The method of predicate least squares refinement

Parameters to be determined in a least squares refinement calculation to fit a set of observed data may sometimes usefully be `predicated' to values obtained from some independent source, such as a theoretical calculation. An algorithm for achieving this in a least squares refinement calculation is described, which leaves the operator in full control of the weight that he may wish to attach to the predicate values of the parameters.

A decoding method of an n length binary BCH code through (n + 1)n length binary cyclic code

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

DEVELOPMENT OF AN ALGORITHM TO ANALYZE CARTOGRAPHIC FEATURES EXTRACTION METHODS IN DIGITAL IMAGES

The algorithm creates a buffer area around the cartographic features of interest in one of the images and compare it with the other one. During the comparison, the algorithm calculates the number of equals and different points and uses it to calculate the statistical values of the analysis. One calculated statistical value is the correctness, which shows the user the percentage of points that were correctly extracted. Another one is the completeness that shows the percentage of points that really belong to the interest feature. And the third value shows the idea of quality obtained by the extraction method, since that in order to calculate the quality the algorithm uses the correctness and completeness previously calculated. All the performed tests using this algorithm were possible to use the statistical values calculated to represent quantitatively the quality obtained by the extraction method executed. So, it is possible to say that the developed algorithm can be used to analyze extraction methods of cartographic features of interest, since that the results obtained were promising.

Parallelization of the algorithm WHAM with NVIDIA CUDA.

The aim of my thesis is to parallelize the Weighting Histogram Analysis Method (WHAM), which is a popular algorithm used to calculate the Free Energy of a molucular system in Molecular Dynamics simulations. WHAM works in post processing in cooperation with another algorithm called Umbrella Sampling. Umbrella Sampling has the purpose to add a biasing in the potential energy of the system in order to force the system to sample a specific region in the configurational space. Several N independent simulations are performed in order to sample all the region of interest. Subsequently, the WHAM algorithm is used to estimate the original system energy starting from the N atomic trajectories. The parallelization of WHAM has been performed through CUDA, a language that allows to work in GPUs of NVIDIA graphic cards, which have a parallel achitecture. The parallel implementation may sensibly speed up the WHAM execution compared to previous serial CPU imlementations. However, the WHAM CPU code presents some temporal criticalities to very high numbers of interactions. The algorithm has been written in C++ and executed in UNIX systems provided with NVIDIA graphic cards. The results were satisfying obtaining an increase of performances when the model was executed on graphics cards with compute capability greater. Nonetheless, the GPUs used to test the algorithm is quite old and not designated for scientific calculations. It is likely that a further performance increase will be obtained if the algorithm would be executed in clusters of GPU at high level of computational efficiency. The thesis is organized in the following way: I will first describe the mathematical formulation of Umbrella Sampling and WHAM algorithm with their apllications in the study of ionic channels and in Molecular Docking (Chapter 1); then, I will present the CUDA architectures used to implement the model (Chapter 2); and finally, the results obtained on model systems will be presented (Chapter 3).

Fast and accurate numerical solutions in some problems of particle and radiation transport: synthetic acceleration for the method of short characteristics, Doppler-broadened scattering kernel, remote sensing of the cryosphere

The aim of this work is to present various aspects of numerical simulation of particle and radiation transport for industrial and environmental protection applications, to enable the analysis of complex physical processes in a fast, reliable, and efficient way. In the first part we deal with speed-up of numerical simulation of neutron transport for nuclear reactor core analysis. The convergence properties of the source iteration scheme of the Method of Characteristics applied to be heterogeneous structured geometries has been enhanced by means of Boundary Projection Acceleration, enabling the study of 2D and 3D geometries with transport theory without spatial homogenization. The computational performances have been verified with the C5G7 2D and 3D benchmarks, showing a sensible reduction of iterations and CPU time. The second part is devoted to the study of temperature-dependent elastic scattering of neutrons for heavy isotopes near to the thermal zone. A numerical computation of the Doppler convolution of the elastic scattering kernel based on the gas model is presented, for a general energy dependent cross section and scattering law in the center of mass system. The range of integration has been optimized employing a numerical cutoff, allowing a faster numerical evaluation of the convolution integral. Legendre moments of the transfer kernel are subsequently obtained by direct quadrature and a numerical analysis of the convergence is presented. In the third part we focus our attention to remote sensing applications of radiative transfer employed to investigate the Earth's cryosphere. The photon transport equation is applied to simulate reflectivity of glaciers varying the age of the layer of snow or ice, its thickness, the presence or not other underlying layers, the degree of dust included in the snow, creating a framework able to decipher spectral signals collected by orbiting detectors.

Method of Detecting System Function by Measuring Frequency Response

Real-time battery impedance spectrum is acquired using a one-time record. Fast Summation Transformation (FST) is a parallel method of acquiring a real-time battery impedance spectrum using a one-time record that enables battery diagnostics. An excitation current to a battery is a sum of equal amplitude sine waves of frequencies that are octave harmonics spread over a range of interest. A sample frequency is also octave and harmonically related to all frequencies in the sum. The time profile of this signal has a duration that is a few periods of the lowest frequency. The voltage response of the battery, average deleted, is the impedance of the battery in the time domain. Since the excitation frequencies are known and octave and harmonically related, a simple algorithm, FST, processes the time record by rectifying relative to the sine and cosine of each frequency. Another algorithm yields real and imaginary components for each frequency.

A framework for benchmarking of homogenisation algorithm performance on the global scale

The International Surface Temperature Initiative (ISTI) is striving towards substantively improving our ability to robustly understand historical land surface air temperature change at all scales. A key recently completed first step has been collating all available records into a comprehensive open access, traceable and version-controlled databank. The crucial next step is to maximise the value of the collated data through a robust international framework of benchmarking and assessment for product intercomparison and uncertainty estimation. We focus on uncertainties arising from the presence of inhomogeneities in monthly mean land surface temperature data and the varied methodological choices made by various groups in building homogeneous temperature products. The central facet of the benchmarking process is the creation of global-scale synthetic analogues to the real-world database where both the "true" series and inhomogeneities are known (a luxury the real-world data do not afford us). Hence, algorithmic strengths and weaknesses can be meaningfully quantified and conditional inferences made about the real-world climate system. Here we discuss the necessary framework for developing an international homogenisation benchmarking system on the global scale for monthly mean temperatures. The value of this framework is critically dependent upon the number of groups taking part and so we strongly advocate involvement in the benchmarking exercise from as many data analyst groups as possible to make the best use of this substantial effort.

Instrumental variable method for the causal relationship between soluble receptor for advanced glycation end-products (sRAGE) and risk of pancreatic cancer

This thesis project is motivated by the potential problem of using observational data to draw inferences about a causal relationship in observational epidemiology research when controlled randomization is not applicable. Instrumental variable (IV) method is one of the statistical tools to overcome this problem. Mendelian randomization study uses genetic variants as IVs in genetic association study. In this thesis, the IV method, as well as standard logistic and linear regression models, is used to investigate the causal association between risk of pancreatic cancer and the circulating levels of soluble receptor for advanced glycation end-products (sRAGE). Higher levels of serum sRAGE were found to be associated with a lower risk of pancreatic cancer in a previous observational study (255 cases and 485 controls). However, such a novel association may be biased by unknown confounding factors. In a case-control study, we aimed to use the IV approach to confirm or refute this observation in a subset of study subjects for whom the genotyping data were available (178 cases and 177 controls). Two-stage IV method using generalized method of moments-structural mean models (GMM-SMM) was conducted and the relative risk (RR) was calculated. In the first stage analysis, we found that the single nucleotide polymorphism (SNP) rs2070600 of the receptor for advanced glycation end-products (AGER) gene meets all three general assumptions for a genetic IV in examining the causal association between sRAGE and risk of pancreatic cancer. The variant allele of SNP rs2070600 of the AGER gene was associated with lower levels of sRAGE, and it was neither associated with risk of pancreatic cancer, nor with the confounding factors. It was a potential strong IV (F statistic = 29.2). However, in the second stage analysis, the GMM-SMM model failed to converge due to non- concaveness probably because of the small sample size. Therefore, the IV analysis could not support the causality of the association between serum sRAGE levels and risk of pancreatic cancer. Nevertheless, these analyses suggest that rs2070600 was a potentially good genetic IV for testing the causality between the risk of pancreatic cancer and sRAGE levels. A larger sample size is required to conduct a credible IV analysis.^

Contribution to the design of waveguide-fed compound-slot arrays by means of equivalent circuit modelling

Los arrays de ranuras son sistemas de antennas conocidos desde los años 40, principalmente destinados a formar parte de sistemas rádar de navíos de combate y grandes estaciones terrenas donde el tamaño y el peso no eran altamente restrictivos. Con el paso de los años y debido sobre todo a importantes avances en materiales y métodos de fabricación, el rango de aplicaciones de este tipo de sistemas radiantes creció en gran medida. Desde nuevas tecnologías biomédicas, sistemas anticolisión en automóviles y navegación en aviones, enlaces de comunicaciones de alta tasa binaria y corta distancia e incluso sistemas embarcados en satélites para la transmisión de señal de televisión. Dentro de esta familia de antennas, existen dos grupos que destacan por ser los más utilizados: las antennas de placas paralelas con las ranuras distribuidas de forma circular o espiral y las agrupaciones de arrays lineales construidos sobre guia de onda. Continuando con las tareas de investigación desarrolladas durante los últimos años en el Instituto de Tecnología de Tokyo y en el Grupo de Radiación de la Universidad Politécnica de Madrid, la totalidad de esta tesis se centra en este último grupo, aunque como se verá se separa en gran medida de las técnicas de diseño y metodologías convencionales. Los arrays de ranuras rectas y paralelas al eje de la guía rectangular que las alimenta son, sin ninguna duda, los modelos más empleados debido a la fiabilidad que presentan a altas frecuencias, su capacidad para gestionar grandes cantidades de potencia y la sencillez de su diseño y fabricación. Sin embargo, también presentan desventajas como estrecho ancho de banda en pérdidas de retorno y rápida degradación del diagrama de radiación con la frecuencia. Éstas son debidas a la naturaleza resonante de sus elementos radiantes: al perder la resonancia, el sistema global se desajusta y sus prestaciones degeneran. En arrays bidimensionales de slots rectos, el campo eléctrico queda polarizado sobre el plano transversal a las ranuras, correspondiéndose con el plano de altos lóbulos secundarios. Esta tesis tiene como objetivo el desarrollo de un método sistemático de diseño de arrays de ranuras inclinadas y desplazadas del centro (en lo sucesivo “ranuras compuestas”), definido en 1971 como uno de los desafíos a superar dentro del mundo del diseño de antennas. La técnica empleada se basa en el Método de los Momentos, la Teoría de Circuitos y la Teoría de Conexión Aleatoria de Matrices de Dispersión. Al tratarse de un método circuital, la primera parte de la tesis se corresponde con el estudio de la aplicabilidad de las redes equivalentes fundamentales, su capacidad para recrear fenómenos físicos de la ranura, las limitaciones y ventajas que presentan para caracterizar las diferentes configuraciones de slot compuesto. Se profundiza en las diferencias entre las redes en T y en ! y se condiciona la selección de una u otra dependiendo del tipo de elemento radiante. Una vez seleccionado el tipo de red a emplear en el diseño del sistema, se ha desarrollado un algoritmo de cascadeo progresivo desde el puerto alimentador hacia el cortocircuito que termina el modelo. Este algoritmo es independiente del número de elementos, la frecuencia central de funcionamiento, del ángulo de inclinación de las ranuras y de la red equivalente seleccionada (en T o en !). Se basa en definir el diseño del array como un Problema de Satisfacción de Condiciones (en inglés, Constraint Satisfaction Problem) que se resuelve por un método de Búsqueda en Retroceso (Backtracking algorithm). Como resultado devuelve un circuito equivalente del array completo adaptado a su entrada y cuyos elementos consumen una potencia acorde a una distribución de amplitud dada para el array. En toda agrupación de antennas, el acoplo mutuo entre elementos a través del campo radiado representa uno de los principales problemas para el ingeniero y sus efectos perjudican a las prestaciones globales del sistema, tanto en adaptación como en capacidad de radiación. El empleo de circuito equivalente se descartó por la dificultad que suponía la caracterización de estos efectos y su inclusión en la etapa de diseño. En esta tesis doctoral el acoplo también se ha modelado como una red equivalente cuyos elementos son transformadores ideales y admitancias, conectada al conjunto de redes equivalentes que representa el array. Al comparar los resultados estimados en términos de pérdidas de retorno y radiación con aquellos obtenidos a partir de programas comerciales populares como CST Microwave Studio se confirma la validez del método aquí propuesto, el primer método de diseño sistemático de arrays de ranuras compuestos alimentados por guía de onda rectangular. Al tratarse de ranuras no resonantes, el ancho de banda en pérdidas de retorno es mucho mas amplio que el que presentan arrays de slots rectos. Para arrays bidimensionales, el ángulo de inclinación puede ajustarse de manera que el campo quede polarizado en los planos de bajos lóbulos secundarios. Además de simulaciones se han diseñado, construido y medido dos prototipos centrados en la frecuencia de 12GHz, de seis y diez elementos. Las medidas de pérdidas de retorno y diagrama de radiación revelan excelentes resultados, certificando la bondad del método genuino Method of Moments - Forward Matching Procedure desarrollado a lo largo de esta tésis. Abstract The slot antenna arrays are well known systems from the decade of 40s, mainly intended to be part of radar systems of large warships and terrestrial stations where size and weight were not highly restrictive. Over the years, mainly due to significant advances in materials and manufacturing methods, the range of applications of this type of radiating systems grew significantly. From new biomedical technologies, collision avoidance systems in cars and aircraft navigation, short communication links with high bit transfer rate and even embedded systems in satellites for television broadcast. Within this family of antennas, two groups stand out as being the most frequent in the literature: parallel plate antennas with slots placed in a circular or spiral distribution and clusters of waveguide linear arrays. To continue the vast research work carried out during the last decades in the Tokyo Institute of Technology and in the Radiation Group at the Universidad Politécnica de Madrid, this thesis focuses on the latter group, although it represents a technique that drastically breaks with traditional design methodologies. The arrays of slots straight and parallel to the axis of the feeding rectangular waveguide are without a doubt the most used models because of the reliability that they present at high frequencies, its ability to handle large amounts of power and their simplicity of design and manufacturing. However, there also exist disadvantages as narrow bandwidth in return loss and rapid degradation of the radiation pattern with frequency. These are due to the resonant nature of radiating elements: away from the resonance status, the overall system performance and radiation pattern diminish. For two-dimensional arrays of straight slots, the electric field is polarized transverse to the radiators, corresponding to the plane of high side-lobe level. This thesis aims to develop a systematic method of designing arrays of angled and displaced slots (hereinafter "compound slots"), defined in 1971 as one of the challenges to overcome in the world of antenna design. The used technique is based on the Method of Moments, Circuit Theory and the Theory of Scattering Matrices Connection. Being a circuitry-based method, the first part of this dissertation corresponds to the study of the applicability of the basic equivalent networks, their ability to recreate the slot physical phenomena, their limitations and advantages presented to characterize different compound slot configurations. It delves into the differences of T and ! and determines the selection of the most suitable one depending on the type of radiating element. Once the type of network to be used in the system design is selected, a progressive algorithm called Forward Matching Procedure has been developed to connect the proper equivalent networks from the feeder port to shorted ending. This algorithm is independent of the number of elements, the central operating frequency, the angle of inclination of the slots and selected equivalent network (T or ! networks). It is based on the definition of the array design as a Constraint Satisfaction Problem, solved by means of a Backtracking Algorithm. As a result, the method returns an equivalent circuit of the whole array which is matched at its input port and whose elements consume a power according to a given amplitude distribution for the array. In any group of antennas, the mutual coupling between elements through the radiated field represents one of the biggest problems that the engineer faces and its effects are detrimental to the overall performance of the system, both in radiation capabilities and return loss. The employment of an equivalent circuit for the array design was discarded by some authors because of the difficulty involved in the characterization of the coupling effects and their inclusion in the design stage. In this thesis the coupling has also been modeled as an equivalent network whose elements are ideal transformers and admittances connected to the set of equivalent networks that represent the antennas of the array. By comparing the estimated results in terms of return loss and radiation with those obtained from popular commercial software as CST Microwave Studio, the validity of the proposed method is fully confirmed, representing the first method of systematic design of compound-slot arrays fed by rectangular waveguide. Since these slots do not work under the resonant status, the bandwidth in return loss is much wider than the longitudinal-slot arrays. For the case of two-dimensional arrays, the angle of inclination can be adjusted so that the field is polarized at the low side-lobe level plane. Besides the performed full-wave simulations two prototypes of six and ten elements for the X-band have been designed, built and measured, revealing excellent results and agreement with the expected results. These facts certify that the genuine technique Method of Moments - Matching Forward Procedure developed along this thesis is valid and trustable.

Computational cost of GNG3D algorithm for mesh simplification

In this paper we present a study of the computational cost of the GNG3D algorithm for mesh optimization. This algorithm has been implemented taking as a basis a new method which is based on neural networks and consists on two differentiated phases: an optimization phase and a reconstruction phase. The optimization phase is developed applying an optimization algorithm based on the Growing Neural Gas model, which constitutes an unsupervised incremental clustering algorithm. The primary goal of this phase is to obtain a simplified set of vertices representing the best approximation of the original 3D object. In the reconstruction phase we use the information provided by the optimization algorithm to reconstruct the faces thus obtaining the optimized mesh. The computational cost of both phases is calculated, showing some examples.

Comparative study of RPSALG algorithm for convex semi-infinite programming

The Remez penalty and smoothing algorithm (RPSALG) is a unified framework for penalty and smoothing methods for solving min-max convex semi-infinite programing problems, whose convergence was analyzed in a previous paper of three of the authors. In this paper we consider a partial implementation of RPSALG for solving ordinary convex semi-infinite programming problems. Each iteration of RPSALG involves two types of auxiliary optimization problems: the first one consists of obtaining an approximate solution of some discretized convex problem, while the second one requires to solve a non-convex optimization problem involving the parametric constraints as objective function with the parameter as variable. In this paper we tackle the latter problem with a variant of the cutting angle method called ECAM, a global optimization procedure for solving Lipschitz programming problems. We implement different variants of RPSALG which are compared with the unique publicly available SIP solver, NSIPS, on a battery of test problems.

Using the Agglomerative Method of Hierarchical Clustering as a Data Mining Tool in Capital Market

The purpose of this paper is to explain the notion of clustering and a concrete clustering method- agglomerative hierarchical clustering algorithm. It shows how a data mining method like clustering can be applied to the analysis of stocks, traded on the Bulgarian Stock Exchange in order to identify similar temporal behavior of the traded stocks. This problem is solved with the aid of a data mining tool that is called XLMiner™ for Microsoft Excel Office.

Implementation of a Heuristic Method of Decomposition of Partial Boolean Functions

An original heuristic algorithm of sequential two-block decomposition of partial Boolean functions is researched. The key combinatorial task is considered: finding of suitable partition on the set of arguments, i. e. such one, on which the function is separable. The search for suitable partition is essentially accelerated by preliminary detection of its traces. Within the framework of the experimental system the efficiency of the algorithm is evaluated, the boundaries of its practical application are determined.

An automatic method of above-water iceberg 3-D profiling based on autonomous surface craft (ASC) using surface images and LIDAR

This thesis reports on a novel method to build a 3-D model of the above-water portion of icebergs using surface imaging. The goal is to work towards the automation of iceberg surveys, allowing an Autonomous Surface Craft (ASC) to acquire shape and size information. After collecting data and images, the core software algorithm is made up of three parts: occluding contour finding, volume intersection, and parameter estimation. A software module is designed that could be used on the ASC to perform automatic and fast processing of above-water surface image data to determine iceberg shape and size measurement and determination. The resolution of the method is calculated using data from the iceberg database of the Program of Energy Research and Development (PERD). The method was investigated using data from field trials conducted through the summer of 2014 by surveying 8 icebergs during 3 expeditions. The results were analyzed to determine iceberg characteristics. Limitations of this method are addressed including its accuracy. Surface imaging system and LIDAR system are developed to profile the above-water iceberg in 2015.

Iterative reconstruction as a novel method of radiation dose reduction at computed tomography in patients with Crohn's disease

Prior work of our research group, that quantified the alarming levels of radiation dose to patients with Crohn’s disease from medical imaging and the notable shift towards CT imaging making these patients an at risk group, provided context for this work. CT delivers some of the highest doses of ionising radiation in diagnostic radiology. Once a medical imaging examination is deemed justified, there is an onus on the imaging team to endeavour to produce diagnostic quality CT images at the lowest possible radiation dose to that patient. The fundamental limitation with conventional CT raw data reconstruction was the inherent coupling of administered radiation dose with observed image noise – the lower the radiation dose, the noisier the image. The renaissance, rediscovery and refinement of iterative reconstruction removes this limitation allowing either an improvement in image quality without increasing radiation dose or maintenance of image quality at a lower radiation dose compared with traditional image reconstruction. This thesis is fundamentally an exercise in optimisation in clinical CT practice with the objectives of assessment of iterative reconstruction as a method for improvement of image quality in CT, exploration of the associated potential for radiation dose reduction, and development of a new split dose CT protocol with the aim of achieving and validating diagnostic quality submillisiever t CT imaging in patients with Crohn’s disease. In this study, we investigated the interplay of user-selected parameters on radiation dose and image quality in phantoms and cadavers, comparing traditional filtered back projection (FBP) with iterative reconstruction algorithms. This resulted in the development of an optimised, refined and appropriate split dose protocol for CT of the abdomen and pelvis in clinical patients with Crohn’s disease allowing contemporaneous acquisition of both modified and conventional dose CT studies. This novel algorithm was then applied to 50 patients with a suspected acute complication of known Crohn’s disease and the raw data reconstructed with FBP, adaptive statistical iterative reconstruction (ASiR) and model based iterative reconstruction (MBIR). Conventional dose CT images with FBP reconstruction were used as the reference standard with which the modified dose CT images were compared in terms of radiation dose, diagnostic findings and image quality indices. As there are multiple possible user-selected strengths of ASiR available, these were compared in terms of image quality to determine the optimal strength for this modified dose CT protocol. Modified dose CT images with MBIR were also compared with contemporaneous abdominal radiograph, where performed, in terms of diagnostic yield and radiation dose. Finally, attenuation measurements in organs, tissues, etc. with each reconstruction algorithm were compared to assess for preservation of tissue characterisation capabilities. In the phantom and cadaveric models, both forms of iterative reconstruction examined (ASiR and MBIR) were superior to FBP across a wide variety of imaging protocols, with MBIR superior to ASiR in all areas other than reconstruction speed. We established that ASiR appears to work to a target percentage noise reduction whilst MBIR works to a target residual level of absolute noise in the image. Modified dose CT images reconstructed with both ASiR and MBIR were non-inferior to conventional dose CT with FBP in terms of diagnostic findings, despite reduced subjective and objective indices of image quality. Mean dose reductions of 72.9-73.5% were achieved with the modified dose protocol with a mean effective dose of 1.26mSv. MBIR was again demonstrated superior to ASiR in terms of image quality. The overall optimal ASiR strength for the modified dose protocol used in this work is ASiR 80%, as this provides the most favourable balance of peak subjective image quality indices with less objective image noise than the corresponding conventional dose CT images reconstructed with FBP. Despite guidelines to the contrary, abdominal radiographs are still often used in the initial imaging of patients with a suspected complication of Crohn’s disease. We confirmed the superiority of modified dose CT with MBIR over abdominal radiographs at comparable doses in detection of Crohn’s disease and non-Crohn’s disease related findings. Finally, we demonstrated (in phantoms, cadavers and in vivo) that attenuation values do not change significantly across reconstruction algorithms meaning preserved tissue characterisation capabilities with iterative reconstruction. Both adaptive statistical and model based iterative reconstruction algorithms represent feasible methods of facilitating acquisition diagnostic quality CT images of the abdomen and pelvis in patients with Crohn’s disease at markedly reduced radiation doses. Our modified dose CT protocol allows dose savings of up to 73.5% compared with conventional dose CT, meaning submillisievert imaging is possible in many of these patients.