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Dagstuhl Seminar Proceedings, Volume 8191

Part of: Series: Dagstuhl Seminar Proceedings (DagSemProc)

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published at: 2008-07-22
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik

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Document

DOI: 10.4230/DagSemProc.08191.1

08191 Abstracts Collection – Graph Drawing with Applications to Bioinformatics and Social Sciences

Authors: Stephen Borgatti, Stephen Kobourov, Oliver Kohlbacher, and Petra Mutzel

Abstract

From May 4 to May 9, 2008, the Dagstuhl Seminar 08191 ``Graph Drawing with Applications to Bioinformatics and Social Sciences'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.

Cite as

Stephen Borgatti, Stephen Kobourov, Oliver Kohlbacher, and Petra Mutzel. 08191 Abstracts Collection – Graph Drawing with Applications to Bioinformatics and Social Sciences. In Graph Drawing with Applications to Bioinformatics and Social Sciences. Dagstuhl Seminar Proceedings, Volume 8191, pp. 1-10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{borgatti_et_al:DagSemProc.08191.1,
  author =	{Borgatti, Stephen and Kobourov, Stephen and Kohlbacher, Oliver and Mutzel, Petra},
  title =	{{08191 Abstracts Collection – Graph Drawing with Applications to Bioinformatics and Social Sciences}},
  booktitle =	{Graph Drawing with Applications to Bioinformatics and Social Sciences},
  pages =	{1--10},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8191},
  editor =	{Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08191.1},
  URN =		{urn:nbn:de:0030-drops-15547},
  doi =		{10.4230/DagSemProc.08191.1},
  annote =	{Keywords: Graph drawing, visualization, social sciences, bioinformatics}
}

Document

DOI: 10.4230/DagSemProc.08191.2

08191 Executive Summary – Graph Drawing with Applications to Bioinformatics and Social Sciences

Authors: Stephen Borgatti, Stephen Kobourov, Oliver Kohlbacher, and Petra Mutzel

Abstract

Graph drawing deals with the problem of communicating the structure of relational data through diagrams, or drawings. The ability to represent relational information in a graphical form is a powerful tool which allows to perform analysis through visual exploration to find important patterns, trends, and correlations. Real-world applications such as bioinformatics and sociology pose challenges to the relational visualization because, e.g., semantic information carried by the diagram has to be used for obtaining meaningful layouts and application-specific drawing conventions need to be fulfilled. Moreover, the underlying data often stems from huge data bases, but only a small fraction shall be displayed at a time; the user interactively selects the data to be displayed and explores the graph by expanding interesting and collapsing irrelevant parts. This requires powerful graph exploration tools with navigation capabilities that allow dynamic adaption of the graph layout in real time. In this seminar we focused on the application of graph drawing in two important application domains: bioinformatics and social sciences. We brought together theoreticians and practitioners from these areas and focused on problems concerning interaction with and navigation in large and dynamic networks arising in these application areas; During the seminar, we identified and defined open graph drawing problems that are motivated by practical applications in the targeted application areas, tackled selected open problems, formulated the findings as a first step to the solution, and defined further research directions.

Cite as

Stephen Borgatti, Stephen Kobourov, Oliver Kohlbacher, and Petra Mutzel. 08191 Executive Summary – Graph Drawing with Applications to Bioinformatics and Social Sciences. In Graph Drawing with Applications to Bioinformatics and Social Sciences. Dagstuhl Seminar Proceedings, Volume 8191, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{borgatti_et_al:DagSemProc.08191.2,
  author =	{Borgatti, Stephen and Kobourov, Stephen and Kohlbacher, Oliver and Mutzel, Petra},
  title =	{{08191 Executive Summary – Graph Drawing with Applications to Bioinformatics and Social Sciences}},
  booktitle =	{Graph Drawing with Applications to Bioinformatics and Social Sciences},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8191},
  editor =	{Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08191.2},
  URN =		{urn:nbn:de:0030-drops-15523},
  doi =		{10.4230/DagSemProc.08191.2},
  annote =	{Keywords: Graph drawing, visualization, social sciences, bioinformatics}
}

Document

DOI: 10.4230/DagSemProc.08191.3

08191 Working Group Report – Edge Thresholding

Authors: Patrick Healy and Tim Dwyer

Abstract

When working with very large networks it is typical for scientists to present a ``thinned out'' version of the network in order to avoid the clutter of the entire network. For example in the hypothetical case of illustrating trading patterns between groups of nations it might be appropriate to limit the inclusion of inter-nation edges to all those that are significant in terms of their weight but do not, say, associate with a country outside the grouping. Arising from a discussion during one of the introductory sessions we became interested in a problem relating to the discovery of ``key events'' in a network, in terms of an ordered addition of edges to the network.

Cite as

Patrick Healy and Tim Dwyer. 08191 Working Group Report – Edge Thresholding. In Graph Drawing with Applications to Bioinformatics and Social Sciences. Dagstuhl Seminar Proceedings, Volume 8191, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{healy_et_al:DagSemProc.08191.3,
  author =	{Healy, Patrick and Dwyer, Tim},
  title =	{{08191 Working Group Report – Edge Thresholding}},
  booktitle =	{Graph Drawing with Applications to Bioinformatics and Social Sciences},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8191},
  editor =	{Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08191.3},
  URN =		{urn:nbn:de:0030-drops-15570},
  doi =		{10.4230/DagSemProc.08191.3},
  annote =	{Keywords: Graph drawing, edge thresholding}
}

Document

DOI: 10.4230/DagSemProc.08191.4

08191 Working Group Report – Visualization of Trajectories

Authors: Stephen Borgatti, Ulrik Brandes, Michael Kaufmann, Stephen Kobourov, Anna Lubiw, and Dorothea Wagner

Abstract

We considered the following problem: Given a set of vertices V and a set of paths P, where each path is a sequence of vertices, represent these paths somehow. We explored representations in different dimensions and with different conditions on the paths.

Cite as

Stephen Borgatti, Ulrik Brandes, Michael Kaufmann, Stephen Kobourov, Anna Lubiw, and Dorothea Wagner. 08191 Working Group Report – Visualization of Trajectories. In Graph Drawing with Applications to Bioinformatics and Social Sciences. Dagstuhl Seminar Proceedings, Volume 8191, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{borgatti_et_al:DagSemProc.08191.4,
  author =	{Borgatti, Stephen and Brandes, Ulrik and Kaufmann, Michael and Kobourov, Stephen and Lubiw, Anna and Wagner, Dorothea},
  title =	{{08191 Working Group Report – Visualization of Trajectories}},
  booktitle =	{Graph Drawing with Applications to Bioinformatics and Social Sciences},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8191},
  editor =	{Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08191.4},
  URN =		{urn:nbn:de:0030-drops-15558},
  doi =		{10.4230/DagSemProc.08191.4},
  annote =	{Keywords: Graph drawing, trajectories, paths}
}

Document

DOI: 10.4230/DagSemProc.08191.5

08191 Working Group Report – X-graphs of Y-graphs and their Representations

Authors: Vladimir Batagelj, Franz J. Brandenburg, Walter Didimo, Guiseppe Liotta, and Maurizio Patrignani

Abstract

We address graph decomposition problems that help the hybrid visualization of large graphs, where different graphic metaphors (node-link, matrix, etc.) are used in the same picture. We generalize the $X$-graphs of $Y$-graphs model introduced by Brandenburg (Brandenburg, F.J.: Graph clustering I: Cycles of cliques. In Di Battista, G., ed.: Graph Drawing (Proc. GD '97). Volume 1353 of Lecture Notes Comput. Sci., Springer-Verlag (1997) 158--168) to formalize the problem of automatically identifying dense subgraphs ($Y$-graphs, clusters) that are prone to be collapsed and shown with a matricial representation when needed. We show that (planar, $K_5$)-recognition, that is, the problem of identifying $K_5$ subgraphs such that the graph obtained by collapsing them is planar, is NP-hard. On the positive side, we show that it is possible to determine the highest value of $k$ such that $G$ is a (planar,$k$-core)-graph in $O(m + n log(n))$ time.

Cite as

Vladimir Batagelj, Franz J. Brandenburg, Walter Didimo, Guiseppe Liotta, and Maurizio Patrignani. 08191 Working Group Report – X-graphs of Y-graphs and their Representations. In Graph Drawing with Applications to Bioinformatics and Social Sciences. Dagstuhl Seminar Proceedings, Volume 8191, pp. 1-17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{batagelj_et_al:DagSemProc.08191.5,
  author =	{Batagelj, Vladimir and Brandenburg, Franz J. and Didimo, Walter and Liotta, Guiseppe and Patrignani, Maurizio},
  title =	{{08191 Working Group Report – X-graphs of Y-graphs and their Representations}},
  booktitle =	{Graph Drawing with Applications to Bioinformatics and Social Sciences},
  pages =	{1--17},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8191},
  editor =	{Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08191.5},
  URN =		{urn:nbn:de:0030-drops-15563},
  doi =		{10.4230/DagSemProc.08191.5},
  annote =	{Keywords: Graph drawing, X-graphs of Y-graphs, visualization of large graphs}
}

Document

DOI: 10.4230/DagSemProc.08191.6

08191 Working Group Summary – Visually Comparing a Set of Graphs

Authors: Mario Albrecht, Alejandro Estrella-Balderrama, Markus Geyer, Carsten Gutwenger, Karsten Klein, Oliver Kohlbacher, and Michael Schulz

Abstract

We consider methods to visually compare graphs, more to focus on the differences of the graphs than on the similarities. Our two-level approach constructs a meaningful overview of the given graphs combined with a detailed view focusing on a local area of change. The actual layout of these graphs has to be evaluated depending on the specific type of biological network to be visualized in each case. We look into different variants and propose properties to be optimized in our visualizations.

Cite as

Mario Albrecht, Alejandro Estrella-Balderrama, Markus Geyer, Carsten Gutwenger, Karsten Klein, Oliver Kohlbacher, and Michael Schulz. 08191 Working Group Summary – Visually Comparing a Set of Graphs. In Graph Drawing with Applications to Bioinformatics and Social Sciences. Dagstuhl Seminar Proceedings, Volume 8191, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{albrecht_et_al:DagSemProc.08191.6,
  author =	{Albrecht, Mario and Estrella-Balderrama, Alejandro and Geyer, Markus and Gutwenger, Carsten and Klein, Karsten and Kohlbacher, Oliver and Schulz, Michael},
  title =	{{08191 Working Group Summary – Visually Comparing a Set of Graphs}},
  booktitle =	{Graph Drawing with Applications to Bioinformatics and Social Sciences},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8191},
  editor =	{Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08191.6},
  URN =		{urn:nbn:de:0030-drops-15536},
  doi =		{10.4230/DagSemProc.08191.6},
  annote =	{Keywords: Graph drawing, visual graph comparison}
}

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