolution issues and provide complementary information necessary to compare graph partitions.

An Approach to Spatiotemporal Trajectory Clustering Based on Community Detection

Nowadays, large volumes of multimodal data have been collected for analysis. An important type of data is trajectory data, which contains both time and space information. Trajectory analysis and clustering are essential to learn the pattern of moving objects. Computing trajectory similarity is a key aspect of trajectory analysis, but it is very time consuming. To address this issue, this paper presents an improved branch and bound strategy based on time slice segmentation, which reduces the time to obtain the similarity matrix by decreasing the number of distance calculations required to compute similarity. Then, the similarity matrix is transformed into a trajectory graph and a community detection algorithm is applied on it for clustering. Extensive experiments were done to compare the proposed algorithms with existing similarity measures and clustering algorithms. Results show that the proposed method can effectively mine the trajectory cluster information from the spatiotemporal trajectories.

Making sense of tweets using sentiment analysis on closely related topics

Microblogging has taken a considerable upturn in recent years, with the growth of microblogging websites like Twitter people have started to share more of their opinions about various pressing issues on such online social networks. A broader understanding of the domain in question is required to make an informed decision. With this motivation, our study focuses on finding overall sentiments of related topics with reference to a given topic. We propose an architecture that combines sentiment analysis and community detection to get an overall sentiment of related topics. We apply that model on the following topics: shopping, politics, covid19 and electric vehicles to understand emerging trends, issues and its possible marketing, business and political implications.

Towards Inferring Influential Facebook Users

Because of the complexity of the actors and the relationships between them, social networks are always represented by graphs. This structure makes it possible to analyze the effectiveness of the network for the social actors who are there. This work presents a social network analysis approach that focused on processing Facebook pages and users who react to posts to infer influential people. In our study, we are particularly interested in studying the relationships between the posts of the page, and the reactions of fans (users) towards these posts. The topics covered include data crawling, graph modeling, and exploratory analysis using statistical tools and machine learning algorithms. We seek to detect influential people in the sense that the influence of a Facebook user lies in their ability to transmit and disseminate information. Once determined, these users have an impact on business for a specific brand. The proposed exploratory analysis has shown that the network structure and its properties have important implications for the outcome of interest.

Understanding digitally enabled complex networks: a plural granulation based hybrid community detection approach

Purpose

Communities representing groups of agents with similar interests or functions are one of the essential features of complex networks. Finding communities in real-world networks is critical for analyzing complex systems in various areas ranging from collaborative information to political systems. Given the different characteristics of networks and the capability of community detection in handling a plethora of societal problems, community detection methods represent an emerging area of research. Contributing to this field, the authors propose a new community detection algorithm based on the hybridization of node and link granulation.

Design/methodology/approach

The proposed algorithm utilizes a rough set-theoretic concept called closure on networks. Initial sets are constructed by using neighborhood topology around the nodes as well as links and represented as two different categories of granules. Subsequently, the authors iteratively obtain the constrained closure of these sets. The authors use node mutuality and link mutuality as merging criteria for node and link granules, respectively, during the iterations. Finally, the constrained closure subsets of nodes and links are combined and refined using the Jaccard similarity coefficient and a local density function to obtain communities in a binary network.

Findings

Extensive experiments conducted on twelve real-world networks followed by a comparison with state-of-the-art methods demonstrate the viability and effectiveness of the proposed algorithm.

Research limitations/implications

The study also contributes to the ongoing effort related to the application of soft computing techniques to model complex systems. The extant literature has integrated a rough set-theoretic approach with a fuzzy granular model (Kundu and Pal, 2015) and spectral clustering (Huang and Xiao, 2012) for node-centric community detection in complex networks. In contributing to this stream of work, the proposed algorithm leverages the unexplored synergy between rough set theory, node granulation and link granulation in the context of complex networks. Combined with experiments of network datasets from various domains, the results indicate that the proposed algorithm can effectively reveal co-occurring disjoint, overlapping and nested communities without necessarily assigning each node to a community.

Practical implications

This study carries important practical implications for complex adaptive systems in business and management sciences, in which entities are increasingly getting organized into communities (Jacucci et al., 2006). The proposed community detection method can be used for network-based fraud detection by enabling experts to understand the formation and development of fraudulent setups with an active exchange of information and resources between the firms (Van Vlasselaer et al., 2017). Products and services are getting connected and mapped in every walk of life due to the emergence of a variety of interconnected devices, social networks and software applications.

Social implications

The proposed algorithm could be extended for community detection on customer trajectory patterns and design recommendation systems for online products and services (Ghose et al., 2019; Liu and Wang, 2017). In line with prior research, the proposed algorithm can aid companies in investigating the characteristics of implicit communities of bloggers or social media users for their services and products so as to identify peer influencers and conduct targeted marketing (Chau and Xu, 2012; De Matos et al., 2014; Zhang et al., 2016). The proposed algorithm can be used to understand the behavior of each group and the appropriate communication strategy for that group. For instance, a group using a specific language or following a specific account might benefit more from a particular piece of content than another group. The proposed algorithm can thus help in exploring the factors defining communities and confronting many real-life challenges.

Originality/value

This work is based on a theoretical argument that communities in networks are not only based on compatibility among nodes but also on the compatibility among links. Building up on the aforementioned argument, the authors propose a community detection method that considers the relationship among both the entities in a network (nodes and links) as opposed to traditional methods, which are predominantly based on relationships among nodes only.

A social media analytics platform visualising the spread of COVID-19 in Italy via exploitation of automatically geotagged tweets

Social media play an important role in the daily life of people around the globe and users have emerged as an active part of news distribution as well as production. The threatening pandemic of COVID-19 has been the lead subject in online discussions and posts, resulting to large amounts of related social media data, which can be utilised to reinforce the crisis management in several ways. Towards this direction, we propose a novel framework to collect, analyse, and visualise Twitter posts, which has been tailored to specifically monitor the virus spread in severely affected Italy. We present and evaluate a deep learning localisation technique that geotags posts based on the locations mentioned in their text, a face detection algorithm to estimate the number of people appearing in posted images, and a community detection approach to identify communities of Twitter users. Moreover, we propose further analysis of the collected posts to predict their reliability and to detect trending topics and events. Finally, we demonstrate an online platform that comprises an interactive map to display and filter analysed posts, utilising the outcome of the localisation technique, and a visual analytics dashboard that visualises the results of the topic, community, and event detection methodologies.

LPA-MNI: An Improved Label Propagation Algorithm Based on Modularity and Node Importance for Community Detection

Community detection is of great significance in understanding the structure of the network. Label propagation algorithm (LPA) is a classical and effective method, but it has the problems of randomness and instability. An improved label propagation algorithm named LPA-MNI is proposed in this study by combining the modularity function and node importance with the original LPA. LPA-MNI first identify the initial communities according to the value of modularity. Subsequently, the label propagation is used to cluster the remaining nodes that have not been assigned to initial communities. Meanwhile, node importance is used to improve the node order of label updating and the mechanism of label selecting when multiple labels are contained by the maximum number of nodes. Extensive experiments are performed on twelve real-world networks and eight groups of synthetic networks, and the results show that LPA-MNI has better accuracy, higher modularity, and more reasonable community numbers when compared with other six algorithms. In addition, LPA-MNI is shown to be more robust than the traditional LPA algorithm.

Disambiguation of author entities in ADS using supervised learning and graph theory methods

Disambiguation of authors in digital libraries is essential for many tasks, including efficient bibliographical searches and scientometric analyses to the level of individuals. The question of how to link documents written by the same person has been given much attention by academic publishers and information retrieval researchers alike. Usual approaches rely on publications’ metadata such as affiliations, email addresses, co-authors, or scholarly topics. Lack of homogeneity in the structure of bibliographic collections and discipline-specific dissimilarities between them make the creation of general-purpose disambiguators arduous. We present an algorithm to disambiguate authorships in the Astrophysics Data System (ADS) following an established semi-supervised approach of training a classifier on authorship pairs and clustering the resulting graphs. Due to the lack of high-signal features such as email addresses and citations, we engineer additional content- and location-based features via text embeddings and named-entity recognition. We train various nonlinear tree-based classifiers and detect communities from the resulting weighted graphs through label propagation, a fast yet efficient algorithm that requires no tuning. The resulting procedure reaches reasonable complexity and offers possibilities for interpretation. We apply our method to the creation of author entities in a recent ADS snapshot. The algorithm is evaluated on 39 manually-labeled author blocks comprising 9545 authorships from 562 author profiles. Our best approach utilizes the Random Forest classifier and yields a micro- and macro-averaged BCubed $$\mathrm {F}_1$$ F 1 score of 0.95 and 0.87, respectively. We release our code and labeled data publicly to foster the development of further disambiguation procedures for ADS.

Persona2vec: a flexible multi-role representations learning framework for graphs

Graph embedding techniques, which learn low-dimensional representations of a graph, are achieving state-of-the-art performance in many graph mining tasks. Most existing embedding algorithms assign a single vector to each node, implicitly assuming that a single representation is enough to capture all characteristics of the node. However, across many domains, it is common to observe pervasively overlapping community structure, where most nodes belong to multiple communities, playing different roles depending on the contexts. Here, we propose persona2vec, a graph embedding framework that efficiently learns multiple representations of nodes based on their structural contexts. Using link prediction-based evaluation, we show that our framework is significantly faster than the existing state-of-the-art model while achieving better performance.

Network community structure of substorms using SuperMAG magnetometers

Geomagnetic substorms are a global magnetospheric reconfiguration, during which energy is abruptly transported to the ionosphere. Central to this are the auroral electrojets, large-scale ionospheric currents that are part of a larger three-dimensional system, the substorm current wedge. Many, often conflicting, magnetospheric reconfiguration scenarios have been proposed to describe the substorm current wedge evolution and structure. SuperMAG is a worldwide collaboration providing easy access to ground based magnetometer data. Here we show application of techniques from network science to analyze data from 137 SuperMAG ground-based magnetometers. We calculate a time-varying directed network and perform community detection on the network, identifying locally dense groups of connections. Analysis of 41 substorms exhibit robust structural change from many small, uncorrelated current systems before substorm onset, to a large spatially-extended coherent system, approximately 10 minutes after onset. We interpret this as strong indication that the auroral electrojet system during substorm expansions is inherently a large-scale phenomenon and is not solely due to many meso-scale wedgelets.

Community detection in networks using graph embeddings

Graph embedding methods are becoming increasingly popular in the machine learning community, where they are widely used for tasks such as node classification and link prediction. Embedding graphs in geometric spaces should aid the identification of network communities as well because nodes in the same community should be projected close to each other in the geometric space, where they can be detected via standard data clustering algorithms. In this paper, we test the ability of several graph embedding techniques to detect communities on benchmark graphs. We compare their performance against that of traditional community detection algorithms. We find that the performance is comparable, if the parameters of the embedding techniques are suitably chosen. However, the optimal parameter set varies with the specific features of the benchmark graphs, like their size, whereas popular community detection algorithms do not require any parameter. So, it is not possible to indicate beforehand good parameter sets for the analysis of real networks. This finding, along with the high computational cost of embedding a network and grouping the points, suggests that, for community detection, current embedding techniques do not represent an improvement over network clustering algorithms.

A landscape for drug-target interactions based on network analysis

In this work, we performed an analysis of the networks of interactions between drugs and their targets to assess how connected the compounds are. For our purpose, the interactions were downloaded from the DrugBank database, and we considered all drugs approved by the FDA. Based on topological analysis of this interaction network, we obtained information on degree, clustering coefficient, connected components, and centrality of these interactions. We identified that this drug-target interaction network cannot be divided into two disjoint and independent sets, i.e., it is not bipartite. In addition, the connectivity or associations between every pair of nodes identified that the drug-target network is constituted of 165 connected components, where one giant component contains 4376 interactions that represent 89.99% of all the elements. In this regard, the histamine H1 receptor, which belongs to the family of rhodopsin-like G-protein-coupled receptors and is activated by the biogenic amine histamine, was found to be the most important node in the centrality of input-degrees. In the case of centrality of output-degrees, fostamatinib was found to be the most important node, as this drug interacts with 300 different targets, including arachidonate 5-lipoxygenase or ALOX5, expressed on cells primarily involved in regulation of immune responses. The top 10 hubs interacted with 33% of the target genes. Fostamatinib stands out because it is used for the treatment of chronic immune thrombocytopenia in adults. Finally, 187 highly connected sets of nodes, structured in communities, were also identified. Indeed, the largest communities have more than 400 elements and are related to metabolic diseases, psychiatric disorders and cancer. Our results demonstrate the possibilities to explore these compounds and their targets to improve drug repositioning and contend against emergent diseases.

Analysis of dynamic networks based on the Ising model for the case of study of co-authorship of scientific articles

Two computational methods based on the Ising model were implemented for studying temporal dynamic in co-authorship networks: an interpretative for real networks and another for simulation via Monte Carlo. The objective of simulation networks is to evaluate if the Ising model describes in similar way the dynamic of the network and of the magnetic system, so that it can be found a generalized explanation to the behaviours observed in real networks. The scientific papers used for building the real networks were acquired from WoS core collection. The variables for each record took into account bibliographic references. The search equation for each network considered specific topics trying to obtain an advanced temporal evolution in terms of the addition of new nodes; that means 3 steps, a time to reach the interest of the scientific community, a gradual increase until reaching a peak and finally, a decreasing trend by losing of novelty. It is possible to conclude that both methods are consistent with each other, showing that the Ising model can predict behaviours such as the number and size of communities (or domains) according to the temporal distribution of new nodes.