Novel graph analytics for enhancing data insight

Graph analytics is a fast growing and significant field in the visualization and data mining community, which is applied on numerous high-impact applications such as, network security, finance, and health care, providing users with adequate knowledge across various patterns within a given system. Although a series of methods have been developed in the past years for the analysis of unstructured collections of multi-dimensional points, graph analytics has only recently been explored. Despite the significant progress that has been achieved recently, there are still many open issues in the area, concerning not only the performance of the graph mining algorithms, but also producing effective graph visualizations in order to enhance human perception. The current thesis deals with the investigation of novel methods for graph analytics, in order to enhance data insight. Towards this direction, the current thesis proposes two methods so as to perform graph mining and visualization. Based on previous works related to graph mining, the current thesis suggests a set of novel graph features that are particularly efficient in identifying the behavioral patterns of the nodes on the graph. The specific features proposed, are able to capture the interaction of the neighborhoods with other nodes on the graph. Moreover, unlike previous approaches, the graph features introduced herein, include information from multiple node neighborhood sizes, thus capture long-range correlations between the nodes, and are able to depict the behavioral aspects of each node with high accuracy. Experimental evaluation on multiple datasets, shows that the use of the proposed graph features for the graph mining procedure, provides better results than the use of other state-of-the-art graph features. Thereafter, the focus is laid on the improvement of graph visualization methods towards enhanced human insight. In order to achieve this, the current thesis uses non-linear deformations so as to reduce visual clutter. Non-linear deformations have been previously used to magnify significant/cluttered regions in data or images for reducing clutter and enhancing the perception of patterns. Extending previous approaches, this work introduces a hierarchical approach for non-linear deformation that aims to reduce visual clutter by magnifying significant regions, and leading to enhanced visualizations of one/two/three-dimensional datasets. In this context, an energy function is utilized, which aims to determine the optimal deformation for every local region in the data, taking the information from multiple single-layer significance maps into consideration. The problem is subsequently transformed into an optimization problem for the minimization of the energy function under specific spatial constraints. Extended experimental evaluation provides evidence that the proposed hierarchical approach for the generation of the significance map surpasses current methods, and manages to effectively identify significant regions and deliver better results. The thesis is concluded with a discussion outlining the major achievements of the current work, as well as some possible drawbacks and other open issues of the proposed approaches that could be addressed in future works.Open Acces

A Comparison of Display Techniques for Large Graphs

Visualizing information focuses on the display of data in order to provide the user a representation that provides understanding of the data. Information visualization systems typically couple interaction mechanisms for providing overviews of the data with more detailed information through a zooming interface. This thesis compares three different techniques for displaying graphs provided by the prefuse visualization system: force-directed node positioning, radial node positioning, and a tree view of graphs. Using a large, real world data set from the South Texas College’s Distance Education department, the three visualization techniques are compared for a set of tasks that users routinely need to perform using standard data access techniques. Though the tree view visualization is the most limited in generality of the three techniques, it is found to best provide support for the tasks, in part because of its ability to provide the abstractions that best match the tasks

Visualization of large molecular trajectories

The analysis of protein-ligand interactions is a time-intensive task. Researchers have to analyze multiple physico-chemical properties of the protein at once and combine them to derive conclusions about the protein-ligand interplay. Typically, several charts are inspected, and 3D animations can be played side-by-side to obtain a deeper understanding of the data. With the advances in simulation techniques, larger and larger datasets are available, with up to hundreds of thousands of steps. Unfortunately, such large trajectories are very difficult to investigate with traditional approaches. Therefore, the need for special tools that facilitate inspection of these large trajectories becomes substantial. In this paper, we present a novel system for visual exploration of very large trajectories in an interactive and user-friendly way. Several visualization motifs are automatically derived from the data to give the user the information about interactions between protein and ligand. Our system offers specialized widgets to ease and accelerate data inspection and navigation to interesting parts of the simulation. The system is suitable also for simulations where multiple ligands are involved. We have tested the usefulness of our tool on a set of datasets obtained from protein engineers, and we describe the expert feedback.Peer ReviewedPostprint (author's final draft

Visualization methods for analysis of 3D multi-scale medical data

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Interactive Visualization Lenses:: Natural Magic Lens Interaction for Graph Visualization

Information visualization is an important research field concerned with making sense and inferring knowledge from data collections. Graph visualizations are specific techniques for data representation relevant in diverse application domains among them biology, software-engineering, and business finance. These data visualizations benefit from the display space provided by novel interactive large display environments. However, these environments also cause new challenges and result in new requirements regarding the need for interaction beyond the desktop and according redesign of analysis tools. This thesis focuses on interactive magic lenses, specialized locally applied tools that temporarily manipulate the visualization. These may include magnification of focus regions but also more graph-specific functions such as pulling in neighboring nodes or locally reducing edge clutter. Up to now, these lenses have mostly been used as single-user, single-purpose tools operated by mouse and keyboard. This dissertation presents the extension of magic lenses both in terms of function as well as interaction for large vertical displays. In particular, this thesis contributes several natural interaction designs with magic lenses for the exploration of graph data in node-link visualizations using diverse interaction modalities. This development incorporates flexible switches between lens functions, adjustment of individual lens properties and function parameters, as well as the combination of lenses. It proposes interaction techniques for fluent multi-touch manipulation of lenses, controlling lenses using mobile devices in front of large displays, and a novel concept of body-controlled magic lenses. Functional extensions in addition to these interaction techniques convert the lenses to user-configurable, personal territories with use of alternative interaction styles. To create the foundation for this extension, the dissertation incorporates a comprehensive design space of magic lenses, their function, parameters, and interactions. Additionally, it provides a discussion on increased embodiment in tool and controller design, contributing insights into user position and movement in front of large vertical displays as a result of empirical investigations and evaluations.Informationsvisualisierung ist ein wichtiges Forschungsfeld, das das Analysieren von Daten unterstützt. Graph-Visualisierungen sind dabei eine spezielle Variante der Datenrepräsentation, deren Nutzen in vielerlei Anwendungsfällen zum Einsatz kommt, u.a. in der Biologie, Softwareentwicklung und Finanzwirtschaft. Diese Datendarstellungen profitieren besonders von großen Displays in neuen Displayumgebungen. Jedoch bringen diese Umgebungen auch neue Herausforderungen mit sich und stellen Anforderungen an Nutzerschnittstellen jenseits der traditionellen Ansätze, die dadurch auch Anpassungen von Analysewerkzeugen erfordern. Diese Dissertation befasst sich mit interaktiven „Magischen Linsen“, spezielle lokal-angewandte Werkzeuge, die temporär die Visualisierung zur Analyse manipulieren. Dabei existieren zum Beispiel Vergrößerungslinsen, aber auch Graph-spezifische Manipulationen, wie das Anziehen von Nachbarknoten oder das Reduzieren von Kantenüberlappungen im lokalen Bereich. Bisher wurden diese Linsen vor allem als Werkzeug für einzelne Nutzer mit sehr spezialisiertem Effekt eingesetzt und per Maus und Tastatur bedient. Die vorliegende Doktorarbeit präsentiert die Erweiterung dieser magischen Linsen, sowohl in Bezug auf die Funktionalität als auch für die Interaktion an großen, vertikalen Displays. Insbesondere trägt diese Dissertation dazu bei, die Exploration von Graphen mit magischen Linsen durch natürliche Interaktion mit unterschiedlichen Modalitäten zu unterstützen. Dabei werden flexible Änderungen der Linsenfunktion, Anpassungen von individuellen Linseneigenschaften und Funktionsparametern, sowie die Kombination unterschiedlicher Linsen ermöglicht. Es werden Interaktionstechniken für die natürliche Manipulation der Linsen durch Multitouch-Interaktion, sowie das Kontrollieren von Linsen durch Mobilgeräte vor einer Displaywand vorgestellt. Außerdem wurde ein neuartiges Konzept körpergesteuerter magischer Linsen entwickelt. Funktionale Erweiterungen in Kombination mit diesen Interaktionskonzepten machen die Linse zu einem vom Nutzer einstellbaren, persönlichen Arbeitsbereich, der zudem alternative Interaktionsstile erlaubt. Als Grundlage für diese Erweiterungen stellt die Dissertation eine umfangreiche analytische Kategorisierung bisheriger Forschungsarbeiten zu magischen Linsen vor, in der Funktionen, Parameter und Interaktion mit Linsen eingeordnet werden. Zusätzlich macht die Arbeit Vor- und Nachteile körpernaher Interaktion für Werkzeuge bzw. ihre Steuerung zum Thema und diskutiert dabei Nutzerposition und -bewegung an großen Displaywänden belegt durch empirische Nutzerstudien

A Runtime Software Visualization Environment

As software systems become more complex, so does the task of understanding them. To modify even a simple component of a complex system, at least a rudimentary understanding of the structure and behavior of the whole system is necessary. Although currently available development tools can provide a static representation of a complex system, these utilities are severely limited and prohibitively expensive. As a result, most programmers working on large software systems today resort to classic debuggers and time-consuming plain-text searches through hundreds or thousands of source files. This proposal describes a software development environment that uses static representations of hierarchically structured source code side by side with dynamic visualizations of software systems as they run. This environment provides an intuitive, visual means of easily comprehending complex systems, and has been provided as an open-source development tool for both professionals and students of software engineering

Hitchhiker's Guide to Super-Resolution: Introduction and Recent Advances

With the advent of Deep Learning (DL), Super-Resolution (SR) has also become a thriving research area. However, despite promising results, the field still faces challenges that require further research e.g., allowing flexible upsampling, more effective loss functions, and better evaluation metrics. We review the domain of SR in light of recent advances, and examine state-of-the-art models such as diffusion (DDPM) and transformer-based SR models. We present a critical discussion on contemporary strategies used in SR, and identify promising yet unexplored research directions. We complement previous surveys by incorporating the latest developments in the field such as uncertainty-driven losses, wavelet networks, neural architecture search, novel normalization methods, and the latests evaluation techniques. We also include several visualizations for the models and methods throughout each chapter in order to facilitate a global understanding of the trends in the field. This review is ultimately aimed at helping researchers to push the boundaries of DL applied to SR.Comment: accepted by IEEE Transactions on Pattern Analysis and Machine Intelligence, 202