Irregular alignment of arbitrarily long DNA sequences on GPU

The use of Graphics Processing Units to accelerate computational applications is increasingly being adopted due to its affordability, flexibility and performance. However, achieving top performance comes at the price of restricted data-parallelism models. In the case of sequence alignment, most GPU-based approaches focus on accelerating the Smith-Waterman dynamic programming algorithm due to its regularity. Nevertheless, because of its quadratic complexity, it becomes impractical when comparing long sequences, and therefore heuristic methods are required to reduce the search space. We present GPUGECKO, a CUDA implementation for the sequential, seed-and-extend sequence-comparison algorithm, GECKO. Our proposal includes optimized kernels based on collective operations capable of producing arbitrarily long alignments while dealing with heterogeneous and unpredictable load. Contrary to other state-of-the-art methods, GPUGECKO employs a batching mechanism that prevents memory exhaustion by not requiring to fit all alignments at once into the device memory, therefore enabling to run massive comparisons exhaustively with improved sensitivity while also providing up to 6x average speedup w.r.t. the CUDA acceleration of BLASTN.Funding for open access publishing: Universidad Málaga/CBUA /// This work has been partially supported by the European project ELIXIR-EXCELERATE (grant no. 676559), the Spanish national project Plataforma de Recursos Biomoleculares y Bioinformáticos (ISCIII-PT13.0001.0012 and ISCIII-PT17.0009.0022), the Fondo Europeo de Desarrollo Regional (UMA18-FEDERJA-156, UMA20-FEDERJA-059), the Junta de Andalucía (P18-FR-3130), the Instituto de Investigación Biomédica de Málaga IBIMA and the University of Málaga

Multivariate relationship specification and visualization

In this dissertation, we present a novel method for multivariate visualization that focuses on multivariate relationshipswithin scientific datasets. Specifically, we explore the considerations of such a problem, i.e. we develop an appropriate visualization approach, provide a framework for the specification of multivariate relationships and analyze the space of such relationships for the purpose of guiding the user toward desired visualizations. The visualization approach is derived from a point classification algorithm that summarizes many variables of a dataset into a single image via the creation of attribute subspaces. Then, we extend the notion of attribute subspaces to encompass multivariate relationships. In addition, we provide an unconstrained framework for the user to define such relationships. Althoughwe intend this approach to be generally applicable, the specification of complicated relationships is a daunting task due to the increasing difficulty for a user to understand and apply these relationships. For this reason, we explore this relationship space with a common information visualization technique well suited for this purpose, parallel coordinates. In manipulating this space, a user is able to discover and select both complex and logically informative relationship specifications

Improving Usability in Procedural Modeling

This work presents new approaches and algorithms for procedural modeling geared towards user convenience and improving usability, in order to increase artists’ productivity. Procedural models create geometry for 3D models from sets of rules. Existing approaches that allow to model trees, buildings, and terrain are reviewed and possible improvements are discussed. A new visual programming language for procedural modeling is discussed, where the user connects operators to visual programs called model graphs. These operators create geometry with textures, assign or evaluate variables or control the sequence of operations. When the user moves control points using the mouse in 3D space, the model graph is executed to change the geometry interactively. Thus, model graphs combine the creativity of freehand modeling with the power of programmed modeling while displaying the program structure more clearly than textbased approaches. Usability is increased as a result of these advantages. Also, an interactive editor for botanical trees is demonstrated. In contrast to previous tree modeling systems, we propose linking rules, parameters and geometry to semantic entities. This has the advantage that problems of associating parameters and instances are completely avoided. When an entity is clicked in the viewport, its parameters are displayed immediately, changes are applied to selected entities, and viewport editing operations are reflected in the parameter set. Furthermore, we store the entities in a hierarchical data structure and allow the user to activate recursive traversal via selection options for all editing operations. The user may choose to apply viewport or parameter changes to a single entity or many entities at once, and only the geometry for the affected entities needs to be updated. The proposed user interface simplifies the modeling process and increases productivity. Interactive editing approaches for 3D models often allow more precise control over a model than a global set of parameters that is used to generate a shape. However, usually scripted procedural modeling generates shapes directly from a fixed set of parameters, and interactive editing mostly uses a fixed set of tools. We propose to use scripts not only to generate models, but also for manipulating the models. A base script would set up the state of an object, and tool scripts would modify that state. The base script and the tool scripts generate geometry when necessary. Together, such a collection of scripts forms a template, and templates can be created for various types of objects. We examine how templates simplify the procedural modeling workflow by allowing for editing operations that are context-sensitive, flexible and powerful at the same time. Many algorithms have been published that produce geometry for fictional landscapes. There are algorithms which produce terrain with minimal setup time, allowing to adapt the level of detail as the user zooms into the landscape. However, these approaches lack plausible river networks, and algorithms that create eroded terrain with river networks require a user to supervise creation and minutes or hours of computation. In contrast to that, this work demonstrates an algorithm that creates terrain with plausible river networks and adaptive level of detail with no more than a few seconds of preprocessing. While the system can be configured using parameters, this text focuses on the algorithm that produces the rivers. However, integrating more tools for user-controlled editing of terrain would be possible.Verbesserung der Usability bei prozeduraler Modellierung Ziel der vorliegenden Arbeit ist es, prozedurale Modellierung durch neue neue Ansätze und Algorithmen einfacher, bequemer und anwendungsfreundlicher zu machen, und damit die Produktivität der Künstler zu erhöhen. Diese Anforderungen werden häufig unter dem Stichwort Usability zusammengefasst. Prozedurale Modelle spezifizieren 3D-Modelle über Regeln. Existierende Ansätze für Bäume, Gebäude und Terrain werden untersucht und es werden mögliche Verbesserungen diskutiert. Eine neue visuelle Programmiersprache für prozedurale Modelle wird vorgestellt, bei der Operatoren zu Modellgraphen verschaltet werden. Die Operatoren erzeugen texturierte Geometrie, weisen Variablen zu und werten sie aus, oder sie steuern den Ablauf der Operationen. Wenn der Benutzer Kontrollpunkte im Viewport mit der Maus verschiebt, wird der Modellgraph ausgeführt, um interaktiv neue Geometrie für das Modell zu erzeugen. Modellgraphen kombinieren die kreativen Möglichkeiten des freihändigen Editierens mit der Mächtigkeit der prozeduralen Modellierung. Darüber hinaus sind Modellgraphen eine visuelle Programmiersprache und stellen die Struktur der Algorithmen deutlicher dar als textbasierte Programmiersprachen. Als Resultat dieser Verbesserungen erhöht sich die Usability. Ein interaktiver Editor für botanische Bäume wird ebenfalls vorgestellt. Im Gegensatz zu früheren Ansätzen schlagen wir vor, Regeln, Parameter und Geometrie zu semantischen Entitäten zu verschmelzen. Auf diese Weise werden Zuordnungsprobleme zwischen Parametern und deren Instanzen komplett vermieden. Wenn im Viewport eine Instanz angeklickt wird, werden sofort ihre Parameter angezeigt, alle Änderungen wirken sich direkt auf die betroffenen Instanzen aus, und Änderungen im Viewport werden sofort in den Parametern reflektiert. Darüber hinaus werden die Entitäten in einer hierarchischen Datenstruktur gespeichert und alle Änderungen können rekursiv auf der Hierarchie ausgeführt werden. Dem Benutzer werden Selektionsoptionen zur Verfügung gestellt, über die er Änderungen an den Parametern oder Änderungen im Viewport an einzelnen oder vielen Instanzen gleichzeitig vornehmen kann. Anschließend muss das System nur die Geometrie der betroffenen Instanzen aktualisieren. Auch hier ist das Ziel, das User Interface möglichst an den Bedürfnissen des Benutzers auszurichten, um Vereinfachungen und eine Erhöhung der Produktivität zu erreichen. Interaktive Editieransätze für 3D-Modelle erlauben häufig eine präzisere Kontrolle über ein Modell als ein globaler Parametersatz, der für die Erzeugung des Modells genutzt wird. Trotzdem erzeugen prozedurale Modellierskripte ihre Modelle meist direkt aus einem festen Parametersatz, während interaktive Tools meist mit hartkodierten Operationen arbeiten. Wir schlagen vor, Skripte nicht nur zur Erzeugung der Modelle zu verwenden, sondern auch um die erzeugten Modelle zu editieren. Ein Basisskript soll die Statusinformationen eines Objekts anlegen, während weitere Skripte diesen Status verändern und passende Geometrie erzeugen. Diese Skripte bilden dann ein Template zum Erzeugen einer Klasse von Objekten. Verschiedene Objekttypen können jeweils ihr eigenes Template haben. Wir zeigen, wie Templates den Workflow mit prozeduralen Modellen vereinfachen können, indem Operationen geschaffen werden, die gleichzeitig kontext-sensitiv, mächtig und flexibel sind. Es existiert eine Reihe von Verfahren, um Geometrie für synthetische Landschaften zu erzeugen. Ein Teil der Algorithmen erzeugt Geometrie mit minimaler Vorberechnung und erlaubt es, den Detailgrad der Landschaft interaktiv an die Perspektive anzupassen. Leider fehlen den so erzeugten Landschaften plausible Flussnetze. Algorithmen, die erodiertes Terrain mit Flussnetzen erzeugen, müssen aufwendig vom Benutzer überwacht werden und brauchen Minuten oder Stunden Rechenzeit. Im Gegensatz dazu stellen wir einen Algorithmus vor, der plausible Flussnetze erzeugt, während sich der Betrachter interaktiv durch die Szene bewegt. Das System kann über Parameter gesteuert werden, aber der Fokus liegt auf dem Algorithmus zur Erzeugung der Flüsse. Dennoch wäre es möglich, Tools zum benutzergesteuerten Editieren von Terrain zu integrieren

Multidimensional projections for the visual exploration of multimedia data

Multidimensional data analysis is considerably important when dealing with such large and complex datasets. Among the possibilities when analyzing such kind of data, applying visualization techniques can help the user find and understand patters, trends and establish new goals. This thesis aims to present several visualization methods to interactively explore multidimensional datasets aimed from specialized to casual users, by making use of both static and dynamic representations created by multidimensional projections

High-dimensional glyph-based visualization and interactive techniques.

The advancement of modern technology and scientific measurements has led to datasets growing in both size and complexity, exposing the need for more efficient and effective ways of visualizing and analysing data. Despite the amount of progress in visualization methods, high-dimensional data still poses a number of significant challenges in terms of the technical ability of realising such a mapping, and how accurate they are actually interpreted. The different data sources and characteristics which arise from a wide range of scientific domains as well as specific design requirements constantly create new special challenges for visualization research. This thesis presents several contributions to the field of glyph-based visualization. Glyphs are parametrised objects which encode one or more data values to its appearance (also referred to as visual channels) such as their size, colour, shape, and position. They have been widely used to convey information visually, and are especially well suited for displaying complex, multi-faceted datasets. Its major strength is the ability to depict patterns of data in the context of a spatial relationship, where multi-dimensional trends can often be perceived more easily. Our research is set in the broad scope of multi-dimensional visualization, addressing several aspects of glyph-based techniques, including visual design, perception, placement, interaction, and applications. In particular, this thesis presents a comprehensive study on one interaction technique, namely sorting, for supporting various analytical tasks. We have outlined the concepts of glyph- based sorting, identified a set of design criteria for sorting interactions, designed and prototyped a user interface for sorting multivariate glyphs, developed a visual analytics technique to support sorting, conducted an empirical study on perceptual orderability of visual channels used in glyph design, and applied glyph-based sorting to event visualization in sports applications. The content of this thesis is organised into two parts. Part I provides an overview of the basic concepts of glyph-based visualization, before describing the state-of-the-art in this field. We then present a collection of novel glyph-based approaches to address challenges created from real-world applications. These are detailed in Part II. Our first approach involves designing glyphs to depict the composition of multiple error-sensitivity fields. This work addresses the problem of single camera positioning, using both 2D and 3D methods to support camera configuration based on various constraints in the context of a real-world environment. Our second approach present glyphs to visualize actions and events "at a glance". We discuss the relative merits of using metaphoric glyphs in comparison to other types of glyph designs to the particular problem of real-time sports analysis. As a result of this research, we delivered a visualization software, MatchPad, on a tablet computer. It successfully helped coaching staff and team analysts to examine actions and events in detail whilst maintaining a clear overview of the match, and assisted in their decision making during the matches. Abstract shortened by ProQuest

Explorative coastal oceanographic visual analytics : oceans of data

The widely acknowledged challenge to data analysis and understanding, resulting from the exponential increase in volumes of data generated by increasingly complex modelling and sampling systems, is a problem experienced by many researchers, including ocean scientists. The thesis explores a visualization and visual analytics solution for predictive studies of coastal shelf and estuarine modelled, hydrodynamics undertaken to understand sea level rise, as a contribution to wider climate change studies, and to underpin coastal zone planning, flood prevention and extreme event management. But these studies are complex and require numerous simulations of estuarine hydrodynamics, generating extremely large datasets of multi-field data. This type\ud of data is acknowledged as difficult to visualize and analyse, as its numerous attributes present significant computational challenges, and ideally require a wide range of approaches to provide the necessary insight. These challenges are not easily overcome with the current visualization and analysis methodologies employed by coastal shelf hydrodynamic researchers, who use several software systems to generate graphs, each taking considerable time to operate, thus it is difficult to explore different scenarios and explore the data interactively and visually. The thesis, therefore, develops novel visualization and visual analytics techniques to help researchers overcome the limitations of existing methods (for example in understanding key tidal components); analyse data in a timely manner and explore different scenarios. There were a number of challenges to this: the size of the data, resulting in lengthy computing time, also many data values becoming plotted on one pixel (overplotting). The thesis presents: (1) a new visualization framework (VINCA) using caching and hierarchical aggregation techniques to make the data more interactive, plus explorative, coordinated multiple views, to enable the scientists to explore the data. (2) A novel estuarine transect profiler and flux tool, which provides instantaneous flux calculations across an estuary. Measures of flux are of great significance in oceanographic studies, yet are notoriously difficult and time consuming to calculate with the commonly used tools. This derived data is added back into the database for further investigation and analysis. (3) New views, including a novel, dynamic, spatially aggregated Parallel Coordinate Plots (Sa-PCP), are developed to provide different perspectives of the spatial, time dependent data, also methodologies for developing high-quality (journal ready) output from the visualization tool. Finally, (4) the dissertation explored the use of hierarchical data-structures and caching techniques to enable fast analysis on a desktop computer and to overcome the overplotting challenge for this data

Comparative Uncertainty Visualization for High-Level Analysis of Scalar- and Vector-Valued Ensembles

With this thesis, I contribute to the research field of uncertainty visualization, considering parameter dependencies in multi valued fields and the uncertainty of automated data analysis. Like uncertainty visualization in general, both of these fields are becoming more and more important due to increasing computational power, growing importance and availability of complex models and collected data, and progress in artificial intelligence. I contribute in the following application areas: Uncertain Topology of Scalar Field Ensembles. The generalization of topology-based visualizations to multi valued data involves many challenges. An example is the comparative visualization of multiple contour trees, complicated by the random nature of prevalent contour tree layout algorithms. I present a novel approach for the comparative visualization of contour trees - the Fuzzy Contour Tree. Uncertain Topological Features in Time-Dependent Scalar Fields. Tracking features in time-dependent scalar fields is an active field of research, where most approaches rely on the comparison of consecutive time steps. I created a more holistic visualization for time-varying scalar field topology by adapting Fuzzy Contour Trees to the time-dependent setting. Uncertain Trajectories in Vector Field Ensembles. Visitation maps are an intuitive and well-known visualization of uncertain trajectories in vector field ensembles. For large ensembles, visitation maps are not applicable, or only with extensive time requirements. I developed Visitation Graphs, a new representation and data reduction method for vector field ensembles that can be calculated in situ and is an optimal basis for the efficient generation of visitation maps. This is accomplished by bringing forward calculation times to the pre-processing. Visually Supported Anomaly Detection in Cyber Security. Numerous cyber attacks and the increasing complexity of networks and their protection necessitate the application of automated data analysis in cyber security. Due to uncertainty in automated anomaly detection, the results need to be communicated to analysts to ensure appropriate reactions. I introduce a visualization system combining device readings and anomaly detection results: the Security in Process System. To further support analysts I developed an application agnostic framework that supports the integration of knowledge assistance and applied it to the Security in Process System. I present this Knowledge Rocks Framework, its application and the results of evaluations for both, the original and the knowledge assisted Security in Process System. For all presented systems, I provide implementation details, illustrations and applications