scholarly journals The parallel computing of node centrality based on GPU

2022 ◽  
Vol 19 (3) ◽  
pp. 2700-2719
Author(s):  
Siyuan Yin ◽  
◽  
Yanmei Hu ◽  
Yuchun Ren
Keyword(s):  
Parallel Computing ◽  
Network Analysis ◽  
Parallel Algorithms ◽  
Betweenness Centrality ◽  
Large Scale ◽  
Rapid Development ◽  
Closeness Centrality ◽  
Node Centrality ◽  
Speed Up ◽  
Large Scale Networks

<abstract> <p>Many systems in real world can be represented as network, and network analysis can help us understand these systems. Node centrality is an important problem and has attracted a lot of attention in the field of network analysis. As the rapid development of information technology, the scale of network data is rapidly increasing. However, node centrality computation in large-scale networks is time consuming. Parallel computing is an alternative to speed up the computation of node centrality. GPU, which has been a core component of modern computer, can make a large number of core tasks work in parallel and has the ability of big data processing, and has been widely used to accelerate computing. Therefore, according to the parallel characteristic of GPU, we design the parallel algorithms to compute three widely used node centralities, i.e., closeness centrality, betweenness centrality and PageRank centrality. Firstly, we classify the three node centralities into two groups according to their definitions; secondly, we design the parallel algorithms by mapping the centrality computation of different nodes into different blocks or threads in GPU; thirdly, we analyze the correlations between different centralities in several networks, benefited from the designed parallel algorithms. Experimental results show that the parallel algorithms designed in this paper can speed up the computation of node centrality in large-scale networks, and the closeness centrality and the betweenness centrality are weakly correlated, although both of them are based on the shortest path.</p> </abstract>

scholarly journals A parallel computational framework for ultra-large-scale sequence clustering analysis

2018 ◽  
Vol 35 (3) ◽  
pp. 380-388 ◽  
Author(s):  
Wei Zheng ◽  
Qi Mao ◽  
Robert J Genco ◽  
Jean Wactawski-Wende ◽  
Michael Buck ◽  
...  
Keyword(s):  
Parallel Computing ◽  
High Performance ◽  
Large Scale ◽  
De Novo ◽  
Rapid Development ◽  
Operational Taxonomic Unit ◽  
Supplementary Information ◽  
Computational Framework ◽  
Speed Up ◽  
Scale Sequence

Abstract Motivation The rapid development of sequencing technology has led to an explosive accumulation of genomic data. Clustering is often the first step to be performed in sequence analysis. However, existing methods scale poorly with respect to the unprecedented growth of input data size. As high-performance computing systems are becoming widely accessible, it is highly desired that a clustering method can easily scale to handle large-scale sequence datasets by leveraging the power of parallel computing. Results In this paper, we introduce SLAD (Separation via Landmark-based Active Divisive clustering), a generic computational framework that can be used to parallelize various de novo operational taxonomic unit (OTU) picking methods and comes with theoretical guarantees on both accuracy and efficiency. The proposed framework was implemented on Apache Spark, which allows for easy and efficient utilization of parallel computing resources. Experiments performed on various datasets demonstrated that SLAD can significantly speed up a number of popular de novo OTU picking methods and meanwhile maintains the same level of accuracy. In particular, the experiment on the Earth Microbiome Project dataset (∼2.2B reads, 437 GB) demonstrated the excellent scalability of the proposed method. Availability and implementation Open-source software for the proposed method is freely available at https://www.acsu.buffalo.edu/~yijunsun/lab/SLAD.html. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals How advocacy affects Twitter migraine conversations: A pilot cross-sectional survey of Northeast American “migraine” landscape on Twitter from May to June 2020

2020 ◽  
Vol 3 ◽  
pp. 251581632097208
Author(s):  
Pengfei Zhang ◽  
Santosh Bhaskarabhatla
Keyword(s):  
United States ◽  
Social Media ◽  
Network Analysis ◽  
Network Model ◽  
Large Scale ◽  
The United States ◽  
Closeness Centrality ◽  
Control Group ◽  
Annual Conference ◽  
Sources Of Information

Background: Twitter is a leading microblogging platform, with over 126 million daily active users as of 2019, which allows for large-scale analysis of tweets related to migraine. June 2020 encompassed the National Migraine and Headache Awareness Month in the United States and the American Headache Society’s virtual annual conference, which offer opportunities for us to study online migraine advocacy. Objective: We aim to study the content of individual tweets about migraine, as well as study patterns of other topics that were discussed in those tweets. In addition, we aim to study the sources of information that people reference within their tweets. Thirdly, we want to study how online awareness and advocacy movements shape these conversations about migraine. Methods: We designed a Twitter robot that records all unique public tweets containing the word “migraine” from May 8th, 2020 to June 23rd, 2020, within a 400 km radius of New Brunswick, New Jersey, United States. We built two network analysis models, one for the months of May 2020 and June 2020. The model for the month of May served as a control group for the model for the month of June, the Migraine Awareness Month. Our network model was developed with the following rule: if two hashtag topics co-exist in a single tweet, they are considered nodes connected by an edge in our network model. We then determine the top 30 most important hashtags in the month of May and June through applications of degree, between-ness, and closeness centrality. We also generated highly connected subgraphs (HCS) to categorize clusters of conversations within each of our models. Finally, we tally the websites referenced by these tweets during each month and categorized these websites according to the HCS subgroups. Results: Migraine advocacy related tweets are more popular in June when compared to May as judged by degree and closeness centrality measurements. They remained unchanged when judged by between-ness centralities. The HCS algorithm categorizes the hashtags into a large single dominant conversation in both months. In each of the months, advocacy related hashtags are apart of each of the dominant conversation. There are more hashtag topics as well as more unique websites referenced in the dominant conversation in June than in May. In addition, there are many smaller subgroups of migraine-related hashtags, and in each of these subgroups, there are a maximum of two websites referenced. Conclusion: We find a network analysis approach to be fruitful in the area of migraine social media research. Migraine advocacy tweets on Twitter not only rise in popularity during migraine awareness month but also may potentially bring in more diverse sources of online references into the Twitter migraine conversation. The smaller subgroups we identified suggest that there are marginalized conversations referencing a limited number of websites, creating a possibility of an “echo chamber” phenomenon. These subgroups provide an opportunity for targeted migraine advocacy. Our study therefore highlights the success as well as potential opportunities for social media advocacy on Twitter.

Interpretive MPI for Parallel Computing

2008 ◽  
Author(s):  
Yu-Cheng Chou ◽  
Harry H. Cheng
Keyword(s):  
Parallel Computing ◽  
Programming Languages ◽  
Message Passing ◽  
Large Scale ◽  
Message Passing Interface ◽  
Rapid Development ◽  
Web Based ◽  
Heterogeneous Platforms ◽  
C Programs ◽  
Computation Speedup

Message Passing Interface (MPI) is a standardized library specification designed for message-passing parallel programming on large-scale distributed systems. A number of MPI libraries have been implemented to allow users to develop portable programs using the scientific programming languages, Fortran, C and C++. Ch is an embeddable C/C++ interpreter that provides an interpretive environment for C/C++ based scripts and programs. Combining Ch with any MPI C/C++ library provides the functionality for rapid development of MPI C/C++ programs without compilation. In this article, the method of interfacing Ch scripts with MPI C implementations is introduced by using the MPICH2 C library as an example. The MPICH2-based Ch MPI package provides users with the ability to interpretively run MPI C program based on the MPICH2 C library. Running MPI programs through the MPICH2-based Ch MPI package across heterogeneous platforms consisting of Linux and Windows machines is illustrated. Comparisons for the bandwidth, latency, and parallel computation speedup between C MPI, Ch MPI, and MPI for Python in an Ethernet-based environment comprising identical Linux machines are presented. A Web-based example is given to demonstrate the use of Ch and MPICH2 in C based CGI scripting to facilitate the development of Web-based applications for parallel computing.

scholarly journals Research on Community Detection in Complex Networks Based on Internode Attraction

Entropy ◽  
2020 ◽  
Vol 22 (12) ◽  
pp. 1383
Author(s):  
Jinfang Sheng ◽  
Cheng Liu ◽  
Long Chen ◽  
Bin Wang ◽  
Junkai Zhang
Keyword(s):  
Community Structure ◽  
Complex Networks ◽  
Community Detection ◽  
Large Scale ◽  
Rapid Development ◽  
Structure Detection ◽  
Detection Approach ◽  
Real World Datasets ◽  
New Community ◽  
Large Scale Networks

With the rapid development of computer technology, the research on complex networks has attracted more and more attention. At present, the research directions of cloud computing, big data, internet of vehicles, and distributed systems with very high attention are all based on complex networks. Community structure detection is a very important and meaningful research hotspot in complex networks. It is a difficult task to quickly and accurately divide the community structure and run it on large-scale networks. In this paper, we put forward a new community detection approach based on internode attraction, named IACD. This algorithm starts from the perspective of the important nodes of the complex network and refers to the gravitational relationship between two objects in physics to represent the forces between nodes in the network dataset, and then perform community detection. Through experiments on a large number of real-world datasets and synthetic networks, it is shown that the IACD algorithm can quickly and accurately divide the community structure, and it is superior to some classic algorithms and recently proposed algorithms.

scholarly journals Penerapan Social Network Analysis dalam Penentuan Centrality Studi Kasus Social Network Twitter

2012 ◽  
Vol 8 (1) ◽  
Author(s):  
Budi Susanto ◽  
Herlina Lina ◽  
Antonius Rachmat Chrismanto
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Betweenness Centrality ◽  
Closeness Centrality ◽  
Specific Form ◽  
Analysis Method ◽  
System User

The twitter provides a kind of relation between users in specific form. When someone follow others, it doesn’t mean that she/he know well about them. We have defined a friend relationship between users in twitter as connection following and follower between two users. Based on this definition we develop a system to get friends and also friends of friends relation from a specific user. We use twitter API to get following and follower list and then construct a graph that represent a social network between those users. From this graph, we analyse the centrality using SNA (Social Network Analysis) method, i.e. closeness and betweeness. We propose to use these methods in order to find out who is the most influence user in the his/her social network to spread out the tweet or information. With this system, user can know about their social network based on their friend list on twitter.   Kata Kunci : Social Network Analysis, Betweenness Centrality, Closeness Centrality

scholarly journals Peran Pers Sebagai Aktor Gerakan Digital Tagar #SolidaritasUntukNTT di Twitter

2021 ◽  
Vol 5 (1) ◽  
pp. 98
Author(s):  
Gema Nusantara Bakry ◽  
Ika Merdekawati Kusmayadi
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Betweenness Centrality ◽  
Closeness Centrality ◽  
Degree Centrality ◽  
Eigenvector Centrality ◽  
Personal Network

Peristiwa banjir bandang yang diakibatkan Siklon Seroja telah mengundang perhatian dan simpati masyarakat Indonesia. Berbagai upaya telah dilakukan untuk berkontribusi dalam upaya penanggulangan dampak yang diterima oleh masyarakat NTT. Salah satu upaya yang dilakukan oleh masyarakat adalah mengampanyekan gerakan sosial digital #SolidaritasUntukNTT di Twitter. Gerakan sosial digital melalui pesan-pesan tertentu dapat menggugah kesadaran bagi penggunanya. Untuk mengetahui efektivitas penyebaran pesan dalam gerakan sosial digital dapat divisualisasikan menggunakan metode Social Network Analysis (SNA).  Penelitian ini bertujuan untuk memvisualisasikan peran pers dalam mendistribusikan pesan gerakan sosial digital dengan tagar #SolidaritasUntukNTT. Metode penelitian yang digunakan adalah analisis jaringan sosial dengan teori graf di Twitter. Hasil analisis dan visualisasi jaringan dilakukan di aplikasi Gephi dengan algoritma Yifan Hu untuk melihat distribusi pola pesan dan peran pers pada tagar #SolidaritasUntukNTT. Penelitian ini menggambarkan tipe jaringan two mode yang terdiri dari interaksi antara individu dan organisasi dengan pola komunikasi radial personal network yang memiliki ciri jaringan terbuka dan kohesivitas yang rendah dengan arah relasi directed dan asimetris. Analisis peran pers diukur melalui sentralitas aktor untuk mengetahui degree centrality, closeness centrality, betweenness centrality dan eigenvector centrality. Aktor @vice_id diketahui sebagai aktor yang memiliki degree dan eigenvector centrality tertinggi dibandingkan dengan aktor pers lainnya. Aktor @idntimes dan @detikcom memiliki nilai closeness dan betweenness centrality yang lebih tinggi dari media lainnya. Analisis jaringan sosial memberikan pemahaman terkait distribusi pesan dalam media sosial untuk mengetahui efektivitas pesan yang didistribusikan oleh beberapa aktor jaringan, khususnya peran pers dalam mengampanyekan gerakan sosial di media. Oleh karena itu, metode SNA dapat digunakan untuk penelitian jurnalisme data. 

scholarly journals A network analysis of character relations in Etienne van Heerden’s Toorberg

Literator ◽  
2013 ◽  
Vol 34 (2) ◽  
Author(s):  
Burgert A. Senekal
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Betweenness Centrality ◽  
Theoretical Framework ◽  
Closeness Centrality ◽  
Degree Centrality ◽  
Eigenvector Centrality ◽  
Traditional Concept ◽  
Family Ties

Etienne van Heerden’s Toorberg can be approached as a modern, postcolonial farm novel, partly because it challenges the concept of lineage of inheritance, which is characteristic of the traditional farm novel. Lineage of inheritance implies a strong family bond, and it is therefore instructive to investigate how family ties function within this novel. The article views family ties within Toorberg using Social Network Analysis (SNA), a largely unknown theoretical framework that can also be applied within the study of literature. It is shown how characters’ positions in this network can be calculated in terms of degree centrality, closeness centrality, Eigenvector centrality and betweenness centrality, and how these measures expose the way in which this novel undermines the traditional concept of inheritance.

scholarly journals Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda

2021 ◽  
Author(s):  
J. J. Johannes Hjorth ◽  
Jeanette Hellgren Kotaleski ◽  
Alexander Kozlov
Keyword(s):  
Large Scale ◽  
Model Building ◽  
Rapid Development ◽  
Dorsal Striatum ◽  
Simulated Data ◽  
Cellular Level ◽  
Simulation Software ◽  
Important Approach ◽  
Set Up ◽  
Large Scale Networks

AbstractSimulation of large-scale networks of neurons is an important approach to understanding and interpreting experimental data from healthy and diseased brains. Owing to the rapid development of simulation software and the accumulation of quantitative data of different neuronal types, it is possible to predict both computational and dynamical properties of local microcircuits in a ‘bottom-up’ manner. Simulated data from these models can be compared with experiments and ‘top-down’ modelling approaches, successively bridging the scales. Here we describe an open source pipeline, using the software Snudda, for predicting microcircuit connectivity and for setting up simulations using the NEURON simulation environment in a reproducible way. We also illustrate how to further ‘curate’ data on single neuron morphologies acquired from public databases. This model building pipeline was used to set up a first version of a full-scale cellular level model of mouse dorsal striatum. Model components from that work are here used to illustrate the different steps that are needed when modelling subcortical nuclei, such as the basal ganglia.

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