scholarly journals An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2

2020 ◽  
Author(s):  
Yunchao Ling ◽  
Ruifang Cao ◽  
Jiaqiang Qian ◽  
Jiefu Li ◽  
Haokui Zhou ◽  
...  
Keyword(s):  
Network Analysis ◽  
Genome Evolution ◽  
Viral Genome ◽  
Large Scale ◽  
Phylogenetic Network ◽  
Detection Algorithm ◽  
Viral Genomes ◽  
Network Analyses ◽  
Community Detection Algorithm ◽  
Analysis System

AbstractComprehensive analyses of viral genomes can provide a global picture on SARS-CoV-2 transmission and help to predict the oncoming trends of pandemic. This molecular tracing is mainly conducted through extensive phylogenetic network analyses. However, the rapid accumulation of SARS-CoV-2 genomes presents an unprecedented data size and complexity that has exceeded the capacity of existing methods in constructing evolution network through virus genotyping. Here we report a Viral genome Evolution Network Analysis System (VENAS), which uses Hamming distances adjusted by the minor allele frequency to construct viral genome evolution network. The resulting network was topologically clustered and divided using community detection algorithm, and potential evolution paths were further inferred with a network disassortativity trimming algorithm. We also employed parallel computing technology to achieve rapid processing and interactive visualization of >10,000 viral genomes, enabling accurate detection and subtyping of the viral mutations through different stages of Covid-19 pandemic. In particular, several core viral mutations can be independently identified and linked to early transmission events in Covid-19 pandemic. As a general platform for comprehensive viral genome analysis, VENAS serves as a useful computational tool in the current and future pandemics.

scholarly journals An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2

2022 ◽  
Author(s):  
Yunchao Ling ◽  
Ruifang Cao ◽  
Jiaqiang Qian ◽  
Jiefu Li ◽  
Haokui Zhou ◽  
...  
Keyword(s):  
Network Analysis ◽  
Genome Evolution ◽  
Viral Genome ◽  
Large Scale ◽  
Analysis System

A novel fuzzy community detection method based on improved community adjacency list

2021 ◽  
pp. 2150186
Author(s):  
Xinyue Zhou
Keyword(s):  
Network Analysis ◽  
Community Detection ◽  
Large Scale ◽  
Detection Algorithm ◽  
Good Effect ◽  
Network Applications ◽  
Adjacency List ◽  
Membership Value ◽  
Community Detection Algorithm ◽  
Partition Structure

With the development of economy and society, network analysis is widely used in more and more fields. Signed network has a good effect in the process of representation and display. As an important part of network analysis, fuzzy community detection plays an increasingly important role in analyzing and visualizing the real world. Fuzzy community detection helps to detect nodes that belong to some communities but are still closely related to other communities. These nodes are helpful for mining information from the network more realistically. However, there is little research in this field. This paper proposes a fuzzy community detection algorithm based on pointer and adjacency list. The model adopts a new ICALF network data structure, which can achieve the effect of storing community partition structure and membership value between community and node at the same time, with low time complexity and storage space. Experiments on real networks verify the correctness of the method, and prove that the method is suitable for large-scale network applications.

scholarly journals Static and dynamic functional connectivity supports the configuration of brain networks associated with creative cognition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Abhishek Uday Patil ◽  
Sejal Ghate ◽  
Deepa Madathil ◽  
Ovid J. L. Tzeng ◽  
Hsu-Wen Huang ◽  
...  
Keyword(s):  
Cognitive Processes ◽  
Large Scale ◽  
Brain Networks ◽  
Blood Oxygen Level Dependent ◽  
Detection Algorithm ◽  
Brain Regions ◽  
Creative Cognition ◽  
Network Flexibility ◽  
Community Detection Algorithm ◽  
Window Approach

AbstractCreative cognition is recognized to involve the integration of multiple spontaneous cognitive processes and is manifested as complex networks within and between the distributed brain regions. We propose that the processing of creative cognition involves the static and dynamic re-configuration of brain networks associated with complex cognitive processes. We applied the sliding-window approach followed by a community detection algorithm and novel measures of network flexibility on the blood-oxygen level dependent (BOLD) signal of 8 major functional brain networks to reveal static and dynamic alterations in the network reconfiguration during creative cognition using functional magnetic resonance imaging (fMRI). Our results demonstrate the temporal connectivity of the dynamic large-scale creative networks between default mode network (DMN), salience network, and cerebellar network during creative cognition, and advance our understanding of the network neuroscience of creative cognition.

scholarly journals Studying Positive and Negative Direct and Extended Contact: Complementing Self-Reports With Social Network Analysis

2017 ◽  
Vol 43 (11) ◽  
pp. 1566-1581 ◽  
Author(s):  
Ralf Wölfer ◽  
Eva Jaspers ◽  
Danielle Blaylock ◽  
Clarissa Wigoder ◽  
Joanne Hughes ◽  
...  
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Intergroup Relations ◽  
Large Scale ◽  
Intergroup Contact ◽  
Network Analyses ◽  
Self Reports ◽  
Extended Contact ◽  
Contact Parameters

Traditionally, studies of intergroup contact have primarily relied on self-reports, which constitute a valid method for studying intergroup contact, but has limitations, especially if researchers are interested in negative or extended contact. In three studies, we apply social network analyses to generate alternative contact parameters. Studies 1 and 2 examine self-reported and network-based parameters of positive and negative contact using cross-sectional datasets ( N = 291, N = 258), indicating that both methods help explain intergroup relations. Study 3 examines positive and negative direct and extended contact using the previously validated network-based contact parameters in a large-scale, international, and longitudinal dataset ( N = 12,988), demonstrating that positive and negative direct and extended contact all uniquely predict intergroup relations (i.e., intergroup attitudes and future outgroup contact). Findings highlight the value of social network analysis for examining the full complexity of contact including positive and negative forms of direct and extended contact.

Clustering Algorithm for Community Detection in Complex Network: A Comprehensive Review

2020 ◽  
Vol 13 (4) ◽  
pp. 542-549
Author(s):  
Smita Agrawal ◽  
Atul Patel
Keyword(s):  
Complex Network ◽  
Community Detection ◽  
Large Scale ◽  
Clustering Algorithm ◽  
Detection Algorithm ◽  
Connected Subgraph ◽  
Comprehensive Review ◽  
Detection Algorithms ◽  
Community Detection Algorithm ◽  
Large Scale Networks

Many real-world social networks exist in the form of a complex network, which includes very large scale networks with structured or unstructured data and a set of graphs. This complex network is available in the form of brain graph, protein structure, food web, transportation system, World Wide Web, and these networks are sparsely connected, and most of the subgraphs are densely connected. Due to the scaling of large scale graphs, efficient way for graph generation, complexity, the dynamic nature of graphs, and community detection are challenging tasks. From large scale graph to find the densely connected subgraph from the complex network, various community detection algorithms using clustering techniques are discussed here. In this paper, we discussed the taxonomy of various community detection algorithms like Structural Clustering Algorithm for Networks (SCAN), Structural-Attribute based Cluster (SA-cluster), Community Detection based on Hierarchical Clustering (CDHC), etc. In this comprehensive review, we provide a classification of community detection algorithm based on their approach, dataset used for the existing algorithm for experimental study and measure to evaluate them. In the end, insights into the future scope and research opportunities for community detection are discussed.

Crowd attraction-driven community evolution on social network

2021 ◽  
pp. 2250009
Author(s):  
Fuzhong Nian ◽  
Li Luo ◽  
Xuelong Yu
Keyword(s):  
Social Networks ◽  
Community Structure ◽  
Social Network ◽  
Large Scale ◽  
Detection Algorithm ◽  
Information Propagation ◽  
Evolution Analysis ◽  
Dynamic Social Networks ◽  
Community Evolution ◽  
Community Detection Algorithm

The evolution analysis of community structure of social network will help us understand the composition of social organizations and the evolution of society better. In order to discover the community structure and the regularity of community evolution in large-scale social networks, this paper analyzes the formation process and influencing factors of communities, and proposes a community evolution analysis method of crowd attraction driven. This method uses the traditional community division method to divide the basic community, and introduces the theory of information propagation into complex network to simulate the information propagation of dynamic social networks. Then defines seed node, the activity of basic community and crowd attraction to research the influence of groups on individuals in social networks. Finally, making basic communities as fixed groups in the network and proposing community detection algorithm based on crowd attraction. Experimental results show that the scheme can effectively detect and identify the community structure in large-scale social networks.

Parallel Network Analysis and Communities Detection (PANC) Pipeline for the Analysis and Visualization of COVID-19 Data

2021 ◽  
pp. 2142002
Author(s):  
Giuseppe Agapito ◽  
Marianna Milano ◽  
Mario Cannataro
Keyword(s):  
Network Analysis ◽  
Real Data ◽  
Detection Algorithm ◽  
Data Sets ◽  
Data Set ◽  
Italian Regions ◽  
Initial Dataset ◽  
Parallel Network ◽  
Community Detection Algorithm ◽  
Similarity Matrices

A new coronavirus, causing a severe acute respiratory syndrome (COVID-19), was started at Wuhan, China, in December 2019. The epidemic has rapidly spread across the world becoming a pandemic that, as of today, has affected more than 70 million people causing over 2 million deaths. To better understand the evolution of spread of the COVID-19 pandemic, we developed PANC (Parallel Network Analysis and Communities Detection), a new parallel preprocessing methodology for network-based analysis and communities detection on Italian COVID-19 data. The goal of the methodology is to analyze set of homogeneous datasets (i.e. COVID-19 data in several regions) using a statistical test to find similar/dissimilar behaviours, mapping such similarity information on a graph and then using community detection algorithm to visualize and analyze the initial dataset. The methodology includes the following steps: (i) a parallel methodology to build similarity matrices that represent similar or dissimilar regions with respect to data; (ii) an effective workload balancing function to improve performance; (iii) the mapping of similarity matrices into networks where nodes represent Italian regions, and edges represent similarity relationships; (iv) the discovering and visualization of communities of regions that show similar behaviour. The methodology is general and can be applied to world-wide data about COVID-19, as well as to all types of data sets in tabular and matrix format. To estimate the scalability with increasing workloads, we analyzed three synthetic COVID-19 datasets with the size of 90.0[Formula: see text]MB, 180.0[Formula: see text]MB, and 360.0[Formula: see text]MB. Experiments was performed on showing the amount of data that can be analyzed in a given amount of time increases almost linearly with the number of computing resources available. Instead, to perform communities detection, we employed the real data set.

scholarly journals Network Analysis Reveals the Latent Structure of Negative Symptoms in Schizophrenia

2018 ◽  
Vol 45 (5) ◽  
pp. 1033-1041 ◽  
Author(s):  
Gregory P Strauss ◽  
Farnaz Zamani Esfahlani ◽  
Silvana Galderisi ◽  
Armida Mucci ◽  
Alessandro Rossi ◽  
...  
Keyword(s):  
Factor Analysis ◽  
Network Analysis ◽  
Negative Symptom ◽  
Negative Symptoms ◽  
Null Model ◽  
Detection Algorithm ◽  
Latent Structure ◽  
Symptom Scale ◽  
Mathematical Techniques ◽  
Community Detection Algorithm

Abstract Prior studies using exploratory factor analysis provide evidence that negative symptoms are best conceptualized as 2 dimensions reflecting diminished motivation and expression. However, the 2-dimensional model has yet to be evaluated using more complex mathematical techniques capable of testing structure. In the current study, network analysis was applied to evaluate the latent structure of negative symptoms using a community-detection algorithm. Two studies were conducted that included outpatients with schizophrenia (SZ; Study 1: n = 201; Study 2: n = 912) who were rated on the Brief Negative Symptom Scale (BNSS). In both studies, network analysis indicated that the 13 BNSS items divided into 6 negative symptom domains consisting of anhedonia, avolition, asociality, blunted affect, alogia, and lack of normal distress. Separation of these domains was statistically significant with reference to a null model of randomized networks. There has been a recent trend toward conceptualizing the latent structure of negative symptoms in relation to 2 distinct dimensions reflecting diminished expression and motivation. However, the current results obtained using network analysis suggest that the 2-dimensional conceptualization is not complex enough to capture the nature of the negative symptom construct. Similar to recent confirmatory factor analysis studies, network analysis revealed that the latent structure of negative symptom is best conceptualized in relation to the 5 domains identified in the 2005 National Institute of Mental Health consensus development conference (anhedonia, avolition, asociality, blunted affect, and alogia) and potentially a sixth domain consisting of lack of normal distress. Findings have implications for identifying pathophysiological mechanisms and targeted treatments.

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