Study of gene expression representation with Treelets and hierarchical clustering algorithms

English: Since the mid-1990's, the field of genomic signal processing has exploded due to the development of DNA microarray technology, which made possible the measurement of mRNA expression of thousands of genes in parallel. Researchers had developed a vast body of knowledge in classification methods. However, microarray data is characterized by extremely high dimensionality and comparatively small number of data points. This makes microarray data analysis quite unique. In this work we have developed various hierarchical clustering algorthims in order to improve the microarray classification task. At first, the original feature set of gene expression values are enriched with new features that are linear combinations of the original ones. These new features are called metagenes and are produced by different proposed hierarchical clustering algorithms. In order to prove the utility of this methodology to classify microarray datasets the building of a reliable classifier via feature selection process is introduced. This methodology has been tested on three public cancer datasets: Colon, Leukemia and Lymphoma. The proposed method has obtained better classification results than if this enhancement is not performed. Confirming the utility of the metagenes generation to improve the final classifier. Secondly, a new technique has been developed in order to use the hierarchical clustering to perform a reduction on the huge microarray datasets, removing the initial genes that will not be relevant for the cancer classification task. The experimental results of this method are also presented and analyzed when it is applied to one public database demonstrating the utility of this new approach.Castellano: Desde finales de la década de los años 90, el campo de la genómica fue revolucionado debido al desarrollo de la tecnología de los DNA microarrays. Con ésta técnica es posible medir la expresión de los mRNA de miles de genes en paralelo. Los investigadores han desarrollado un vasto conocimiento en los métodos de clasificación. Sin embargo, los microarrays están caracterizados por tener un alto número de genes y un número de muestras comparativamente pequeño. Éste hecho convierte al estudio de los microarrays en único. En éste trabajo se ha desarrollado diversos algoritmos de agrupación jerárquica para mejorar la clasificación de los microarrays. La primera y gran aplicación ha sido el enriquecimiento de las bases de datos originales mediante la introducción de nuevos elementos que son obtenidos como combinaciones lineales los genes originales. Estos nuevos elementos se han denominado metagenes y son producidos mediante los diferentes algoritmos propuestos de agrupación jerárquica. A fin de demostrar la utilidad de esta metodología para clasificar las bases de datos de microarrays se ha introducido la construcción de un clasificador fiable a través de un proceso de selección de características. Esta metodología ha sido probada en tres bases de datos de cáncer públicas: Colon, Leucemia y Linfoma. El método propuesto ha obtenido mejores resultados en la clasificación que cuando éste enriquecimiento no se ha llevado a cabo. De ésta manera se ha confirmado la utilidad de la generación de los metagenes para mejorar el clasificador. En segundo lugar, se ha desarrollado una nueva técnica para realizar una reducción inicial en las bases de datos, consistente en eliminar los genes que no son relevantes para realizar la clasificación. Éste método se ha aplicado a una de las bases de datos públicas, y los resultados experimentales se presentan y analizan demostrando la utilidad de éste nuevo enfoque.Català: Des de finals de la dècada dels 90, el camp de la genómica va ser revolucionat gràcies al desenvolupament de la tecnología dels DNA microarrays. Amb aquesta tècnica es possible mesurar l'expresió dels mRNA de milers de gens en paralel. Els investigadors han desenvolupat un ample coneixement dels mètodes de classificació. No obstant, els microarrays estàn caracteritzats per tindre una alt nombre de genes i comparativament un nombre petit de mostres. Aquest fet fa que l'estudi dels microarrays sigui únic. Amb aquest treball s' han desenvolupat diversos algoritmes d'agrupació jeràrquica per millorar la classificació dels microarrays. La primera i gran aplicació ha sigut l'enriqueiment de les bases de dades originals mitjançant l'introducció de nous elements que s'obtenen com combinacions lineals dels gens originals. Aquests nous elements han sigut denominats com metagens i són calculats mitjantçant els diferents algoritmes d'agrupació jerárquica proposats. Per a demostrar l'utilitat d'aquesta metodología per a classificar les bases de dades de microarrays s'ha introduït la construcció d'un classificador fiable mitjantçant un procés de selecció de característiques. Aquesta metodología ha sigut aplicada a tres bases de dades públiques de càncer: Colon, Leucèmia i Limfoma. El métode proposat ha obtenigut millors resultats en la classificació que quan aquest enriqueiment no ha sigut realitzat. D'aquesta manera s'ha confirmat l'utilitat de la generació dels metagens per a millorar els classificadors. En segon lloc, s'ha desenvolupat una nova técnica per a realitzar una reducció inicial en les bases de dades, aquest mètode consisteix en l'eliminació dels gens que no són relevants a l'hora de realitzar la classificació dels pacients. Aquest mètode ha sigut aplicat a una de les bases de dades públiques. Els resultats experimentals es presenten i analitzen demostrant l'utilitat d'aquesta nova tècnica

Lichttransportsimulation auf Spezialhardware

It cannot be denied that the developments in computer hardware and in computer algorithms strongly influence each other, with new instructions added to help with video processing, encryption, and in many other areas. At the same time, the current cap on single threaded performance and wide availability of multi-threaded processors has increased the focus on parallel algorithms. Both influences are extremely prominent in computer graphics, where the gaming and movie industries always strive for the best possible performance on the current, as well as future, hardware. In this thesis we examine the hardware-algorithm synergies in the context of ray tracing and Monte-Carlo algorithms. First, we focus on the very basic element of all such algorithms - the casting of rays through a scene, and propose a dedicated hardware unit to accelerate this common operation. Then, we examine existing and novel implementations of many Monte-Carlo rendering algorithms on massively parallel hardware, as full hardware utilization is essential for peak performance. Lastly, we present an algorithm for tackling complex interreflections of glossy materials, which is designed to utilize both powerful processing units present in almost all current computers: the Centeral Processing Unit (CPU) and the Graphics Processing Unit (GPU). These three pieces combined show that it is always important to look at hardware-algorithm mapping on all levels of abstraction: instruction, processor, and machine.Zweifelsohne beeinflussen sich Computerhardware und Computeralgorithmen gegenseitig in ihrer Entwicklung: Prozessoren bekommen neue Instruktionen, um zum Beispiel Videoverarbeitung, Verschlüsselung oder andere Anwendungen zu beschleunigen. Gleichzeitig verstärkt sich der Fokus auf parallele Algorithmen, bedingt durch die limitierte Leistung von für einzelne Threads und die inzwischen breite Verfügbarkeit von multi-threaded Prozessoren. Beide Einflüsse sind im Grafikbereich besonders stark , wo es z.B. für die Spiele- und Filmindustrie wichtig ist, die bestmögliche Leistung zu erreichen, sowohl auf derzeitiger und zukünftiger Hardware. In Rahmen dieser Arbeit untersuchen wir die Synergie von Hardware und Algorithmen anhand von Ray-Tracing- und Monte-Carlo-Algorithmen. Zuerst betrachten wir einen grundlegenden Hardware-Bausteins für alle diese Algorithmen, die Strahlenverfolgung in einer Szene, und präsentieren eine spezielle Hardware-Einheit zur deren Beschleunigung. Anschließend untersuchen wir existierende und neue Implementierungen verschiedener MonteCarlo-Algorithmen auf massiv-paralleler Hardware, wobei die maximale Auslastung der Hardware im Fokus steht. Abschließend stellen wir dann einen Algorithmus zur Berechnung von komplexen Beleuchtungseffekten bei glänzenden Materialien vor, der versucht, die heute fast überall vorhandene Kombination aus Hauptprozessor (CPU) und Grafikprozessor (GPU) optimal auszunutzen. Zusammen zeigen diese drei Aspekte der Arbeit, wie wichtig es ist, Hardware und Algorithmen auf allen Ebenen gleichzeitig zu betrachten: Auf den Ebenen einzelner Instruktionen, eines Prozessors bzw. eines gesamten Systems

A Programmable Streaming Framework for Extreme-Scale Scientific Visualizations

Emerging computational and acquisition technologies are empowering scientists to conduct simulations and experiments on an unprecedented scale. These advancements can push the frontiers of science and technology with groundbreaking discoveries. However, they also pose significant challenges to traditional scientific visualization workflows. Firstly, the data generated by modern scientific studies using these technologies tends to be extremely large and complex, often resulting in slow processing and rendering times. This demands the development of visualization algorithms that can effectively scale with the size of the data. Secondly, state-of-the-art simulations and experiments produce data at extraordinary rates, complicating the task of generating valuable visualization results for scientists. Therefore, there's a pressing need for more adaptive and intelligent visualization workflows. Lastly, although new computer hardware and architecture can speed up the visualization process, significant performance variations still exist among visualization algorithms due to differing design choices. As a result, optimizing algorithms to better leverage emerging hardware features for enhanced efficiency remains an ongoing necessity.This dissertation addresses the aforementioned challenges by introducing a programmable streaming framework enhanced with implicit neural representation, designed for visualizing extreme-scale scientific data. Specifically, it unfolds three innovative methodologies:Firstly, the framework offers a reactive and declarative programming language for streamlining image generation, layout and interaction creation, and I/O processes, eliminating the need for users to manually control all visualization parameters and procedures. This language enables scientists to define highly adaptive visualization workflows through high-level, rule-based grammars. The system then automatically optimizes the low-level implementation according to these specifications, facilitating the creation of more efficient visualization workflows with simpler coding.Secondly, the framework features a scalable, hardware-accelerated streaming visualization system that allows visualization processes to run concurrently with I/O operations. This system not only achieves state-of-the-art scalability but can also effectively manages complex, multi-resolution data structures. It delivers accurate rendering outcomes, reduces memory usage, and leverages emerging hardware capabilities more efficiently.Finally, the framework integrates implicit neural representation (INR) techniques for data compression and interactive visualization. The use of INRs significantly reduces data size while preserving high-frequency details. Additionally, it enables direct access to spatial locations at any desired resolution, obviating the need for decompression or interpolation.In summary, this dissertation research addresses long-standing challenges inherent in extreme-scale scientific visualization by introducing novel designs and methodologies. The presented framework not only enables more efficient and adaptive visualization workflows but also leverages the latest hardware acceleration and data compression techniques. The implications of these advancements extend beyond mere technical improvements; they pave the way for deeper insights and discoveries across a broad spectrum of scientific studies. This research, therefore, represents a significant leap forward, with the potential to transform the landscape of scientific visualization

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

Wrightia.

v.7 (1981-1984

Ray tracing techniques for computer games and isosurface visualization

Ray tracing is a powerful image synthesis technique, that has been used for high-quality offline rendering since decades. In recent years, this technique has become more important for realtime applications, but still plays only a minor role in many areas. Some of the reasons are that ray tracing is compute intensive and has to rely on preprocessed data structures to achieve fast performance. This dissertation investigates methods to broaden the applicability of ray tracing and is divided into two parts. The first part explores the opportunities offered by ray tracing based game technology in the context of current and expected future performance levels. In this regard, novel methods are developed to efficiently support certain kinds of dynamic scenes, while avoiding the burden to fully recompute the required data structures. Furthermore, todays ray tracing performance levels are below what is needed for 3D games. Therefore, the multi-core CPU of the Playstation 3 is investigated, and an optimized ray tracing architecture presented to take steps towards the required performance. In part two, the focus shifts to isosurface raytracing. Isosurfaces are particularly important to understand the distribution of certain values in volumetric data. Since the structure of volumetric data sets is diverse, op- timized algorithms and data structures are developed for rectilinear as well as unstructured data sets which allow for realtime rendering of isosurfaces including advanced shading and visualization effects. This also includes tech- niques for out-of-core and time-varying data sets.Ray-tracing ist ein flexibles Bildgebungsverfahren, das schon seit Jahrzehnten für hoch qualitative, aber langsame Bilderzeugung genutzt wird. In den letzten Jahren wurde Ray-tracing auch für Echtzeitanwendungen immer interessanter, spielt aber in vielen Anwendungsbereichen noch immer eine untergeordnete Rolle. Einige der Gründe sind die Rechenintensität von Ray-tracing sowie die Abhängigkeit von vorberechneten Datenstrukturen um hohe Geschwindigkeiten zu erreichen. Diese Dissertation untersucht Methoden um die Anwendbarkeit von Ray-tracing in zwei verschiedenen Bereichen zu erhöhen. Im ersten Teil dieser Dissertation werden die Möglichkeiten, die Ray- tracing basierte Spieletechnologie bietet, im Kontext mit aktueller sowie zukünftig erwarteten Geschwindigkeiten untersucht. Darüber hinaus werden in diesem Zusammenhang Methoden entwickelt um bestimmte zeitveränderliche Szenen darstellen zu können ohne die dafür benötigen Datenstrukturen von Grund auf neu erstellen zu müssen. Da die Geschwindigkeit von Ray-tracing für Spiele bisher nicht ausreichend ist, wird die Mehrkern- CPU der Playstation 3 untersucht, und ein optimiertes Ray-tracing System beschrieben, das Ray-tracing näher an die benötigte Geschwindigkeit heranbringt. Der zweite Teil beschäftigt sich mit der Darstellung von Isoflächen mittels Ray-tracing. Isoflächen sind insbesonders wichtig um die Verteilung einzelner Werte in volumetrischen Datensätzen zu verstehen. Da diese Datensätze verschieden strukturiert sein können, werden für gitterförmige und unstrukturierte Datensätze optimierte Algorithmen und Datenstrukturen entwickelt, die die Echtzeitdarstellung von Isoflächen erlauben. Dies beinhaltet auch Erweiterungen für extrem große und zeitveränderliche Datensätze

Faster data structures and graphics hardware techniques for high performance rendering

Computer generated imagery is used in a wide range of disciplines, each with different requirements. As an example, real-time applications such as computer games have completely different restrictions and demands than offline rendering of feature films. A game has to render quickly using only limited resources, yet present visually adequate images. Film and visual effects rendering may not have strict time requirements but are still required to render efficiently utilizing huge render systems with hundreds or even thousands of CPU cores. In real-time rendering, with limited time and hardware resources, it is always important to produce as high rendering quality as possible given the constraints available. The first paper in this thesis presents an analytical hardware model together with a feed-back system that guarantees the highest level of image quality subject to a limited time budget. As graphics processing units grow more powerful, power consumption becomes a critical issue. Smaller handheld devices have only a limited source of energy, their battery, and both small devices and high-end hardware are required to minimize energy consumption not to overheat. The second paper presents experiments and analysis which consider power usage across a range of real-time rendering algorithms and shadow algorithms executed on high-end, integrated and handheld hardware. Computing accurate reflections and refractions effects has long been considered available only in offline rendering where time isn’t a constraint. The third paper presents a hybrid approach, utilizing the speed of real-time rendering algorithms and hardware with the quality of offline methods to render high quality reflections and refractions in real-time. The fourth and fifth paper present improvements in construction time and quality of Bounding Volume Hierarchies (BVH). Building BVHs faster reduces rendering time in offline rendering and brings ray tracing a step closer towards a feasible real-time approach. Bonsai, presented in the fourth paper, constructs BVHs on CPUs faster than contemporary competing algorithms and produces BVHs of a very high quality. Following Bonsai, the fifth paper presents an algorithm that refines BVH construction by allowing triangles to be split. Although splitting triangles increases construction time, it generally allows for higher quality BVHs. The fifth paper introduces a triangle splitting BVH construction approach that builds BVHs with quality on a par with an earlier high quality splitting algorithm. However, the method presented in paper five is several times faster in construction time

Report on shape analysis and matching and on semantic matching

In GRAVITATE, two disparate specialities will come together in one working platform for the archaeologist: the fields of shape analysis, and of metadata search. These fields are relatively disjoint at the moment, and the research and development challenge of GRAVITATE is precisely to merge them for our chosen tasks. As shown in chapter 7 the small amount of literature that already attempts join 3D geometry and semantics is not related to the cultural heritage domain. Therefore, after the project is done, there should be a clear ‘before-GRAVITATE’ and ‘after-GRAVITATE’ split in how these two aspects of a cultural heritage artefact are treated.This state of the art report (SOTA) is ‘before-GRAVITATE’. Shape analysis and metadata description are described separately, as currently in the literature and we end the report with common recommendations in chapter 8 on possible or plausible cross-connections that suggest themselves. These considerations will be refined for the Roadmap for Research deliverable.Within the project, a jargon is developing in which ‘geometry’ stands for the physical properties of an artefact (not only its shape, but also its colour and material) and ‘metadata’ is used as a general shorthand for the semantic description of the provenance, location, ownership, classification, use etc. of the artefact. As we proceed in the project, we will find a need to refine those broad divisions, and find intermediate classes (such as a semantic description of certain colour patterns), but for now the terminology is convenient – not least because it highlights the interesting area where both aspects meet.On the ‘geometry’ side, the GRAVITATE partners are UVA, Technion, CNR/IMATI; on the metadata side, IT Innovation, British Museum and Cyprus Institute; the latter two of course also playing the role of internal users, and representatives of the Cultural Heritage (CH) data and target user’s group. CNR/IMATI’s experience in shape analysis and similarity will be an important bridge between the two worlds for geometry and metadata. The authorship and styles of this SOTA reflect these specialisms: the first part (chapters 3 and 4) purely by the geometry partners (mostly IMATI and UVA), the second part (chapters 5 and 6) by the metadata partners, especially IT Innovation while the joint overview on 3D geometry and semantics is mainly by IT Innovation and IMATI. The common section on Perspectives was written with the contribution of all

Non-photorealistic rendering: a critical examination and proposed system.

In the first part of the program the emergent field of Non-Photorealistic Rendering is explored from a cultural perspective. This is to establish a clear understanding of what Non-Photorealistic Rendering (NPR) ought to be in its mature form in order to provide goals and an overall infrastructure for future development. This thesis claims that unless we understand and clarify NPR's relationship with other media (photography, photorealistic computer graphics and traditional media) we will continue to manufacture "new solutions" to computer based imaging which are confused and naive in their goals. Such solutions will be rejected by the art and design community, generally condemned as novelties of little cultural worth ( i.e. they will not sell). This is achieved by critically reviewing published systems that are naively described as Non-photorealistic or "painterly" systems. Current practices and techniques are criticised in terms of their low ability to articulate meaning in images; solutions to this problem are given. A further argument claims that NPR, while being similar to traditional "natural media" techniques in certain aspects, is fundamentally different in other ways. This similarity has lead NPR to be sometimes proposed as "painting simulation" — something it can never be. Methods for avoiding this position are proposed. The similarities and differences to painting and drawing are presented and NPR's relationship to its other counterpart, Photorealistic Rendering (PR), is then delineated. It is shown that NPR is paradigmatically different to other forms of representation — i.e. it is not an "effect", but rather something basically different. The benefits of NPR in its mature form are discussed in the context of Architectural Representation and Design in general. This is done in conjunction with consultations with designers and architects. From this consultation a "wish-list" of capabilities is compiled by way of a requirements capture for a proposed system. A series of computer-based experiments resulting in the systems "Expressive Marks" and 'Magic Painter" are carried out; these practical experiments add further understanding to the problems of NPR. The exploration concludes with a prototype system "Piranesi" which is submitted as a good overall solution to the problem of NPR. In support of this written thesis are : - • The Expressive Marks system • Magic Painter system • The Piranesi system (which includes the EPixel and Sketcher systems) • A large portfolio of images generated throughout the exploration