A parent-centered radial layout algorithm for interactive graph visualization and animation

We have developed (1) a graph visualization system that allows users to explore graphs by viewing them as a succession of spanning trees selected interactively, (2) a radial graph layout algorithm, and (3) an animation algorithm that generates meaningful visualizations and smooth transitions between graphs while minimizing edge crossings during transitions and in static layouts. Our system is similar to the radial layout system of Yee et al. (2001), but differs primarily in that each node is positioned on a coordinate system centered on its own parent rather than on a single coordinate system for all nodes. Our system is thus easy to define recursively and lends itself to parallelization. It also guarantees that layouts have many nice properties, such as: it guarantees certain edges never cross during an animation. We compared the layouts and transitions produced by our algorithms to those produced by Yee et al. Results from several experiments indicate that our system produces fewer edge crossings during transitions between graph drawings, and that the transitions more often involve changes in local scaling rather than structure. These findings suggest the system has promise as an interactive graph exploration tool in a variety of settings

Asynchronous Execution of Python Code on Task Based Runtime Systems

Despite advancements in the areas of parallel and distributed computing, the complexity of programming on High Performance Computing (HPC) resources has deterred many domain experts, especially in the areas of machine learning and artificial intelligence (AI), from utilizing performance benefits of such systems. Researchers and scientists favor high-productivity languages to avoid the inconvenience of programming in low-level languages and costs of acquiring the necessary skills required for programming at this level. In recent years, Python, with the support of linear algebra libraries like NumPy, has gained popularity despite facing limitations which prevent this code from distributed runs. Here we present a solution which maintains both high level programming abstractions as well as parallel and distributed efficiency. Phylanx, is an asynchronous array processing toolkit which transforms Python and NumPy operations into code which can be executed in parallel on HPC resources by mapping Python and NumPy functions and variables into a dependency tree executed by HPX, a general purpose, parallel, task-based runtime system written in C++. Phylanx additionally provides introspection and visualization capabilities for debugging and performance analysis. We have tested the foundations of our approach by comparing our implementation of widely used machine learning algorithms to accepted NumPy standards

Clear Visual Separation of Temporal Event Sequences

Extracting and visualizing informative insights from temporal event sequences becomes increasingly difficult when data volume and variety increase. Besides dealing with high event type cardinality and many distinct sequences, it can be difficult to tell whether it is appropriate to combine multiple events into one or utilize additional information about event attributes. Existing approaches often make use of frequent sequential patterns extracted from the dataset, however, these patterns are limited in terms of interpretability and utility. In addition, it is difficult to assess the role of absolute and relative time when using pattern mining techniques. In this paper, we present methods that addresses these challenges by automatically learning composite events which enables better aggregation of multiple event sequences. By leveraging event sequence outcomes, we present appropriate linked visualizations that allow domain experts to identify critical flows, to assess validity and to understand the role of time. Furthermore, we explore information gain and visual complexity metrics to identify the most relevant visual patterns. We compare composite event learning with two approaches for extracting event patterns using real world company event data from an ongoing project with the Danish Business Authority.Comment: In Proceedings of the 3rd IEEE Symposium on Visualization in Data Science (VDS), 201

ROOT - A C++ Framework for Petabyte Data Storage, Statistical Analysis and Visualization

ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, ROOT offers packages for complex data modeling and fitting, as well as multivariate classification based on machine learning techniques. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks - e.g. data mining in HEP - by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way

PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform

Security, Privacy and Safety Risk Assessment for Virtual Reality Learning Environment Applications

Social Virtual Reality based Learning Environments (VRLEs) such as vSocial render instructional content in a three-dimensional immersive computer experience for training youth with learning impediments. There are limited prior works that explored attack vulnerability in VR technology, and hence there is a need for systematic frameworks to quantify risks corresponding to security, privacy, and safety (SPS) threats. The SPS threats can adversely impact the educational user experience and hinder delivery of VRLE content. In this paper, we propose a novel risk assessment framework that utilizes attack trees to calculate a risk score for varied VRLE threats with rate and duration of threats as inputs. We compare the impact of a well-constructed attack tree with an adhoc attack tree to study the trade-offs between overheads in managing attack trees, and the cost of risk mitigation when vulnerabilities are identified. We use a vSocial VRLE testbed in a case study to showcase the effectiveness of our framework and demonstrate how a suitable attack tree formalism can result in a more safer, privacy-preserving and secure VRLE system.Comment: Tp appear in the CCNC 2019 Conferenc