Predição de sítios de ligação para a cisplatina e transplatina baseada em ligações de hidrogênio

Pós-graduação em Biofísica Molecular - IBILCE

Implementação do algoritmo de treinamento do classificador floresta de caminhos ótimos em GPU

Técnicas de reconhecimento de padrões tem como principal objetivo classificar um conjunto de amostras, sendo o processo de aprendizado a fase de maior consumo de tempo. O problema pode piorar em ferramentas de classificação interativas, o que pode ser inaceitável para grandes bases de dados. Um exemplo de classificador é o baseado em Floresta de Caminhos Ótimos [8] - OPF. Dado que muitos trabalhos tem sido orientados à implementação de algoritmos de reconhecimento de padrões em ambiente General Purpose Graphics Processing Unit - GPGPU, o presente estudo objetivou a implementação da etapa de treinamento do classificador Floresta de Caminhos Ótimos em CUDA, visando aumentar a sua eficiência. A otimização do classificador em CUDA demonstrou uma fase de treinamento mais rápida que a versão original.

Tecnologie per la mobilità verso un middleware general-purpose

L'obiettivo della tesi è esplorare i più avanzati dispositivi, sensori e processori per la computazione spaziale, correlarli con i modelli di spatial computing, e derivarne un'architettura concettuale di middleware distribuito che possa supportare le più avanzate applicazioni in mobilità.

Elastic computing on Cloud resources for the CMS experiment

Nowadays, data handling and data analysis in High Energy Physics requires a vast amount of computational power and storage. In particular, the world-wide LHC Com- puting Grid (LCG), an infrastructure and pool of services developed and deployed by a ample community of physicists and computer scientists, has demonstrated to be a game changer in the efficiency of data analyses during Run-I at the LHC, playing a crucial role in the Higgs boson discovery. Recently, the Cloud computing paradigm is emerging and reaching a considerable adoption level by many different scientific organizations and not only. Cloud allows to access and utilize not-owned large computing resources shared among many scientific communities. Considering the challenging requirements of LHC physics in Run-II and beyond, the LHC computing community is interested in exploring Clouds and see whether they can provide a complementary approach - or even a valid alternative - to the existing technological solutions based on Grid. In the LHC community, several experiments have been adopting Cloud approaches, and in particular the experience of the CMS experiment is of relevance to this thesis. The LHC Run-II has just started, and Cloud-based solutions are already in production for CMS. However, other approaches of Cloud usage are being thought of and are at the prototype level, as the work done in this thesis. This effort is of paramount importance to be able to equip CMS with the capability to elastically and flexibly access and utilize the computing resources needed to face the challenges of Run-III and Run-IV. The main purpose of this thesis is to present forefront Cloud approaches that allow the CMS experiment to extend to on-demand resources dynamically allocated as needed. Moreover, a direct access to Cloud resources is presented as suitable use case to face up with the CMS experiment needs. Chapter 1 presents an overview of High Energy Physics at the LHC and of the CMS experience in Run-I, as well as preparation for Run-II. Chapter 2 describes the current CMS Computing Model, and Chapter 3 provides Cloud approaches pursued and used within the CMS Collaboration. Chapter 4 and Chapter 5 discuss the original and forefront work done in this thesis to develop and test working prototypes of elastic extensions of CMS computing resources on Clouds, and HEP Computing “as a Service”. The impact of such work on a benchmark CMS physics use-cases is also demonstrated.

Reduced neuronal efficacy in progressive mild cognitive impairment: a prospective fMRI study on visuospatial processing

Mild cognitive impairment (MCI) often refers to the preclinical stage of dementia, where the majority develop Alzheimer's disease (AD). Given that neurodegenerative burden and compensatory mechanisms might exist before accepted clinical symptoms of AD are noticeable, the current prospective study aimed to investigate the functioning of brain regions in the visuospatial networks responsible for preclinical symptoms in AD using event-related functional magnetic resonance imaging (fMRI). Eighteen MCI patients were evaluated and clinically followed for approximately 3 years. Five progressed to AD (PMCI) and eight remained stable (SMCI). Thirteen age-, gender- and education-matched controls also participated. An angle discrimination task with varying task demands was used. Brain activation patterns as well as task demand-dependent and -independent signal changes between the groups were investigated by using an extended general linear model including individual performance (reaction time [RT]) of each single trial. Similar behavioral (RT and accuracy) responses were observed between MCI patients and controls. A network of bilateral activations, e.g. dorsal pathway, which increased linearly with increasing task demand, was engaged in all subjects. Compared with SMCI patients and controls, PMCI patients showed a stronger relation between task demand and brain activity in left superior parietal lobules (SPL) as well as a general task demand-independent increased activation in left precuneus. Altered brain function can be detected at a group level in individuals that progress to AD before changes occur at the behavioral level. Increased parietal activation in PMCI could reflect a reduced neuronal efficacy due to accumulating AD pathology and might predict future clinical decline in patients with MCI.

Hierarchical Markov Random Fields Applied to Model Soft Tissue Deformations on Graphics Hardware

Many methodologies dealing with prediction or simulation of soft tissue deformations on medical image data require preprocessing of the data in order to produce a different shape representation that complies with standard methodologies, such as mass–spring networks, finite element method s (FEM). On the other hand, methodologies working directly on the image space normally do not take into account mechanical behavior of tissues and tend to lack physics foundations driving soft tissue deformations. This chapter presents a method to simulate soft tissue deformations based on coupled concepts from image analysis and mechanics theory. The proposed methodology is based on a robust stochastic approach that takes into account material properties retrieved directly from the image, concepts from continuum mechanics and FEM. The optimization framework is solved within a hierarchical Markov random field (HMRF) which is implemented on the graphics processor unit (GPU See Graphics processing unit ).

Optimal polygonal L1 linearization and fast interpolation of nonlinear systems

The analysis of complex nonlinear systems is often carried out using simpler piecewise linear representations of them. A principled and practical technique is proposed to linearize and evaluate arbitrary continuous nonlinear functions using polygonal (continuous piecewise linear) models under the L1 norm. A thorough error analysis is developed to guide an optimal design of two kinds of polygonal approximations in the asymptotic case of a large budget of evaluation subintervals N. The method allows the user to obtain the level of linearization (N) for a target approximation error and vice versa. It is suitable for, but not limited to, an efficient implementation in modern Graphics Processing Units (GPUs), allowing real-time performance of computationally demanding applications. The quality and efficiency of the technique has been measured in detail on two nonlinear functions that are widely used in many areas of scientific computing and are expensive to evaluate.

Large scale multiphysics modeling of neurites

Situado en el límite entre Ingeniería, Informática y Biología, la mecánica computacional de las neuronas aparece como un nuevo campo interdisciplinar que potencialmente puede ser capaz de abordar problemas clínicos desde una perspectiva diferente. Este campo es multiescala por naturaleza, yendo desde la nanoescala (como, por ejemplo, los dímeros de tubulina) a la macroescala (como, por ejemplo, el tejido cerebral), y tiene como objetivo abordar problemas que son complejos, y algunas veces imposibles, de estudiar con medios experimentales. La modelización computacional ha sido ampliamente empleada en aplicaciones Neurocientíficas tan diversas como el crecimiento neuronal o la propagación de los potenciales de acción compuestos. Sin embargo, en la mayoría de los enfoques de modelización hechos hasta ahora, la interacción entre la célula y el medio/estímulo que la rodea ha sido muy poco explorada. A pesar de la tremenda importancia de esa relación en algunos desafíos médicos—como, por ejemplo, lesiones traumáticas en el cerebro, cáncer, la enfermedad del Alzheimer—un puente que relacione las propiedades electrofisiológicas-químicas y mecánicas desde la escala molecular al nivel celular todavía no existe. Con ese objetivo, esta investigación propone un marco computacional multiescala particularizado para dos escenarios respresentativos: el crecimiento del axón y el acomplamiento electrofisiológicomecánico de las neuritas. En el primer caso, se explora la relación entre los constituyentes moleculares del axón durante su crecimiento y sus propiedades mecánicas resultantes, mientras que en el último, un estímulo mecánico provoca deficiencias funcionales a nivel celular como consecuencia de sus alteraciones electrofisiológicas-químicas. La modelización computacional empleada en este trabajo es el método de las diferencias finitas, y es implementada en un nuevo programa llamado Neurite. Aunque el método de los elementos finitos es también explorado en parte de esta investigación, el método de las diferencias finitas tiene la flexibilidad y versatilidad necesaria para implementar mode los biológicos, así como la simplicidad matemática para extenderlos a simulaciones a gran escala con un coste computacional bajo. Centrándose primero en el efecto de las propiedades electrofisiológicas-químicas sobre las propiedades mecánicas, una versión adaptada de Neurite es desarrollada para simular la polimerización de los microtúbulos en el crecimiento del axón y proporcionar las propiedades mecánicas como función de la ocupación de los microtúbulos. Después de calibrar el modelo de crecimiento del axón frente a resultados experimentales disponibles en la literatura, las características mecánicas pueden ser evaluadas durante la simulación. Las propiedades mecánicas del axón muestran variaciones dramáticas en la punta de éste, donde el cono de crecimiento soporta las señales químicas y mecánicas. Bansándose en el conocimiento ganado con el modelo de diferencias finitas, y con el objetivo de ir de 1D a 3D, este esquema preliminar pero de una naturaleza innovadora allana el camino a futuros estudios con el método de los elementos finitos. Centrándose finalmente en el efecto de las propiedades mecánicas sobre las propiedades electrofisiológicas- químicas, Neurite es empleado para relacionar las cargas mecánicas macroscópicas con las deformaciones y velocidades de deformación a escala microscópica, y simular la propagación de la señal eléctrica en las neuritas bajo carga mecánica. Las simulaciones fueron calibradas con resultados experimentales publicados en la literatura, proporcionando, por tanto, un modelo capaz de predecir las alteraciones de las funciones electrofisiológicas neuronales bajo cargas externas dañinas, y uniendo lesiones mecánicas con las correspondientes deficiencias funcionales. Para abordar simulaciones a gran escala, aunque otras arquitecturas avanzadas basadas en muchos núcleos integrados (MICs) fueron consideradas, los solvers explícito e implícito se implementaron en unidades de procesamiento central (CPU) y unidades de procesamiento gráfico (GPUs). Estudios de escalabilidad fueron llevados acabo para ambas implementaciones mostrando resultados prometedores para casos de simulaciones extremadamente grandes con GPUs. Esta tesis abre la vía para futuros modelos mecánicos con el objetivo de unir las propiedades electrofisiológicas-químicas con las propiedades mecánicas. El objetivo general es mejorar el conocimiento de las comunidades médicas y de bioingeniería sobre la mecánica de las neuronas y las deficiencias funcionales que aparecen de los daños producidos por traumatismos mecánicos, como lesiones traumáticas en el cerebro, o enfermedades neurodegenerativas como la enfermedad del Alzheimer. ABSTRACT Sitting at the interface between Engineering, Computer Science and Biology, Computational Neuron Mechanics appears as a new interdisciplinary field potentially able to tackle clinical problems from a new perspective. This field is multiscale by nature, ranging from the nanoscale (e.g., tubulin dimers) to the macroscale (e.g., brain tissue), and aims at tackling problems that are complex, and sometime impossible, to study through experimental means. Computational modeling has been widely used in different Neuroscience applications as diverse as neuronal growth or compound action potential propagation. However, in the majority of the modeling approaches done in this field to date, the interactions between the cell and its surrounding media/stimulus have been rarely explored. Despite of the tremendous importance of such relationship in several medical challenges—e.g., traumatic brain injury (TBI), cancer, Alzheimer’s disease (AD)—a bridge between electrophysiological-chemical and mechanical properties of neurons from the molecular scale to the cell level is still lacking. To this end, this research proposes a multiscale computational framework particularized for two representative scenarios: axon growth and electrophysiological-mechanical coupling of neurites. In the former case, the relation between the molecular constituents of the axon during its growth and its resulting mechanical properties is explored, whereas in the latter, a mechanical stimulus provokes functional deficits at cell level as a consequence of its electrophysiological-chemical alterations. The computational modeling approach chosen in this work is the finite difference method (FDM), and was implemented in a new program called Neurite. Although the finite element method (FEM) is also explored as part of this research, the FDM provides the necessary flexibility and versatility to implement biological models, as well as the mathematical simplicity to extend them to large scale simulations with a low computational cost. Focusing first on the effect of electrophysiological-chemical properties on the mechanical proper ties, an adaptation of Neurite was developed to simulate microtubule polymerization in axonal growth and provide the axon mechanical properties as a function of microtubule occupancy. After calibrating the axon growth model against experimental results available in the literature, the mechanical characteristics can be tracked during the simulation. The axon mechanical properties show dramatic variations at the tip of the axon, where the growth cone supports the chemical and mechanical signaling. Based on the knowledge gained from the FDM scheme, and in order to go from 1D to 3D, this preliminary yet novel scheme paves the road for future studies with FEM. Focusing then on the effect of mechanical properties on the electrophysiological-chemical properties, Neurite was used to relate macroscopic mechanical loading to microscopic strains and strain rates, and simulate the electrical signal propagation along neurites under mechanical loading. The simulations were calibrated against experimental results published in the literature, thus providing a model able to predict the alteration of neuronal electrophysiological function under external damaging load, and linking mechanical injuries to subsequent acute functional deficits. To undertake large scale simulations, although other state-of-the-art architectures based on many integrated cores (MICs) were considered, the explicit and implicit solvers were implemented for central processing units (CPUs) and graphics processing units (GPUs). Scalability studies were done for both implementations showing promising results for extremely large scale simulations with GPUs. This thesis opens the avenue for future mechanical modeling approaches aimed at linking electrophysiological- chemical properties to mechanical properties. Its overarching goal is to enhance the bioengineering and medical communities knowledge on neuronal mechanics and functional deficits arising from damages produced by direct mechanical insults, such as TBI, or neurodegenerative evolving illness, such as AD.

A General Purpose Configurable Controller for Indoors and Outdoors GPS-Denied Navigation for Multirotor Unmanned Aerial Vehicles

This research on odometry based GPS-denied navigation on multirotor Unmanned Aerial Vehicles is focused among the interactions between the odometry sensors and the navigation controller. More precisely, we present a controller architecture that allows to specify a speed specified flight envelope where the quality of the odometry measurements is guaranteed. The controller utilizes a simple point mass kinematic model, described by a set of configurable parameters, to generate a complying speed plan. For experimental testing, we have used down-facing camera optical-flow as odometry measurement. This work is a continuation of prior research to outdoors environments using an AR Drone 2.0 vehicle, as it provides reliable optical flow on a wide range of flying conditions and floor textures. Our experiments show that the architecture is realiable for outdoors flight on altitudes lower than 9 m. A prior version of our code was utilized to compete in the International Micro Air Vehicle Conference and Flight Competition IMAV 2012. The code will be released as an open-source ROS stack hosted on GitHub.

A General Purpose Configurable Navigation Controller for Micro Aerial Multirotor Vehicles

In this paper, we consider the problem of autonomous navigation of multirotor platforms in GPS-denied environments. The focus of this work is on safe navigation based on unperfect odometry measurements, such as on-board optical flow measurements. The multirotor platform is modeled as a flying object with specific kinematic constraints that must be taken into account in order to obtain successful results. A navigation controller is proposed featuring a set of configurable parameters that allow, for instance, to have a configuration setup for fast trajectory following, and another to soften the control laws and make the vehicle navigation more precise and slow whenever necessary. The proposed controller has been successfully implemented in two different multirotor platforms with similar sensoring capabilities showing the openness and tolerance of the approach. This research is focused around the Computer Vision Group's objective of applying multirotor vehicles to civilian service applications. The presented work was implemented to compete in the International Micro Air Vehicle Conference and Flight Competition IMAV 2012, gaining two awards: the Special Award on "Best Automatic Performance - IMAV 2012" and the second overall prize in the participating category "Indoor Flight Dynamics - Rotary Wing MAV". Most of the code related to the present work is available as two open-source projects hosted in GitHub.

A general-purpose tunable landscape generator

The research literature on metalieuristic and evolutionary computation has proposed a large number of algorithms for the solution of challenging real-world optimization problems. It is often not possible to study theoretically the performance of these algorithms unless significant assumptions are made on either the algorithm itself or the problems to which it is applied, or both. As a consequence, metalieuristics are typically evaluated empirically using a set of test problems. Unfortunately, relatively little attention has been given to the development of methodologies and tools for the large-scale empirical evaluation and/or comparison of metaheuristics. In this paper, we propose a landscape (test-problem) generator that can be used to generate optimization problem instances for continuous, bound-constrained optimization problems. The landscape generator is parameterized by a small number of parameters, and the values of these parameters have a direct and intuitive interpretation in terms of the geometric features of the landscapes that they produce. An experimental space is defined over algorithms and problems, via a tuple of parameters for any specified algorithm and problem class (here determined by the landscape generator). An experiment is then clearly specified as a point in this space, in a way that is analogous to other areas of experimental algorithmics, and more generally in experimental design. Experimental results are presented, demonstrating the use of the landscape generator. In particular, we analyze some simple, continuous estimation of distribution algorithms, and gain new insights into the behavior of these algorithms using the landscape generator.

Processing and rendering of Fourier domain optical coherence tomography images at a line rate over 524 kHz using a graphics processing unit

In Fourier domain optical coherence tomography (FD-OCT), a large amount of interference data needs to be resampled from the wavelength domain to the wavenumber domain prior to Fourier transformation. We present an approach to optimize this data processing, using a graphics processing unit (GPU) and parallel processing algorithms. We demonstrate an increased processing and rendering rate over that previously reported by using GPU paged memory to render data in the GPU rather than copying back to the CPU. This avoids unnecessary and slow data transfer, enabling a processing and display rate of well over 524,000 A-scan/s for a single frame. To the best of our knowledge this is the fastest processing demonstrated to date and the first time that FD-OCT processing and rendering has been demonstrated entirely on a GPU.

Multi-Tenant Virtual GPUs for Optimising Performance of a Financial Risk Application

Graphics Processing Units (GPUs) are becoming popular accelerators in modern High-Performance Computing (HPC) clusters. Installing GPUs on each node of the cluster is not efficient resulting in high costs and power consumption as well as underutilisation of the accelerator. The research reported in this paper is motivated towards the use of few physical GPUs by providing cluster nodes access to remote GPUs on-demand for a financial risk application. We hypothesise that sharing GPUs between several nodes, referred to as multi-tenancy, reduces the execution time and energy consumed by an application. Two data transfer modes between the CPU and the GPUs, namely concurrent and sequential, are explored. The key result from the experiments is that multi-tenancy with few physical GPUs using sequential data transfers lowers the execution time and the energy consumed, thereby improving the overall performance of the application.

A fast parallel hyperspectral coded aperture algorithm for compressive sensing using OpenCL

In this paper, we develop a fast implementation of an hyperspectral coded aperture (HYCA) algorithm on different platforms using OpenCL, an open standard for parallel programing on heterogeneous systems, which includes a wide variety of devices, from dense multicore systems from major manufactures such as Intel or ARM to new accelerators such as graphics processing units (GPUs), field programmable gate arrays (FPGAs), the Intel Xeon Phi and other custom devices. Our proposed implementation of HYCA significantly reduces its computational cost. Our experiments have been conducted using simulated data and reveal considerable acceleration factors. This kind of implementations with the same descriptive language on different architectures are very important in order to really calibrate the possibility of using heterogeneous platforms for efficient hyperspectral imaging processing in real remote sensing missions.