Graph Models for Biological Pathway Visualization: State of the Art and Future Challenges

Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
Graph Models for Biological Pathway Visualization: State of the Art and Future Challenges, 20. October 2019, Vis 2019 Workshop, Canada
[paper]

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Abstract

The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an exam- ple of complex real-world networks, where vertices represent biolog- ical entities, and edges indicate the underlying connectivity. For this reason, using multilayer networks to model biological knowledge allows us to formally cover essential properties and theories in the field, which also raises challenges in visualization. This is because, in the early days of pathway visualization research, only restricted types of graphs, such as simple graphs, clustered graphs, and others were adopted. In this paper, we revisit a heterogeneous definition of biological networks and aim to provide an overview to see the gaps between data modeling and visual representation. The contribution will, therefore, lie in providing guidelines and challenges of using multilayer networks as a unified data structure for the biological pathway visualization.

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BibTeX

@WorkshopTalk{wu-2019-visworkshop,
  title =      "Graph Models for Biological Pathway Visualization: State of
               the Art and Future Challenges",
  author =     "Hsiang-Yun Wu and Martin N\"{o}llenburg and Ivan Viola",
  year =       "2019",
  abstract =   "The concept of multilayer networks has become recently
               integrated into complex systems modeling since it
               encapsulates a very general concept of complex
               relationships. Biological pathways are an exam- ple of
               complex real-world networks, where vertices represent
               biolog- ical entities, and edges indicate the underlying
               connectivity. For this reason, using multilayer networks to
               model biological knowledge allows us to formally cover
               essential properties and theories in the field, which also
               raises challenges in visualization. This is because, in the
               early days of pathway visualization research, only
               restricted types of graphs, such as simple graphs, clustered
               graphs, and others were adopted. In this paper, we revisit a
               heterogeneous definition of biological networks and aim to
               provide an overview to see the gaps between data modeling
               and visual representation. The contribution will, therefore,
               lie in providing guidelines and challenges of using
               multilayer networks as a unified data structure for the
               biological pathway visualization. ",
  month =      oct,
  event =      "Vis 2019 Workshop",
  location =   "Canada",
  keywords =   "Graph drawing, multilayer network, biological pathway",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2019/wu-2019-visworkshop/",
}