A map visualization of a graph consists of a node-link diagram in which groups of nodes are enclosed in one or more polygonal regions, similar to countries in a geographic map. Many real-world graphs have naturally defined groups, e.g., a graph that represents collaborations between faculty members within a university, where the departments are the groups. A good visualization of such a graph should place departments that collaborate frequently as adjacent or nearby groups. While some set visualization methods can be used to create map visualizations for graphs with groups, the results can be poor and difficult to read due to fragmented groups or complicated polygonal shapes of the enclosing regions. With this in mind, we propose a new approach that constructs the polygons first and then renders the graph to obtain better control over the drawing properties. We design two methods based on this new approach and compare them with three prior techniques using seven quantitative metrics on several real-world datasets. Our experimental results demonstrate the proposed methods to outperform prior techniques in capturing the intended drawing features and have good performance in most of the metrics.

When visualizing a high-dimensional dataset, dimension reduction techniques are commonly employed which provide a single 2 dimensional view of the data. We describe ENS-t-SNE: an algorithm for Embedding Neighborhoods Simultaneously that generalizes the t-Stochastic Neighborhood Embedding approach. By using different viewpoints in ENS-t-SNE’s 3D embedding, one can visualize different types of clusters within the same high-dimensional dataset. This enables the viewer to see and keep track of the different types of clusters, which is harder to do when providing multiple 2D embeddings, where corresponding points cannot be easily identified. We illustrate the utility of ENS-t-SNE with real-world applications and provide an extensive quantitative evaluation with datasets of different types and sizes.

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.

We describe MPSE: a Multi-Perspective Simultaneous Embedding method for visualizing high-dimensional data, based on multiple pairwise distances between the data points. Specifically, MPSE computes positions for the points in 3D and provides different views into the data by means of 2D projections (planes) that preserve each of the given distance matrices. We consider two versions of the problem: fixed projections and variable projections. MPSE with fixed projections takes as input a set of pairwise distance matrices defined on the data points, along with the same number of projections and embeds the points in 3D so that the pairwise distances are preserved in the given projections. MPSE with variable projections takes as input a set of pairwise distance matrices and embeds the points in 3D while also computing the appropriate projections that preserve the pairwise distances. The proposed approach can be useful in multiple scenarios: from creating simultaneous embedding of multiple graphs on the same set of vertices, to reconstructing a 3D object from multiple 2D snapshots, to analyzing data from multiple points of view. We provide a functional prototype of MPSE that is based on an adaptive and stochastic generalization of multi-dimensional scaling to multiple distances and multiple variable projections. We provide an extensive quantitative evaluation with datasets of different sizes and using different number of projections, as well as several examples that illustrate the quality of the resulting solutions.

The Global Research Activity Map (GRAM) is an interactive web-based system for visualizing and analyzing worldwide scholarship activity as represented by research topics. The underlying data for GRAM is obtained from Google Scholar academic research profiles and is used to create a weighted topic graph. Nodes correspond to self-reported research topics and edges indicate co-occurring topics in the profiles. The GRAM system supports map-based interactive features, including semantic zooming, panning, and searching. Map overlays can be used to compare human resource investment, displayed as the relative number of active researchers in particular topic areas, as well scholarly output in terms of citations and normalized citation counts. Evaluation of the GRAM system, with the help of university research management stakeholders, reveals interesting patterns in research investment and output for universities across the world (USA, Europe, Asia) and for different types of universities. While some of these patterns are expected, others are surprising. Overall, GRAM can be a useful tool to visualize human resource investment and research productivity in comparison to peers at a local, regional and global scale. Such information is needed by university administrators to identify institutional strengths and weaknesses and to make strategic data-driven decisions.