Highly Parallel Geometric Characterization and Visualization of Volumetric Data Sets

Volumetric 3D data sets are being generated in many different application areas. Some examples are CAT scans and MRI data, 3D models of protein molecules represented by implicit surfaces, multi-dimensional numeric simulations of plasma turbulence, and stacks of confocal microscopy images of cells. The size of these data sets has been increasing, requiring the speed of analysis and visualization techniques to also increase to keep up. Recent advances in processor technology have stopped increasing clock speed and instead begun increasing parallelism, resulting in multi-core CPUS and many-core GPUs. To take advantage of these new parallel architectures, algorithms must be explicitly written to exploit parallelism. In this thesis we describe several algorithms and techniques for volumetric data set analysis and visualization that are amenable to these modern parallel architectures. We first discuss modeling volumetric data with Gaussian Radial Basis Functions (RBFs). RBF representation of a data set has several advantages, including lossy compression, analytic differentiability, and analytic application of Gaussian blur. We also describe a parallel volume rendering algorithm that can create images of the data directly from the RBF representation. Next we discuss a parallel, stochastic algorithm for measuring the surface area of volumetric representations of molecules. The algorithm is suitable for implementation on a GPU and is also progressive, allowing it to return a rough answer almost immediately and refine the answer over time to the desired level of accuracy. After this we discuss the concept of Confluent Visualization, which allows the visualization of the interaction between a pair of volumetric data sets. The interaction is visualized through volume rendering, which is well suited to implementation on parallel architectures. Finally we discuss a parallel, stochastic algorithm for classifying stem cells as having been grown on a surface that induces differentiation or on a surface that does not induce differentiation. The algorithm takes as input 3D volumetric models of the cells generated from confocal microscopy. This algorithm builds on our algorithm for surface area measurement and, like that algorithm, this algorithm is also suitable for implementation on a GPU and is progressive

Approximation and Relaxation Approaches for Parallel and Distributed Machine Learning

Large scale machine learning requires tradeoffs. Commonly this tradeoff has led practitioners to choose simpler, less powerful models, e.g. linear models, in order to process more training examples in a limited time. In this work, we introduce parallelism to the training of non-linear models by leveraging a different tradeoff--approximation. We demonstrate various techniques by which non-linear models can be made amenable to larger data sets and significantly more training parallelism by strategically introducing approximation in certain optimization steps. For gradient boosted regression tree ensembles, we replace precise selection of tree splits with a coarse-grained, approximate split selection, yielding both faster sequential training and a significant increase in parallelism, in the distributed setting in particular. For metric learning with nearest neighbor classification, rather than explicitly train a neighborhood structure we leverage the implicit neighborhood structure induced by task-specific random forest classifiers, yielding a highly parallel method for metric learning. For support vector machines, we follow existing work to learn a reduced basis set with extremely high parallelism, particularly on GPUs, via existing linear algebra libraries. We believe these optimization tradeoffs are widely applicable wherever machine learning is put in practice in large scale settings. By carefully introducing approximation, we also introduce significantly higher parallelism and consequently can process more training examples for more iterations than competing exact methods. While seemingly learning the model with less precision, this tradeoff often yields noticeably higher accuracy under a restricted training time budget

On continuous maximum ow image segmentation algorithm

Ces dernières années avec les progrès matériels, les dimensions et le contenu des images acquises se sont complexifiés de manière notable. Egalement, le différentiel de performance entre les architectures classiques mono-processeur et parallèles est passé résolument en faveur de ces dernières. Pourtant, les manières de programmer sont restées largement les mêmes, instituant un manque criant de performance même sur ces architectures. Dans cette thèse, nous explorons en détails un algorithme particulier, les flots maximaux continus. Nous explicitons pourquoi cet algorithme est important et utile, et nous proposons plusieurs implémentations sur diverses architectures, du mono-processeur à l'architecture SMP et NUMA, ainsi que sur les architectures massivement parallèles des GPGPU. Nous explorons aussi des applications et nous évaluons ses performances sur des images de grande taille en science des matériaux et en biologie à l'échelle nanoIn recent years, with the advance of computing equipment and image acquisition techniques, the sizes, dimensions and content of acquired images have increased considerably. Unfortunately as time passes there is a steadily increasing gap between the classical and parallel programming paradigms and their actual performance on modern computer hardware. In this thesis we consider in depth one particular algorithm, the continuous maximum flow computation. We review in detail why this algorithm is useful and interesting, and we propose efficient and portable implementations on various architectures. We also examine how it performs in the terms of segmentation quality on some recent problems of materials science and nano-scale biologyPARIS-EST-Université (770839901) / SudocSudocFranceF

Efficient and High-Quality Rendering of Higher-Order Geometric Data Representations

Computer-Aided Design (CAD) bezeichnet den Entwurf industrieller Produkte mit Hilfe von virtuellen 3D Modellen. Ein CAD-Modell besteht aus parametrischen Kurven und Flächen, in den meisten Fällen non-uniform rational B-Splines (NURBS). Diese mathematische Beschreibung wird ebenfalls zur Analyse, Optimierung und Präsentation des Modells verwendet. In jeder dieser Entwicklungsphasen wird eine unterschiedliche visuelle Darstellung benötigt, um den entsprechenden Nutzern ein geeignetes Feedback zu geben. Designer bevorzugen beispielsweise illustrative oder realistische Darstellungen, Ingenieure benötigen eine verständliche Visualisierung der Simulationsergebnisse, während eine immersive 3D Darstellung bei einer Benutzbarkeitsanalyse oder der Designauswahl hilfreich sein kann. Die interaktive Darstellung von NURBS-Modellen und -Simulationsdaten ist jedoch aufgrund des hohen Rechenaufwandes und der eingeschränkten Hardwareunterstützung eine große Herausforderung. Diese Arbeit stellt vier neuartige Verfahren vor, welche sich mit der interaktiven Darstellung von NURBS-Modellen und Simulationensdaten befassen. Die vorgestellten Algorithmen nutzen neue Fähigkeiten aktueller Grafikkarten aus, um den Stand der Technik bezüglich Qualität, Effizienz und Darstellungsgeschwindigkeit zu verbessern. Zwei dieser Verfahren befassen sich mit der direkten Darstellung der parametrischen Beschreibung ohne Approximationen oder zeitaufwändige Vorberechnungen. Die dabei vorgestellten Datenstrukturen und Algorithmen ermöglichen die effiziente Unterteilung, Klassifizierung, Tessellierung und Darstellung getrimmter NURBS-Flächen und einen interaktiven Ray-Casting-Algorithmus für die Isoflächenvisualisierung von NURBSbasierten isogeometrischen Analysen. Die weiteren zwei Verfahren beschreiben zum einen das vielseitige Konzept der programmierbaren Transparenz für illustrative und verständliche Visualisierungen tiefenkomplexer CAD-Modelle und zum anderen eine neue hybride Methode zur Reprojektion halbtransparenter und undurchsichtiger Bildinformation für die Beschleunigung der Erzeugung von stereoskopischen Bildpaaren. Die beiden letztgenannten Ansätze basieren auf rasterisierter Geometrie und sind somit ebenfalls für normale Dreiecksmodelle anwendbar, wodurch die Arbeiten auch einen wichtigen Beitrag in den Bereichen der Computergrafik und der virtuellen Realität darstellen. Die Auswertung der Arbeit wurde mit großen, realen NURBS-Datensätzen durchgeführt. Die Resultate zeigen, dass die direkte Darstellung auf Grundlage der parametrischen Beschreibung mit interaktiven Bildwiederholraten und in subpixelgenauer Qualität möglich ist. Die Einführung programmierbarer Transparenz ermöglicht zudem die Umsetzung kollaborativer 3D Interaktionstechniken für die Exploration der Modelle in virtuellenUmgebungen sowie illustrative und verständliche Visualisierungen tiefenkomplexer CAD-Modelle. Die Erzeugung stereoskopischer Bildpaare für die interaktive Visualisierung auf 3D Displays konnte beschleunigt werden. Diese messbare Verbesserung wurde zudem im Rahmen einer Nutzerstudie als wahrnehmbar und vorteilhaft befunden.In computer-aided design (CAD), industrial products are designed using a virtual 3D model. A CAD model typically consists of curves and surfaces in a parametric representation, in most cases, non-uniform rational B-splines (NURBS). The same representation is also used for the analysis, optimization and presentation of the model. In each phase of this process, different visualizations are required to provide an appropriate user feedback. Designers work with illustrative and realistic renderings, engineers need a comprehensible visualization of the simulation results, and usability studies or product presentations benefit from using a 3D display. However, the interactive visualization of NURBS models and corresponding physical simulations is a challenging task because of the computational complexity and the limited graphics hardware support. This thesis proposes four novel rendering approaches that improve the interactive visualization of CAD models and their analysis. The presented algorithms exploit latest graphics hardware capabilities to advance the state-of-the-art in terms of quality, efficiency and performance. In particular, two approaches describe the direct rendering of the parametric representation without precomputed approximations and timeconsuming pre-processing steps. New data structures and algorithms are presented for the efficient partition, classification, tessellation, and rendering of trimmed NURBS surfaces as well as the first direct isosurface ray-casting approach for NURBS-based isogeometric analysis. The other two approaches introduce the versatile concept of programmable order-independent semi-transparency for the illustrative and comprehensible visualization of depth-complex CAD models, and a novel method for the hybrid reprojection of opaque and semi-transparent image information to accelerate stereoscopic rendering. Both approaches are also applicable to standard polygonal geometry which contributes to the computer graphics and virtual reality research communities. The evaluation is based on real-world NURBS-based models and simulation data. The results show that rendering can be performed directly on the underlying parametric representation with interactive frame rates and subpixel-precise image results. The computational costs of additional visualization effects, such as semi-transparency and stereoscopic rendering, are reduced to maintain interactive frame rates. The benefit of this performance gain was confirmed by quantitative measurements and a pilot user study

Fundamentals

Volume 1 establishes the foundations of this new field. It goes through all the steps from data collection, their summary and clustering, to different aspects of resource-aware learning, i.e., hardware, memory, energy, and communication awareness. Machine learning methods are inspected with respect to resource requirements and how to enhance scalability on diverse computing architectures ranging from embedded systems to large computing clusters

Fundamentals

Volume 1 establishes the foundations of this new field. It goes through all the steps from data collection, their summary and clustering, to different aspects of resource-aware learning, i.e., hardware, memory, energy, and communication awareness. Machine learning methods are inspected with respect to resource requirements and how to enhance scalability on diverse computing architectures ranging from embedded systems to large computing clusters

Geospatial Data Science to Identify Patterns of Evasion

University of Minnesota Ph.D. dissertation.January 2018. Major: Computer Science. Advisor: Shashi Shekhar. 1 computer file (PDF); x, 153 pages.Over the last decade, there has been a significant growth in the availability of cheap raw spatial data in the form of GPS trajectories, activity/event locations, temporally detailed road networks, satellite imagery, etc. These data are being collected, often around the clock, from location-aware applications, sensor technologies, etc. and represent an unprecedented opportunity to study our economic, social, and natural systems and their interactions. For example, finding hotspots (areas with unusually high concentration of activities/events) from activity/event locations plays a crucial role in epidemiology since it may help public health officials prevent further spread of an infectious disease. In order to extract useful information from these datasets, many geospatial data tools have been proposed in recent years. However, these tools are often used as a “black box”, where a trial-error strategy is used with multiple approaches from different scientific disciplines (e.g. statistics, mathematics and computer science) to find the best solution with little or no consideration of the actual phenomena being investigated. Hence, the results may be biased or some important information may be missed. To address this problem, we need geospatial data science with a stronger scientific foundation to understand the actual phenomena, develop reliable and trustworthy models and extract information through a scientific process. Thus, my thesis investigates a wide-lens perspective on geospatial data science, considering it as a transdisciplinary field comprising statistics, mathematics, and computer science. This approach aims to reduce the redundant work across disciplines as well as define scientific boundaries of geospatial data science to distinguish it from being a black box that claims to solve every possible geospatial problem. In my proposed approaches, I used ideas from those three disciplines, e.g. spatial scan statistics from statistical science to reduce chance patterns in the output and provide statistical robustness; mathematical definitions of geometric shapes of the patterns, which maintain correctness and completeness; and computational approaches (along with prune and refine framework and dynamic programming ideas) to scale up to large spatial datasets. In addition, the proposed approaches incorporate domain-specific geographic theories (e.g., routine activity theory in criminology) for applicability in those domains that are interested in specific patterns, which occur due to the actual phenomena, from geospatial datasets. The proposed techniques have been applied to real world disease and crime datasets and the evaluations confirmed that our techniques outperform current state-of-the-art such as density based clustering approaches as well as circular hotspot detection methods

Fluka Raytracer

The project described in this document was developed as the work for a technical student position at CERN in Geneva, Switzerland. CERN is the European Organization for Nuclear Research and is one of the leading physics laboratories across the world. The development of the current project was held by the section EN-STI-EET (Engineering; Sources Targets and Interactions; Emerging Energy Technologies), which in collaboration with INFN Institute, Italy is in charge of developing and maintaining the Monte Carlo generator FLUKA . FLUKA is a general purpose tool for calculations of particle transport and interactions with matter, covering an extended range of applications spanning from proton and electron accelerator shielding to target design, calorimetry, activation, dosimetry, detector design, Accelerator Driven Systems, cosmic rays, neutrino physics, radiotherapy etc.Siñuela Pastor, D. (2013). Fluka Raytracer. http://hdl.handle.net/10251/27328.Archivo delegad

Higher Performance Traversal and Construction of Tree-Based Raytracing Acceleration Structures

Ray tracing is an important computational primitive used in different algorithms including collision detection, line-of-sight computations, ray tracing-based sound propagation, and most prominently light transport algorithms. It computes the closest intersections for a given set of rays and geometry. The geometry is usually modeled with a set of geometric primitives such as triangles or quadrangles which define a scene. An efficient ray tracing implementation needs to rely on an acceleration structure to decouple ray tracing complexity from scene complexity as far as possible. The most common ray tracing acceleration structures are kd-trees and bounding volume hierarchies (BVHs) which have an O(log n) ray tracing complexity in the number of scene primitives. Both structures offer similar ray tracing performance in practice. This thesis presents theoretical insights and practical approaches for higher quality, improved graphics processing unit (GPU) ray tracing performance, and faster construction of BVHs and kd-trees, where the focus is on BVHs. The chosen construction strategy for BVHs and kd-trees has a significant impact on final ray tracing performance. The most common measure for the quality of BVHs and kd-trees is the surface area metric (SAM). Using assumptions on the distribution of ray origins and directions the SAM gives an approximation for the cost of traversing an acceleration structure without having to trace a single ray. High quality construction algorithms aim at reducing the SAM cost. The most widespread high quality greedy plane-sweep algorithm applies the surface area heuristic (SAH) which is a simplification of the SAM. Advances in research on quality metrics for BVHs have shown that greedy SAH-based plane-sweep builders often construct BVHs with superior traversal performance despite the fact that the resulting SAM costs are higher than those created by more sophisticated builders. Motivated by this observation we examine different construction algorithms that use the SAM cost of temporarily constructed SAH-built BVHs to guide the construction to higher quality BVHs. An extensive evaluation reveals that the resulting BVHs indeed achieve significantly higher trace performance for primary and secondary diffuse rays compared to BVHs constructed with standard plane-sweeping. Compared to the Spatial-BVH, a kd-tree/BVH hybrid, we still achieve an acceptable increase in performance. We show that the proposed algorithm has subquadratic computational complexity in the number of primitives, which renders it usable in practical applications. An alternative construction algorithm to the plane-sweep BVH builder is agglomerative clustering, which constructs BVHs in a bottom-up fashion. It clusters primitives with a SAM-inspired heuristic and gives mixed quality BVHs compared to standard plane-sweeping construction. While related work only focused on the construction speed of this algorithm we examine clustering heuristics, which aim at higher hierarchy quality. We propose a fully SAM-based clustering heuristic which on average produces better performing BVHs compared to original agglomerative clustering. The definitions of SAM and SAH are based on assumptions on the distribution of ray origins and directions to define a conditional geometric probability for intersecting nodes in kd-trees and BVHs. We analyze the probability function definition and show that the assumptions allow for an alternative probability definition. Unlike the conventional probability, our definition accounts for directional variation in the likelihood of intersecting objects from different directions. While the new probability does not result in improved practical tracing performance, we are able to provide an interesting insight on the conventional probability. We show that the conventional probability function is directly linked to our examined probability function and can be interpreted as covertly accounting for directional variation. The path tracing light transport algorithm can require tracing of billions of rays. Thus, it can pay off to construct high quality acceleration structures to reduce the ray tracing cost of each ray. At the same time, the arising number of trace operations offers a tremendous amount of data parallelism. With CPUs moving towards many-core architectures and GPUs becoming more general purpose architectures, path tracing can now be well parallelized on commodity hardware. While parallelization is trivial in theory, properties of real hardware make efficient parallelization difficult, especially when tracing so called incoherent rays. These rays cause execution flow divergence, which reduces efficiency of SIMD-based parallelism and memory read efficiency due to incoherent memory access. We investigate how different BVH and node memory layouts as well as storing the BVH in different memory areas impacts the ray tracing performance of a GPU path tracer. We also optimize the BVH layout using information gathered in a pre-processing pass by applying a number of different BVH reordering techniques. This results in increased ray tracing performance. Our final contribution is in the field of fast high quality BVH and kd-tree construction. Increased quality usually comes at the cost of higher construction time. To reduce construction time several algorithms have been proposed to construct acceleration structures in parallel on GPUs. These are able to perform full rebuilds in realtime for moderate scene sizes if all data completely fits into GPU memory. The sheer amount of data arising from geometric detail used in production rendering makes construction on GPUs, however, infeasible due to GPU memory limitations. Existing out-of-core GPU approaches perform hybrid bottom-up top-down construction which suffers from reduced acceleration structure quality in the critical upper levels of the tree. We present an out-of-core multi-GPU approach for full top-down SAH-based BVH and kd-tree construction, which is designed to work on larger scenes than conventional approaches and yields high quality trees. The algorithm is evaluated for scenes consisting of up to 1 billion triangles and performance scales with an increasing number of GPUs