Persistent Homology Guided Force-Directed Graph Layouts

Graphs are commonly used to encode relationships among entities, yet their abstractness makes them difficult to analyze. Node-link diagrams are popular for drawing graphs, and force-directed layouts provide a flexible method for node arrangements that use local relationships in an attempt to reveal the global shape of the graph. However, clutter and overlap of unrelated structures can lead to confusing graph visualizations. This paper leverages the persistent homology features of an undirected graph as derived information for interactive manipulation of force-directed layouts. We first discuss how to efficiently extract 0-dimensional persistent homology features from both weighted and unweighted undirected graphs. We then introduce the interactive persistence barcode used to manipulate the force-directed graph layout. In particular, the user adds and removes contracting and repulsing forces generated by the persistent homology features, eventually selecting the set of persistent homology features that most improve the layout. Finally, we demonstrate the utility of our approach across a variety of synthetic and real datasets

Interactive visualisation and exploration of biological data

International audienceno abstrac

Museum Experience Design: A Modern Storytelling Methodology

In this paper we propose a new direction for design, in the context of the theme “Next Digital Technologies in Arts and Culture”, by employing modern methods based on Interaction Design, Interactive Storytelling and Artificial Intelligence. Focusing on Cultural Heritage, we propose a new paradigm for Museum Experience Design, facilitating on the one hand traditional visual and multimedia communication and, on the other, a new type of interaction with artefacts, in the form of a Storytelling Experience. Museums are increasingly being transformed into hybrid spaces, where virtual (digital) information coexists with tangible artefacts. In this context, “Next Digital Technologies” play a new role, providing methods to increase cultural accessibility and enhance experience. Not only is the goal to convey stories hidden inside artefacts, as well as items or objects connected to them, but it is also to pave the way for the creation of new ones through an interactive museum experience that continues after the museum visit ends. Social sharing, in particular, can greatly increase the value of dissemination

Speculative practices : utilizing InfoVis to explore untapped literary collections

Funding: Canadian Social Sciences and Humanities Research CouncilIn this paper we exemplify how information visualization supports speculative thinking, hypotheses testing, and preliminary interpretation processes as part of literary research. While InfoVis has become a buzz topic in the digital humanities, skepticism remains about how effectively it integrates into and expands on traditional humanities research approaches. From an InfoVis perspective, we lack case studies that show the specific design challenges that make literary studies and humanities research at large a unique application area for information visualization. We examine these questions through our case study of the Speculative W@nderverse, a visualization tool that was designed to enable the analysis and exploration of an untapped literary collection consisting of thousands of science fiction short stories. We present the results of two empirical studies that involved general-interest readers and literary scholars who used the evolving visualization prototype as part of their research for over a year. Our findings suggest a design space for visualizing literary collections that is defined by (1) their academic and public relevance, (2) the tension between qualitative vs. quantitative methods of interpretation, (3) result- vs. process-driven approaches to InfoVis, and (4) the unique material and visual qualities of cultural collections. Through the Speculative W@nderverse we demonstrate how visualization can bridge these sometimes contradictory perspectives by cultivating curiosity and providing entry points into literary collections while, at the same time, supporting multiple aspects of humanities research processes.PostprintPeer reviewe

TreeViewJ: An Application for Viewing and Analyzing Phylogenetic Trees

BACKGROUND. Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images. RESULTS. We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order. CONCLUSION. TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net

Visualization of back pain data-A 3-D solution

Traditional approaches to gathering and visualizing pain data rely on two-dimensional (2-D) human body models, where different types of sensation are recorded with various monochrome symbols. We proposean alternative that uses a three-dimensional (3-D) representation of the human body, which can be marked in color to visualize and record pain data

Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm

Peer reviewedPublisher PD