An Adaptation of the Hoshen-Kopelman Cluster Counting Algorithm for Honeycomb Networks

We develop a simplified implementation of the Hoshen-Kopelman cluster counting algorithm adapted for honeycomb networks. In our implementation of the algorithm we assume that all nodes in the network are occupied and links between nodes can be intact or broken. The algorithm counts how many clusters there are in the network and determines which nodes belong to each cluster. The network information is stored into two sets of data. The first one is related to the connectivity of the nodes and the second one to the state of links. The algorithm finds all clusters in only one scan across the network and thereafter cluster relabeling operates on a vector whose size is much smaller than the size of the network. Counting the number of clusters of each size, the algorithm determines the cluster size probability distribution from which the mean cluster size parameter can be estimated. Although our implementation of the Hoshen-Kopelman algorithm works only for networks with a honeycomb (hexagonal) structure, it can be easily changed to be applied for networks with arbitrary connectivity between the nodes (triangular, square, etc.). The proposed adaptation of the Hoshen-Kopelman cluster counting algorithm is applied to studying the thermal degradation of a graphene-like honeycomb membrane by means of Molecular Dynamics simulation with a Langevin thermostat. ACM Computing Classification System (1998): F.2.2, I.5.3.

DEVELOPMENT OF AN OFF-LINE RAINFLOW COUNTING ALGORITHM WITH TEMPORAL PARAMETERS AND DATA REDUCTION

Rainflow counting methods convert a complex load time history into a set of load reversals for use in fatigue damage modeling. Rainflow counting methods were originally developed to assess fatigue damage associated with mechanical cycling where creep of the material under load was not considered to be a significant contributor to failure. However, creep is a significant factor in some cyclic loading cases such as solder interconnects under temperature cycling. In this case, fatigue life models require the dwell time to account for stress relaxation and creep. This study develops a new version of the multi-parameter rainflow counting algorithm that provides a range-based dwell time estimation for use with time-dependent fatigue damage models. To show the applicability, the method is used to calculate the life of solder joints under a complex thermal cycling regime and is verified by experimental testing. An additional algorithm is developed in this study to provide data reduction in the results of the rainflow counting. This algorithm uses a damage model and a statistical test to determine which of the resultant cycles are statistically insignificant to a given confidence level. This makes the resulting data file to be smaller, and for a simplified load history to be reconstructed.

THE VORONOI TESSELLATION CLUSTER FINDER IN 2+1 DIMENSIONS

We present a detailed description of the Voronoi Tessellation (VT) cluster finder algorithm in 2+1 dimensions, which improves on past implementations of this technique. The need for cluster finder algorithms able to produce reliable cluster catalogs up to redshift 1 or beyond and down to 10(13.5) solar masses is paramount especially in light of upcoming surveys aiming at cosmological constraints from galaxy cluster number counts. We build the VT in photometric redshift shells and use the two-point correlation function of the galaxies in the field to both determine the density threshold for detection of cluster candidates and to establish their significance. This allows us to detect clusters in a self-consistent way without any assumptions about their astrophysical properties. We apply the VT to mock catalogs which extend to redshift 1.4 reproducing the ACDM cosmology and the clustering properties observed in the Sloan Digital Sky Survey data. An objective estimate of the cluster selection function in terms of the completeness and purity as a function of mass and redshift is as important as having a reliable cluster finder. We measure these quantities by matching the VT cluster catalog with the mock truth table. We show that the VT can produce a cluster catalog with completeness and purity > 80% for the redshift range up to similar to 1 and mass range down to similar to 10(13.5) solar masses.

GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms. (c) 2005 Elsevier Ltd. All rights reserved.

A system for classification of time-series data from industrial non-destructive device

This work proposes a system for classification of industrial steel pieces by means of magnetic nondestructive device. The proposed classification system presents two main stages, online system stage and off-line system stage. In online stage, the system classifies inputs and saves misclassification information in order to perform posterior analyses. In the off-line optimization stage, the topology of a Probabilistic Neural Network is optimized by a Feature Selection algorithm combined with the Probabilistic Neural Network to increase the classification rate. The proposed Feature Selection algorithm searches for the signal spectrogram by combining three basic elements: a Sequential Forward Selection algorithm, a Feature Cluster Grow algorithm with classification rate gradient analysis and a Sequential Backward Selection. Also, a trash-data recycling algorithm is proposed to obtain the optimal feedback samples selected from the misclassified ones.

Applicability of Process Mining Techniques in Business Environments

This thesis analyses problems related to the applicability, in business environments, of Process Mining tools and techniques. The first contribution is a presentation of the state of the art of Process Mining and a characterization of companies, in terms of their "process awareness". The work continues identifying circumstance where problems can emerge: data preparation; actual mining; and results interpretation. Other problems are the configuration of parameters by not-expert users and computational complexity. We concentrate on two possible scenarios: "batch" and "on-line" Process Mining. Concerning the batch Process Mining, we first investigated the data preparation problem and we proposed a solution for the identification of the "case-ids" whenever this field is not explicitly indicated. After that, we concentrated on problems at mining time and we propose the generalization of a well-known control-flow discovery algorithm in order to exploit non instantaneous events. The usage of interval-based recording leads to an important improvement of performance. Later on, we report our work on the parameters configuration for not-expert users. We present two approaches to select the "best" parameters configuration: one is completely autonomous; the other requires human interaction to navigate a hierarchy of candidate models. Concerning the data interpretation and results evaluation, we propose two metrics: a model-to-model and a model-to-log. Finally, we present an automatic approach for the extension of a control-flow model with social information, in order to simplify the analysis of these perspectives. The second part of this thesis deals with control-flow discovery algorithms in on-line settings. We propose a formal definition of the problem, and two baseline approaches. The actual mining algorithms proposed are two: the first is the adaptation, to the control-flow discovery problem, of a frequency counting algorithm; the second constitutes a framework of models which can be used for different kinds of streams (stationary versus evolving).

A soft-tetramer model for diblock copolymer melts: structure formation and geometric characterization

The ability of block copolymers to spontaneously self-assemble into a variety of ordered nano-structures not only makes them a scientifically interesting system for the investigation of order-disorder phase transitions, but also offers a wide range of nano-technological applications. The architecture of a diblock is the most simple among the block copolymer systems, hence it is often used as a model system in both experiment and theory. We introduce a new soft-tetramer model for efficient computer simulations of diblock copolymer melts. The instantaneous non-spherical shape of polymer chains in molten state is incorporated by modeling each of the two blocks as two soft spheres. The interactions between the spheres are modeled in a way that the diblock melt tends to microphase separate with decreasing temperature. Using Monte Carlo simulations, we determine the equilibrium structures at variable values of the two relevant control parameters, the diblock composition and the incompatibility of unlike components. The simplicity of the model allows us to scan the control parameter space in a completeness that has not been reached in previous molecular simulations.The resulting phase diagram shows clear similarities with the phase diagram found in experiments. Moreover, we show that structural details of block copolymer chains can be reproduced by our simple model.We develop a novel method for the identification of the observed diblock copolymer mesophases that formalizes the usual approach of direct visual observation,using the characteristic geometry of the structures. A cluster analysis algorithm is used to determine clusters of each component of the diblock, and the number and shape of the clusters can be used to determine the mesophase.We also employ methods from integral geometry for the identification of mesophases and compare their usefulness to the cluster analysis approach.To probe the properties of our model in confinement, we perform molecular dynamics simulations of atomistic polyethylene melts confined between graphite surfaces. The results from these simulations are used as an input for an iterative coarse-graining procedure that yields a surface interaction potential for the soft-tetramer model. Using the interaction potential derived in that way, we perform an initial study on the behavior of the soft-tetramer model in confinement. Comparing with experimental studies, we find that our model can reflect basic features of confined diblock copolymer melts.

Toward reduction of artifacts in fused images

Most fusion satellite image methodologies at pixel-level introduce false spatial details, i.e.artifacts, in the resulting fusedimages. In many cases, these artifacts appears because image fusion methods do not consider the differences in roughness or textural characteristics between different land covers. They only consider the digital values associated with single pixels. This effect increases as the spatial resolution image increases. To minimize this problem, we propose a new paradigm based on local measurements of the fractal dimension (FD). Fractal dimension maps (FDMs) are generated for each of the source images (panchromatic and each band of the multi-spectral images) with the box-counting algorithm and by applying a windowing process. The average of source image FDMs, previously indexed between 0 and 1, has been used for discrimination of different land covers present in satellite images. This paradigm has been applied through the fusion methodology based on the discrete wavelet transform (DWT), using the à trous algorithm (WAT). Two different scenes registered by optical sensors on board FORMOSAT-2 and IKONOS satellites were used to study the behaviour of the proposed methodology. The implementation of this approach, using the WAT method, allows adapting the fusion process to the roughness and shape of the regions present in the image to be fused. This improves the quality of the fusedimages and their classification results when compared with the original WAT method

Localization and activity detection Based on the fusion of environment And inertial sensors = Localización y detección de actividad Basadas en integración de sensores y dispositivos inerciales

Los sensores inerciales (acelerómetros y giróscopos) se han ido introduciendo poco a poco en dispositivos que usamos en nuestra vida diaria gracias a su minituarización. Hoy en día todos los smartphones contienen como mínimo un acelerómetro y un magnetómetro, siendo complementados en losmás modernos por giróscopos y barómetros. Esto, unido a la proliferación de los smartphones ha hecho viable el diseño de sistemas basados en las medidas de sensores que el usuario lleva colocados en alguna parte del cuerpo (que en un futuro estarán contenidos en tejidos inteligentes) o los integrados en su móvil. El papel de estos sensores se ha convertido en fundamental para el desarrollo de aplicaciones contextuales y de inteligencia ambiental. Algunos ejemplos son el control de los ejercicios de rehabilitación o la oferta de información referente al sitio turístico que se está visitando. El trabajo de esta tesis contribuye a explorar las posibilidades que ofrecen los sensores inerciales para el apoyo a la detección de actividad y la mejora de la precisión de servicios de localización para peatones. En lo referente al reconocimiento de la actividad que desarrolla un usuario, se ha explorado el uso de los sensores integrados en los dispositivos móviles de última generación (luz y proximidad, acelerómetro, giróscopo y magnetómetro). Las actividades objetivo son conocidas como ‘atómicas’ (andar a distintas velocidades, estar de pie, correr, estar sentado), esto es, actividades que constituyen unidades de actividades más complejas como pueden ser lavar los platos o ir al trabajo. De este modo, se usan algoritmos de clasificación sencillos que puedan ser integrados en un móvil como el Naïve Bayes, Tablas y Árboles de Decisión. Además, se pretende igualmente detectar la posición en la que el usuario lleva el móvil, no sólo con el objetivo de utilizar esa información para elegir un clasificador entrenado sólo con datos recogidos en la posición correspondiente (estrategia que mejora los resultados de estimación de la actividad), sino también para la generación de un evento que puede producir la ejecución de una acción. Finalmente, el trabajo incluye un análisis de las prestaciones de la clasificación variando el tipo de parámetros y el número de sensores usados y teniendo en cuenta no sólo la precisión de la clasificación sino también la carga computacional. Por otra parte, se ha propuesto un algoritmo basado en la cuenta de pasos utilizando informaiii ción proveniente de un acelerómetro colocado en el pie del usuario. El objetivo final es detectar la actividad que el usuario está haciendo junto con la estimación aproximada de la distancia recorrida. El algoritmo de cuenta pasos se basa en la detección de máximos y mínimos usando ventanas temporales y umbrales sin requerir información específica del usuario. El ámbito de seguimiento de peatones en interiores es interesante por la falta de un estándar de localización en este tipo de entornos. Se ha diseñado un filtro extendido de Kalman centralizado y ligeramente acoplado para fusionar la información medida por un acelerómetro colocado en el pie del usuario con medidas de posición. Se han aplicado también diferentes técnicas de corrección de errores como las de velocidad cero que se basan en la detección de los instantes en los que el pie está apoyado en el suelo. Los resultados han sido obtenidos en entornos interiores usando las posiciones estimadas por un sistema de triangulación basado en la medida de la potencia recibida (RSS) y GPS en exteriores. Finalmente, se han implementado algunas aplicaciones que prueban la utilidad del trabajo desarrollado. En primer lugar se ha considerado una aplicación de monitorización de actividad que proporciona al usuario información sobre el nivel de actividad que realiza durante un período de tiempo. El objetivo final es favorecer el cambio de comportamientos sedentarios, consiguiendo hábitos saludables. Se han desarrollado dos versiones de esta aplicación. En el primer caso se ha integrado el algoritmo de cuenta pasos en una plataforma OSGi móvil adquiriendo los datos de un acelerómetro Bluetooth colocado en el pie. En el segundo caso se ha creado la misma aplicación utilizando las implementaciones de los clasificadores en un dispositivo Android. Por otro lado, se ha planteado el diseño de una aplicación para la creación automática de un diario de viaje a partir de la detección de eventos importantes. Esta aplicación toma como entrada la información procedente de la estimación de actividad y de localización además de información almacenada en bases de datos abiertas (fotos, información sobre sitios) e información sobre sensores reales y virtuales (agenda, cámara, etc.) del móvil. Abstract Inertial sensors (accelerometers and gyroscopes) have been gradually embedded in the devices that people use in their daily lives thanks to their miniaturization. Nowadays all smartphones have at least one embedded magnetometer and accelerometer, containing the most upto- date ones gyroscopes and barometers. This issue, together with the fact that the penetration of smartphones is growing steadily, has made possible the design of systems that rely on the information gathered by wearable sensors (in the future contained in smart textiles) or inertial sensors embedded in a smartphone. The role of these sensors has become key to the development of context-aware and ambient intelligent applications. Some examples are the performance of rehabilitation exercises, the provision of information related to the place that the user is visiting or the interaction with objects by gesture recognition. The work of this thesis contributes to explore to which extent this kind of sensors can be useful to support activity recognition and pedestrian tracking, which have been proven to be essential for these applications. Regarding the recognition of the activity that a user performs, the use of sensors embedded in a smartphone (proximity and light sensors, gyroscopes, magnetometers and accelerometers) has been explored. The activities that are detected belong to the group of the ones known as ‘atomic’ activities (e.g. walking at different paces, running, standing), that is, activities or movements that are part of more complex activities such as doing the dishes or commuting. Simple, wellknown classifiers that can run embedded in a smartphone have been tested, such as Naïve Bayes, Decision Tables and Trees. In addition to this, another aim is to estimate the on-body position in which the user is carrying the mobile phone. The objective is not only to choose a classifier that has been trained with the corresponding data in order to enhance the classification but also to start actions. Finally, the performance of the different classifiers is analysed, taking into consideration different features and number of sensors. The computational and memory load of the classifiers is also measured. On the other hand, an algorithm based on step counting has been proposed. The acceleration information is provided by an accelerometer placed on the foot. The aim is to detect the activity that the user is performing together with the estimation of the distance covered. The step counting strategy is based on detecting minima and its corresponding maxima. Although the counting strategy is not innovative (it includes time windows and amplitude thresholds to prevent under or overestimation) no user-specific information is required. The field of pedestrian tracking is crucial due to the lack of a localization standard for this kind of environments. A loosely-coupled centralized Extended Kalman Filter has been proposed to perform the fusion of inertial and position measurements. Zero velocity updates have been applied whenever the foot is detected to be placed on the ground. The results have been obtained in indoor environments using a triangulation algorithm based on RSS measurements and GPS outdoors. Finally, some applications have been designed to test the usefulness of the work. The first one is called the ‘Activity Monitor’ whose aim is to prevent sedentary behaviours and to modify habits to achieve desired objectives of activity level. Two different versions of the application have been implemented. The first one uses the activity estimation based on the step counting algorithm, which has been integrated in an OSGi mobile framework acquiring the data from a Bluetooth accelerometer placed on the foot of the individual. The second one uses activity classifiers embedded in an Android smartphone. On the other hand, the design of a ‘Travel Logbook’ has been planned. The input of this application is the information provided by the activity and localization modules, external databases (e.g. pictures, points of interest, weather) and mobile embedded and virtual sensors (agenda, camera, etc.). The aim is to detect important events in the journey and gather the information necessary to store it as a journal page.

Computer aided process planning (CAPP) for flat rolling of copper alloys

The manufacture of copper alloy flat rolled metals involves hot and cold rolling operations, together with annealing and other secondary processes, to transform castings (mainly slabs and cakes) into such shapes as strip, plate, sheet, etc. Production is mainly to customer orders in a wide range of specifications for dimensions and properties. However, order quantities are often small and so process planning plays an important role in this industry. Much research work has been done in the past in relation to the technology of flat rolling and the details of the operations, however, there is little or no evidence of any research in the planning of processes for this type of manufacture. Practical observation in a number of rolling mills has established the type of manual process planning traditionally used in this industry. This manual approach, however, has inherent drawbacks, being particularly dependent on the individual planners who gain their knowledge over a long span of practical experience. The introduction of the retrieval CAPP approach to this industry was a first step to reduce these problems. But this could not provide a long-term answer because of the need for an experienced planner to supervise generation of any plan. It also fails to take account of the dynamic nature of the parameters involved in the planning, such as the availability of resources, operation conditions and variations in the costs. The other alternative is the use of a generative approach to planning in the rolling mill context. In this thesis, generative methods are developed for the selection of optimal routes for single orders and then for batches of orders, bearing in mind equipment restrictions, production costs and material yield. The batch order process planning involves the use of a special cluster analysis algorithm for optimal grouping of the orders. This research concentrates on cold-rolling operations. A prototype model of the proposed CAPP system, including both single order and batch order planning options, has been developed and tested on real order data in the industry. The results were satisfactory and compared very favourably with the existing manual and retrieval methods.

Analysis of slip distribution of large earthquakes oriented to tsunamigenesis characterisation

The present thesis focuses on the on-fault slip distribution of large earthquakes in the framework of tsunami hazard assessment and tsunami warning improvement. It is widely known that ruptures on seismic faults are strongly heterogeneous. In the case of tsunamigenic earthquakes, the slip heterogeneity strongly influences the spatial distribution of the largest tsunami effects along the nearest coastlines. Unfortunately, after an earthquake occurs, the so-called finite-fault models (FFM) describing the coseismic on-fault slip pattern becomes available over time scales that are incompatible with early tsunami warning purposes, especially in the near field. Our work aims to characterize the slip heterogeneity in a fast, but still suitable way. Using finite-fault models to build a starting dataset of seismic events, the characteristics of the fault planes are studied with respect to the magnitude. The patterns of the slip distribution on the rupture plane, analysed with a cluster identification algorithm, reveal a preferential single-asperity representation that can be approximated by a two-dimensional Gaussian slip distribution (2D GD). The goodness of the 2D GD model is compared to other distributions used in literature and its ability to represent the slip heterogeneity in the form of the main asperity is proven. The magnitude dependence of the 2D GD parameters is investigated and turns out to be of primary importance from an early warning perspective. The Gaussian model is applied to the 16 September 2015 Illapel, Chile, earthquake and used to compute early tsunami predictions that are satisfactorily compared with the available observations. The fast computation of the 2D GD and its suitability in representing the slip complexity of the seismic source make it a useful tool for the tsunami early warning assessments, especially for what concerns the near field.

Bayesian Linear Regression for estimation of the Fractal Dimension of the Cerebral Cortex

The cerebral cortex presents self-similarity in a proper interval of spatial scales, a property typical of natural objects exhibiting fractal geometry. Its complexity therefore can be characterized by the value of its fractal dimension (FD). In the computation of this metric, it has usually been employed a frequentist approach to probability, with point estimator methods yielding only the optimal values of the FD. In our study, we aimed at retrieving a more complete evaluation of the FD by utilizing a Bayesian model for the linear regression analysis of the box-counting algorithm. We used T1-weighted MRI data of 86 healthy subjects (age 44.2 ± 17.1 years, mean ± standard deviation, 48% males) in order to gain insights into the confidence of our measure and investigate the relationship between mean Bayesian FD and age. Our approach yielded a stronger and significant (P < .001) correlation between mean Bayesian FD and age as compared to the previous implementation. Thus, our results make us suppose that the Bayesian FD is a more truthful estimation for the fractal dimension of the cerebral cortex compared to the frequentist FD.

A robust algorithm for segmenting fluorescence images and its application to single-molecule counting

La microscopie par fluorescence de cellules vivantes produit de grandes quantités de données. Ces données sont composées d’une grande diversité au niveau de la forme des objets d’intérêts et possèdent un ratio signaux/bruit très bas. Pour concevoir un pipeline d’algorithmes efficaces en traitement d’image de microscopie par fluorescence, il est important d’avoir une segmentation robuste et fiable étant donné que celle-ci constitue l’étape initiale du traitement d’image. Dans ce mémoire, je présente MinSeg, un algorithme de segmentation d’image de microscopie par fluorescence qui fait peu d’assomptions sur l’image et utilise des propriétés statistiques pour distinguer le signal par rapport au bruit. MinSeg ne fait pas d’assomption sur la taille ou la forme des objets contenus dans l’image. Par ce fait, il est donc applicable sur une grande variété d’images. Je présente aussi une suite d’algorithmes pour la quantification de petits complexes dans des expériences de microscopie par fluorescence de molécules simples utilisant l’algorithme de segmentation MinSeg. Cette suite d’algorithmes a été utilisée pour la quantification d’une protéine nommée CENP-A qui est une variante de l’histone H3. Par cette technique, nous avons trouvé que CENP-A est principalement présente sous forme de dimère.

A cluster-based implementation of a fault-tolerant parallel reduction algorithm using swarm-array computing

Recent research in multi-agent systems incorporate fault tolerance concepts. However, the research does not explore the extension and implementation of such ideas for large scale parallel computing systems. The work reported in this paper investigates a swarm array computing approach, namely ‘Intelligent Agents’. In the approach considered a task to be executed on a parallel computing system is decomposed to sub-tasks and mapped onto agents that traverse an abstracted hardware layer. The agents intercommunicate across processors to share information during the event of a predicted core/processor failure and for successfully completing the task. The agents hence contribute towards fault tolerance and towards building reliable systems. The feasibility of the approach is validated by simulations on an FPGA using a multi-agent simulator and implementation of a parallel reduction algorithm on a computer cluster using the Message Passing Interface.