Community Fabric: Visualizing communities and structure in dynamic networks

2021 ◽  
pp. 147387162110560
Author(s):  
Evan Ezell ◽  
Seung-Hwan Lim ◽  
David Anderson ◽  
Robert Stewart
Keyword(s):  
Dynamic Networks ◽  
Dynamic Network ◽  
Data Sets ◽  
Dynamic Graphs ◽  
Visualization Technique ◽  
Web Based ◽  
New Approach ◽  
Community Evolution ◽  
Underlying Network ◽  
Flow Diagrams

We present Community Fabric, a novel visualization technique for simultaneously visualizing communities and structure within dynamic networks. In dynamic networks, the structure of the network is continuously evolving throughout time and these underlying topological shifts tend to lead to communal changes. Community Fabric helps the viewer more easily interpret and understand the interplay of structural change and community evolution in dynamic graphs. To achieve this, we take a new approach, hybridizing two popular network and community visualizations. Community Fabric combines the likes of the Biofabric static network visualization method with traditional community alluvial flow diagrams to visualize communities in a dynamic network while also displaying the underlying network structure. Our approach improves upon existing state-of-the-art techniques in several key areas. We describe the methodologies of Community Fabric, implement the visualization using modern web-based tools, and apply our approach to three example data sets.

Effective Temporal Graph Layout: A Comparative Study of Animation versus Static Display Methods

2011 ◽  
Vol 10 (1) ◽  
pp. 47-64 ◽  
Author(s):  
Michael Farrugia ◽  
Aaron Quigley
Keyword(s):  
Graph Drawing ◽  
Dynamic Networks ◽  
Experimental System ◽  
Graph Layout ◽  
Dynamic Graphs ◽  
Social Scientists ◽  
Web Based ◽  
Time Performance ◽  
Level Information ◽  
Micro Level

Graph drawing algorithms have classically addressed the layout of static graphs. However, the need to draw evolving or dynamic graphs has brought into question many of the assumptions, conventions and layout methods designed to date. For example, social scientists studying evolving social networks have created a demand for visual representations of graphs changing over time. Two common approaches to represent temporal information in graphs include animation of the network and use of static snapshots of the network at different points in time. Here, we report on two experiments, one in a laboratory environment and another using an asynchronous remote web-based platform, Mechanical Turk, to compare the efficiency of animated displays versus static displays. Four tasks are studied with each visual representation, where two characterise overview level information presentation, and two characterise micro level analytical tasks. For the tasks studied in these experiments and within the limits of the experimental system, the results of this study indicate that static representations are generally more effective particularly in terms of time performance, when compared to fully animated movie representations of dynamic networks.

Survey Data Quality in Analyzing Harmonized Indicators of Protest Behavior: A Survey Data Recycling Approach

2021 ◽  
pp. 000276422110216
Author(s):  
Kazimierz M. Slomczynski ◽  
Irina Tomescu-Dubrow ◽  
Ilona Wysmulek
Keyword(s):  
Data Processing ◽  
Data Quality ◽  
Survey Data ◽  
A Priori ◽  
Data Sets ◽  
New Approach ◽  
Survey Quality ◽  
Survey Error ◽  
Ex Post ◽  
The Impact

This article proposes a new approach to analyze protest participation measured in surveys of uneven quality. Because single international survey projects cover only a fraction of the world’s nations in specific periods, researchers increasingly turn to ex-post harmonization of different survey data sets not a priori designed as comparable. However, very few scholars systematically examine the impact of the survey data quality on substantive results. We argue that the variation in source data, especially deviations from standards of survey documentation, data processing, and computer files—proposed by methodologists of Total Survey Error, Survey Quality Monitoring, and Fitness for Intended Use—is important for analyzing protest behavior. In particular, we apply the Survey Data Recycling framework to investigate the extent to which indicators of attending demonstrations and signing petitions in 1,184 national survey projects are associated with measures of data quality, controlling for variability in the questionnaire items. We demonstrate that the null hypothesis of no impact of measures of survey quality on indicators of protest participation must be rejected. Measures of survey documentation, data processing, and computer records, taken together, explain over 5% of the intersurvey variance in the proportions of the populations attending demonstrations or signing petitions.

scholarly journals DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations

2021 ◽  
Vol 12 (15) ◽  
pp. 5473-5483
Author(s):  
Zhixin Zhou ◽  
Jianbang Wang ◽  
R. D. Levine ◽  
Francoise Remacle ◽  
Itamar Willner
Keyword(s):  
Nucleic Acid ◽  
Dynamic Networks ◽  
Dynamic Network ◽  
Logic Gates ◽  
Functional Modules ◽  
Logic Operations

A nucleic acid-based constitutional dynamic network (CDN) provides a single functional computational module for diverse input-guided logic operations and computing circuits.

Recent and Planned Developments of the Program OxCal

Radiocarbon ◽  
2013 ◽  
Vol 55 (2) ◽  
pp. 720-730 ◽  
Author(s):  
Christopher Bronk Ramsey ◽  
Sharen Lee
Keyword(s):  
Statistical Analysis ◽  
Statistical Methods ◽  
Software Package ◽  
Model Averaging ◽  
Data Sets ◽  
Radiocarbon Dates ◽  
New Approach ◽  
New Models ◽  
Multiphase Models ◽  
Deposition Models

OxCal is a widely used software package for the calibration of radiocarbon dates and the statistical analysis of 14C and other chronological information. The program aims to make statistical methods easily available to researchers and students working in a range of different disciplines. This paper will look at the recent and planned developments of the package. The recent additions to the statistical methods are primarily aimed at providing more robust models, in particular through model averaging for deposition models and through different multiphase models. The paper will look at how these new models have been implemented and explore the implications for researchers who might benefit from their use. In addition, a new approach to the evaluation of marine reservoir offsets will be presented. As the quantity and complexity of chronological data increase, it is also important to have efficient methods for the visualization of such extensive data sets and methods for the presentation of spatial and geographical data embedded within planned future versions of OxCal will also be discussed.

Quasi-2D inversion of DCR and TDEM data for shallow investigations

Geophysics ◽  
2011 ◽  
Vol 76 (4) ◽  
pp. F239-F250 ◽  
Author(s):  
Fernando A. Monteiro Santos ◽  
Hesham M. El-Kaliouby
Keyword(s):  
Joint Inversion ◽  
Synthetic Data ◽  
Data Sets ◽  
Complex Environments ◽  
Inversion Algorithm ◽  
2D Inversion ◽  
New Approach ◽  
Earth Models ◽  
Time Domain Electromagnetic ◽  
Inversion Techniques

Joint or sequential inversion of direct current resistivity (DCR) and time-domain electromagnetic (TDEM) data commonly are performed for individual soundings assuming layered earth models. DCR and TDEM have different and complementary sensitivity to resistive and conductive structures, making them suitable methods for the application of joint inversion techniques. This potential joint inversion of DCR and TDEM methods has been used by several authors to reduce the ambiguities of the models calculated from each method separately. A new approach for joint inversion of these data sets, based on a laterally constrained algorithm, was found. The method was developed for the interpretation of soundings collected along a line over a 1D or 2D geology. The inversion algorithm was tested on two synthetic data sets, as well as on field data from Saudi Arabia. The results show that the algorithm is efficient and stable in producing quasi-2D models from DCR and TDEM data acquired in relatively complex environments.

scholarly journals Giovanni: The Bridge Between Data and Science

Eos ◽  
2017 ◽  
Author(s):  
Zhong Liu ◽  
James Acker
Keyword(s):  
Remote Sensing ◽  
Satellite Remote Sensing ◽  
Earth Science ◽  
Remote Sensing Data ◽  
Data Sets ◽  
Science Data ◽  
Web Based ◽  
Sensing Data ◽  
Daunting Task ◽  
Earth Science Data

Using satellite remote sensing data sets can be a daunting task. Giovanni, a Web-based tool, facilitates access, visualization, and exploration for many of NASA’s Earth science data sets.

scholarly journals WONKAandOOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design

2017 ◽  
Vol 73 (3) ◽  
pp. 279-285
Author(s):  
Charlotte M. Deane ◽  
Ian D. Wall ◽  
Darren V. S. Green ◽  
Brian D. Marsden ◽  
Anthony R. Bradley
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Data Sets ◽  
Interaction Data ◽  
Activity Data ◽  
Ligand Interaction ◽  
Structure Based Drug Design ◽  
Web Based ◽  
Protein Ligand Interaction ◽  
Ligand Activity

In this work, two freely available web-based interactive computational tools that facilitate the analysis and interpretation of protein–ligand interaction data are described. Firstly,WONKA, which assists in uncovering interesting and unusual features (for example residue motions) within ensembles of protein–ligand structures and enables the facile sharing of observations between scientists. Secondly,OOMMPPAA, which incorporates protein–ligand activity data with protein–ligand structural data using three-dimensional matched molecular pairs.OOMMPPAAhighlights nuanced structure–activity relationships (SAR) and summarizes available protein–ligand activity data in the protein context. In this paper, the background that led to the development of both tools is described. Their implementation is outlined and their utility using in-house Structural Genomics Consortium (SGC) data sets and openly available data from the PDB and ChEMBL is described. Both tools are freely available to use and download at http://wonka.sgc.ox.ac.uk/WONKA/ and http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/.

scholarly journals PRISMA2020: an R package and Shiny app for producing PRISMA 2020-compliant flow diagrams, with interactivity for optimised digital transparency and Open Synthesis

2021 ◽  
Author(s):  
Neal R Haddaway ◽  
Matthew J Page ◽  
Christopher C Pritchard ◽  
Luke A McGuinness
Keyword(s):  
Systematic Review ◽  
Systematic Reviews ◽  
Science Communication ◽  
Review Process ◽  
Evidence Synthesis ◽  
R Package ◽  
Web Based ◽  
Shiny App ◽  
Data Files ◽  
Flow Diagrams

Background Reporting standards, such as PRISMA aim to ensure that the methods and results of systematic reviews are described in sufficient detail to allow full transparency. Flow diagrams in evidence syntheses allow the reader to rapidly understand the core procedures used in a review and examine the attrition of irrelevant records throughout the review process. Recent research suggests that use of flow diagrams in systematic reviews is poor and of low quality and called for standardised templates to facilitate better reporting in flow diagrams. The increasing options for interactivity provided by the Internet gives us an opportunity to support easy-to-use evidence synthesis tools, and here we report on the development of tools for the production of PRISMA 2020-compliant systematic review flow diagrams. Methods and Findings We developed a free-to-use, Open Source R package and web-based Shiny app to allow users to design PRISMA flow diagrams for their own systematic reviews. Our tools allow users to produce standardised visualisations that transparently document the methods and results of a systematic review process in a variety of formats. In addition, we provide the opportunity to produce interactive, web-based flow diagrams (exported as HTML files), that allow readers to click on boxes of the diagram and navigate to further details on methods, results or data files. We provide an interactive example here; https://driscoll.ntu.ac.uk/prisma/. Conclusions We have developed a user-friendly suite of tools for producing PRISMA 2020-compliant flow diagrams for users with coding experience and, importantly, for users without prior experience in coding by making use of Shiny. These free-to-use tools will make it easier to produce clear and PRISMA 2020-compliant systematic review flow diagrams. Significantly, users can also produce interactive flow diagrams for the first time, allowing readers of their reviews to smoothly and swiftly explore and navigate to further details of the methods and results of a review. We believe these tools will increase use of PRISMA flow diagrams, improve the compliance and quality of flow diagrams, and facilitate strong science communication of the methods and results of systematic reviews by making use of interactivity. We encourage the systematic review community to make use of these tools, and provide feedback to streamline and improve their usability and efficiency.

An experimental evaluation and guideline for path finding in weighted dynamic network

2021 ◽  
Vol 14 (11) ◽  
pp. 2127-2140
Author(s):  
Mengxuan Zhang ◽  
Lei Li ◽  
Xiaofang Zhou
Keyword(s):  
Shortest Path ◽  
State Of The Art ◽  
Dynamic Networks ◽  
Real Life ◽  
Dynamic Network ◽  
Problem Space ◽  
Network Applications ◽  
Complete Problem ◽  
Path Computation ◽  
Shortest Path Computation

Shortest path computation is a building block of various network applications. Since real-life networks evolve as time passes, the Dynamic Shortest Path (DSP) problem has drawn lots of attention in recent years. However, as DSP has many factors related to network topology, update patterns, and query characteristics, existing works only test their algorithms on limited situations without sufficient comparisons with other approaches. Thus, it is still hard to choose the most suitable method in practice. To this end, we first identify the determinant dimensions and constraint dimensions of the DSP problem and create a complete problem space to cover all possible situations. Then we evaluate the state-of-the-art DSP methods under the same implementation standard and test them systematically under a set of synthetic dynamic networks. Furthermore, we propose the concept of dynamic degree to classify the dynamic environments and use throughput to evaluate their performance. These results can serve as a guideline to find the best solution for each situation during system implementation and also identify research opportunities. Finally, we validate our findings on real-life dynamic networks.

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