Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms

Fog Computing

Everything that is not a computer, in the traditional sense, is being connected to the Internet. These devices are also referred to as the Internet of Things and they are pressuring the current network infrastructure. Not all devices are intensive data producers and part of them can be used beyond their original intent by sharing their computational resources. The combination of those two factors can be used either to perform insight over the data closer where is originated or extend into new services by making available computational resources, but not exclusively, at the edge of the network. Fog computing is a new computational paradigm that provides those devices a new form of cloud at a closer distance where IoT and other devices with connectivity capabilities can offload computation. In this dissertation, we have explored the fog computing paradigm, and also comparing with other paradigms, namely cloud, and edge computing. Then, we propose a novel architecture that can be used to form or be part of this new paradigm. The implementation was tested on two types of applications. The first application had the main objective of demonstrating the correctness of the implementation while the other application, had the goal of validating the characteristics of fog computing.Tudo o que não é um computador, no sentido tradicional, está sendo conectado à Internet. Esses dispositivos também são chamados de Internet das Coisas e estão pressionando a infraestrutura de rede atual. Nem todos os dispositivos são produtores intensivos de dados e parte deles pode ser usada além de sua intenção original, compartilhando seus recursos computacionais. A combinação desses dois fatores pode ser usada para realizar processamento dos dados mais próximos de onde são originados ou estender para a criação de novos serviços, disponibilizando recursos computacionais periféricos à rede. Fog computing é um novo paradigma computacional que fornece a esses dispositivos uma nova forma de nuvem a uma distância mais próxima, onde “Things” e outros dispositivos com recursos de conectividade possam delegar processamento. Nesta dissertação, exploramos fog computing e também comparamos com outros paradigmas, nomeadamente cloud e edge computing. Em seguida, propomos uma nova arquitetura que pode ser usada para formar ou fazer parte desse novo paradigma. A implementação foi testada em dois tipos de aplicativos. A primeira aplicação teve o objetivo principal de demonstrar a correção da implementação, enquanto a outra aplicação, teve como objetivo validar as características de fog computing

Surface Deformation Potentials on Meshes for Computer Graphics and Visualization

Shape deformation models have been used in computer graphics primarily to describe the dynamics of physical deformations like cloth draping, collisions of elastic bodies, fracture, or animation of hair. Less frequent is their application to problems not directly related to a physical process. In this thesis we apply deformations to three problems in computer graphics that do not correspond to physical deformations. To this end, we generalize the physical model by modifying the energy potential. Originally, the energy potential amounts to the physical work needed to deform a body from its rest state into a given configuration and relates material strain to internal restoring forces that act to restore the original shape. For each of the three problems considered, this potential is adapted to reflect an application specific notion of shape. Under the influence of further constraints, our generalized deformation results in shapes that balance preservation of certain shape properties and application specific objectives similar to physical equilibrium states. The applications discussed in this thesis are surface parameterization, interactive shape editing and automatic design of panorama maps. For surface parameterization, we interpret parameterizations over a planar domain as deformations from a flat initial configuration onto a given surface. In this setting, we review existing parameterization methods by analyzing properties of their potential functions and derive potentials accounting for distortion of geometric properties. Interactive shape editing allows an untrained user to modify complex surfaces, be simply grabbing and moving parts of interest. A deformation model interactively extrapolates the transformation from those parts to the rest of the surface. This thesis proposes a differential shape representation for triangle meshes leading to a potential that can be optimized interactively with a simple, tailored algorithm. Although the potential is not physically accurate, it results in intuitive deformation behavior and can be parameterized to account for different material properties. Panorama maps are blends between landscape illustrations and geographic maps that are traditionally painted by an artist to convey geographic surveyknowledge on public places like ski resorts or national parks. While panorama maps are not drawn to scale, the shown landscape remains recognizable and the observer can easily recover details necessary for self location and orientation. At the same time, important features as trails or ski slopes appear not occluded and well visible. This thesis proposes the first automatic panorama generation method. Its basis is again a surface deformation, that establishes the necessary compromise between shape preservation and feature visibility.Potentiale zur Flächendeformation auf Dreiecksnetzen für Anwendungen in der Computergrafik und Visualisierung Deformationsmodelle werden in der Computergrafik bislang hauptsächlich eingesetzt, um die Dynamik physikalischer Deformationsprozesse zu modellieren. Gängige Beispiele sind Bekleidungssimulationen, Kollisionen elastischer Körper oder Animation von Haaren und Frisuren. Deutlich seltener ist ihre Anwendung auf Probleme, die nicht direkt physikalischen Prozessen entsprechen. In der vorliegenden Arbeit werden Deformationsmodelle auf drei Probleme der Computergrafik angewandt, die nicht unmittelbar einem physikalischen Deformationsprozess entsprechen. Zu diesem Zweck wird das physikalische Modell durch eine passende Änderung der potentiellen Energie verallgemeinert. Die potentielle Energie entspricht normalerweise der physikalischen Arbeit, die aufgewendet werden muss, um einen Körper aus dem Ruhezustand in eine bestimmte Konfiguration zu verformen. Darüber hinaus setzt sie die aktuelle Verformung in Beziehung zu internen Spannungskräften, die wirken um die ursprüngliche Form wiederherzustellen. In dieser Arbeit passen wir für jedes der drei betrachteten Problemfelder die potentielle Energie jeweils so an, dass sie eine anwendungsspezifische Definition von Form widerspiegelt. Unter dem Einfluss weiterer Randbedingungen führt die so verallgemeinerte Deformation zu einer Fläche, die eine Balance zwischen der Erhaltung gewisser Formeigenschaften und Zielvorgaben der Anwendung findet. Diese Balance entspricht dem Equilibrium einer physikalischen Deformation. Die drei in dieser Arbeit diskutierten Anwendungen sind Oberflächenparameterisierung, interaktives Bearbeiten von Flächen und das vollautomatische Erzeugen von Panoramakarten im Stile von Heinrich Berann. Zur Oberflächenparameterisierung interpretieren wir Parameterisierungen über einem flachen Parametergebiet als Deformationen, die ein ursprünglich ebenes Flächenstück in eine gegebene Oberfläche verformen. Innerhalb dieses Szenarios vergleichen wir dann existierende Methoden zur planaren Parameterisierung, indem wir die resultierenden potentiellen Energien analysieren, und leiten weitere Potentiale her, die die Störung geometrischer Eigenschaften wie Fläche und Winkel erfassen. Verfahren zur interaktiven Flächenbearbeitung ermöglichen schnelle und intuitive Änderungen an einer komplexen Oberfläche. Dazu wählt der Benutzer Teile der Fläche und bewegt diese durch den Raum. Ein Deformationsmodell extrapoliert interaktiv die Transformation der gewählten Teile auf die restliche Fläche. Diese Arbeit stellt eine neue differentielle Flächenrepräsentation für diskrete Flächen vor, die zu einem einfach und interaktiv zu optimierendem Potential führt. Obwohl das vorgeschlagene Potential nicht physikalisch korrekt ist, sind die resultierenden Deformationen intuitiv. Mittels eines Parameters lassen sich außerdem bestimmte Materialeigenschaften einstellen. Panoramakarten im Stile von Heinrich Berann sind eine Verschmelzung von Landschaftsillustration und geographischer Karte. Traditionell werden sie so von Hand gezeichnet, dass bestimmt Merkmale wie beispielsweise Skipisten oder Wanderwege in einem Gebiet unverdeckt und gut sichtbar bleiben, was große Kunstfertigkeit verlangt. Obwohl diese Art der Darstellung nicht maßstabsgetreu ist, sind Abweichungen auf den ersten Blick meistens nicht zu erkennen. Dadurch kann der Betrachter markante Details schnell wiederfinden und sich so innerhalb des Gebietes orientieren. Diese Arbeit stellt das erste, vollautomatische Verfahren zur Erzeugung von Panoramakarten vor. Grundlage ist wiederum eine verallgemeinerte Oberflächendeformation, die sowohl auf Formerhaltung als auch auf die Sichtbarkeit vorgegebener geographischer Merkmale abzielt

Load forecasting: a cross-field study on server and energy load forecasting Impact of temporal factors on generalization ability and performance of regression models

The server load prediction and energy load forecasting have available a wide range of approaches and applications, with their general goal being the prediction of future load for a specific period of time on a given system. Depending on the specific goal, different methodologies can be applied. In this dissertation, the integration of additional temporal information to datasets, as a mean to create a more generalized model is studied. The main steps involve a deep literature review in order to find the most suited methodologies and/or learning methods. A novel dataset enrichment process through the integration of extra temporal information and lastly, a cross-model testing stage, where trained models for server load prediction and energy load forecast are applied to the opposite field. This last stage, tests and analyses the generalization level of the created models through the temporal information integration procedure. The created models were both oriented to short-term load forecasting problems, with the use of data from single and combined months, regarding real data from Wikipedia servers of the year 2016 in the case of server load prediction and real data regarding the consumption levels in April 2016 of the city of Leiria/Portugal for the energy load forecasting case study. The learning methods used for creating the different models were linear regression, artificial neural networks and support vector machines oriented to regression problems, more precisely the Smoreg implementation. Results prove that it is possible to tune the dataset features, e.g., granularity and time window to improve prediction results and generalization. Results from this work, as well as an optimization approach through the use of genetic algorithms, normalization effects, split ratio vs crossvalidation influence and different granularities and time windows were peer-reviewed published

Information Bottleneck

The celebrated information bottleneck (IB) principle of Tishby et al. has recently enjoyed renewed attention due to its application in the area of deep learning. This collection investigates the IB principle in this new context. The individual chapters in this collection: • provide novel insights into the functional properties of the IB; • discuss the IB principle (and its derivates) as an objective for training multi-layer machine learning structures such as neural networks and decision trees; and • offer a new perspective on neural network learning via the lens of the IB framework. Our collection thus contributes to a better understanding of the IB principle specifically for deep learning and, more generally, of information–theoretic cost functions in machine learning. This paves the way toward explainable artificial intelligence

Computer Aided Verification

This open access two-volume set LNCS 13371 and 13372 constitutes the refereed proceedings of the 34rd International Conference on Computer Aided Verification, CAV 2022, which was held in Haifa, Israel, in August 2022. The 40 full papers presented together with 9 tool papers and 2 case studies were carefully reviewed and selected from 209 submissions. The papers were organized in the following topical sections: Part I: Invited papers; formal methods for probabilistic programs; formal methods for neural networks; software Verification and model checking; hyperproperties and security; formal methods for hardware, cyber-physical, and hybrid systems. Part II: Probabilistic techniques; automata and logic; deductive verification and decision procedures; machine learning; synthesis and concurrency. This is an open access book

Proceedings of the 8th Workshop on Detection and Classification of Acoustic Scenes and Events (DCASE 2023)

This volume gathers the papers presented at the Detection and Classification of Acoustic Scenes and Events 2023 Workshop (DCASE2023), Tampere, Finland, during 21–22 September 2023