Taxonomic classification has always been important to the study of any biological system. Many biological species will go unclassified and become lost forever at the current rate of classification. The current state of computer technology makes image storage and retrieval possible on a global level. As a result, computer-aided taxonomy is now possible. Content based image retrieval techniques utilize visual features of the image for classification. By utilizing image content and computer technology, the gap between taxonomic classification and species destruction is shrinking. This content based study utilizes the Fourier Descriptors of fifteen known landmark features on three Carpiodes species: C.carpio, C.velifer, and C.cyprinus. Classification analysis involves both unsupervised and supervised machine learning algorithms. Fourier Descriptors of the fifteen known landmarks provide for strong classification power on image data. Feature reduction analysis indicates feature reduction is possible. This proves useful for increasing generalization power of classification.

Abstract Cluster analysis has become one of the main tools used in extracting knowledge from data, which is known as data mining. In this area of data analysis, data of large dimensions are often processed, both in the number of objects and in the number of variables, which characterize the objects. Many methods for data clustering have been developed. One of the most widely used is a k-means method, which is suitable for clustering data sets containing large number of objects. It is based on finding the best clustering in relation to the initial distribution of objects into clusters and subsequent step-by-step redistribution of objects belonging to the clusters by the optimization function. The aim of this Ph.D. thesis was a comparison of selected variants of existing k-means methods, detailed characterization of their positive and negative characte- ristics, new alternatives of this method and experimental comparisons with existing approaches. These objectives were met. I focused on modifications of the k-means method for clustering of large number of objects in my work, specifically on the algorithms BIRCH k-means, filtering, k-means++ and two-phases. I watched the time complexity of algorithms, the effect of initialization distribution and outliers, the validity of the resulting clusters. Two real data files and some generated data sets were used. The common and different features of method, which are under investigation, are summarized at the end of the work. The main aim and benefit of the work is to devise my modifications, solving the bottlenecks of the basic procedure and of the existing variants, their programming and verification. Some modifications brought accelerate the processing. The application of the main ideas of algorithm k-means++ brought to other variants of k-means method better results of clustering. The most significant of the proposed changes is a modification of the filtering algorithm, which brings an entirely new feature of the algorithm, which is the detection of outliers. The accompanying CD is enclosed. It includes the source code of programs written in MATLAB development environment. Programs were created specifically for the purpose of this work and are intended for experimental use. The CD also contains the data files used for various experiments.

O comportamento individual relativo a viagens sofre a influência de fatores individuais e do meio urbano. Assim, a vizinhança seria uma das variáveis a serem consideradas na análise comportamental relacionada aos deslocamentos. O objetivo principal deste trabalho é analisar a influência da vizinhança no comportamento individual relativo a viagens, através de dados em painel. Dados em painel constituem importante ferramenta em análises comportamentais subjacentes a viagens urbanas, uma vez que propiciam maior quantidade de informações quando comparados aos dados seccionais. Padrões de viagens são mais bem evidenciados, através de dados em painel, caracterizando as habituais rotinas de atividades e viagens, além de melhor identificar comportamentos atípicos. Todavia, a obtenção desses dados comumente não é atividade trivial, demandando recursos monetários e de tempo. Um dos objetivos secundários deste trabalho é apresentar uma maneira prática e pouco onerosa de obtenção de dados em painel através de Smartphones. Tais dados, posteriormente, são aplicados à classificação de indivíduos segundo comportamento relacionado às viagens. A potencialidade da proposta sugerida é validada por meio de um estudo de caso relativo aos estudantes universitários do município de São Carlos - SP, Brasil. Através dos dados em painel, fornecidos pelos estudantes, utilizou-se o algoritmo k-médias considerando quatro variáveis relativas aos deslocamentos. As três categorias obtidas apresentam estrutura espacial e, portanto, possibilitam análises espaciais exploratórias e confirmatórias, almejando a compreensão de influências da vizinhança nas dinâmicas cotidianas. Este trabalho atesta a existência de autocorrelação espacial do conjunto de dados por meio de dois indicadores: Moran e SivarG (Global Spatial Indicator Based on Variogram). A corroboração da dependência espacial, apontada pelos indicadores globais, é confirmada por meio de dois modelos de escolha discreta. Um contendo apenas variáveis originais da base de dados. Outro, análogo ao primeiro, porém adicionado de covariáveis regionais, obtidas por preceitos da geoestatística. A incorporação das covariáveis regionais aumenta a precisão do modelo e promove um incremento das taxas de acertos em validações cruzadas. / Individual travel behaviour is influenced by individual factors and the urban environment. Thus, the neighborhood influence would be one of the variables to be considered in travel behavior analysis related to urban displacements. The main objective of this work is to analyze the influence of neighborhood on travel behavior by panel data. Panel data is an important tool in urban travel behavioral analyzes, since they provide a greater amount of information when compared to sectional data. Travel patterns are more evident through panel data, characterizing the usual routines of activities, as well the atypical behaviors. However, obtaining these data is not a simple task, requiring monetary and time resources. Secondary goals of this work aim to present a practical and inexpensive way to obtain panel data through Smartphones. These data are then applied to the classification of individuals according to travel behavior. The potential of the proposal is validated by a case of study concerning undergraduate and PhD students from São Carlos - SP, Brazil. Using the data provided by the students, a k-means algorithm was used considering four variables regarding displacements. These three categories have spatial structure and allow exploratory and confirmatory spatial data analyzes aiming the comprehension of the nearby influence of data at daily dynamics. This work attests to the existence of spatial autocorrelation of the data set by two indicators: Moran and SivarG (Global Spatial Indicator Based on Variogram). Corroboration of spatial dependence, pointed by the global indicators, is confirmed by two discrete choice models. The first one includes just the original database variables. The second one, analogous to the first, but added of regional covariates obtained by geostatistical concepts. The addition of regional variables leads to a more accurate model, increasing cross-validations hit rates.

O comportamento individual relativo a viagens sofre a influência de fatores individuais e do meio urbano. Assim, a vizinhança seria uma das variáveis a serem consideradas na análise comportamental relacionada aos deslocamentos. O objetivo principal deste trabalho é analisar a influência da vizinhança no comportamento individual relativo a viagens, através de dados em painel. Dados em painel constituem importante ferramenta em análises comportamentais subjacentes a viagens urbanas, uma vez que propiciam maior quantidade de informações quando comparados aos dados seccionais. Padrões de viagens são mais bem evidenciados, através de dados em painel, caracterizando as habituais rotinas de atividades e viagens, além de melhor identificar comportamentos atípicos. Todavia, a obtenção desses dados comumente não é atividade trivial, demandando recursos monetários e de tempo. Um dos objetivos secundários deste trabalho é apresentar uma maneira prática e pouco onerosa de obtenção de dados em painel através de Smartphones. Tais dados, posteriormente, são aplicados à classificação de indivíduos segundo comportamento relacionado às viagens. A potencialidade da proposta sugerida é validada por meio de um estudo de caso relativo aos estudantes universitários do município de São Carlos - SP, Brasil. Através dos dados em painel, fornecidos pelos estudantes, utilizou-se o algoritmo k-médias considerando quatro variáveis relativas aos deslocamentos. As três categorias obtidas apresentam estrutura espacial e, portanto, possibilitam análises espaciais exploratórias e confirmatórias, almejando a compreensão de influências da vizinhança nas dinâmicas cotidianas. Este trabalho atesta a existência de autocorrelação espacial do conjunto de dados por meio de dois indicadores: Moran e SivarG (Global Spatial Indicator Based on Variogram). A corroboração da dependência espacial, apontada pelos indicadores globais, é confirmada por meio de dois modelos de escolha discreta. Um contendo apenas variáveis originais da base de dados. Outro, análogo ao primeiro, porém adicionado de covariáveis regionais, obtidas por preceitos da geoestatística. A incorporação das covariáveis regionais aumenta a precisão do modelo e promove um incremento das taxas de acertos em validações cruzadas. / Individual travel behaviour is influenced by individual factors and the urban environment. Thus, the neighborhood influence would be one of the variables to be considered in travel behavior analysis related to urban displacements. The main objective of this work is to analyze the influence of neighborhood on travel behavior by panel data. Panel data is an important tool in urban travel behavioral analyzes, since they provide a greater amount of information when compared to sectional data. Travel patterns are more evident through panel data, characterizing the usual routines of activities, as well the atypical behaviors. However, obtaining these data is not a simple task, requiring monetary and time resources. Secondary goals of this work aim to present a practical and inexpensive way to obtain panel data through Smartphones. These data are then applied to the classification of individuals according to travel behavior. The potential of the proposal is validated by a case of study concerning undergraduate and PhD students from São Carlos - SP, Brazil. Using the data provided by the students, a k-means algorithm was used considering four variables regarding displacements. These three categories have spatial structure and allow exploratory and confirmatory spatial data analyzes aiming the comprehension of the nearby influence of data at daily dynamics. This work attests to the existence of spatial autocorrelation of the data set by two indicators: Moran and SivarG (Global Spatial Indicator Based on Variogram). Corroboration of spatial dependence, pointed by the global indicators, is confirmed by two discrete choice models. The first one includes just the original database variables. The second one, analogous to the first, but added of regional covariates obtained by geostatistical concepts. The addition of regional variables leads to a more accurate model, increasing cross-validations hit rates.

<p>The Swedish National Debt Office (SNDO) is the Swedish Government’s financial administration. It has several tasks and the main one is to manage the central government’s debt in a way that minimizes the cost with due regard to risk. The debt management problem is to choose currency composition and maturity profile - a problem made difficult because of the many stochastic factors involved. </p><p>The SNDO has created a simulation model to quantitatively analyze different aspects of this problem by evaluating a set of static strategies in a great number of simulated futures. This approach has a number of drawbacks, which might be handled by using a financial optimization approach based on Stochastic Programming. </p><p>The objective of this master’s thesis is thus to apply financial optimization on the Swedish government’s strategic debt management problem, using the SNDO’s simulation model to generate scenarios, and to evaluate this approach against a set of static strategies in fictitious future macroeconomic developments. </p><p>In this report we describe how the SNDO’s simulation model is used along with a clustering algorithm to form future scenarios, which are then used by an optimization model to find an optimal decision regarding the debt management problem. </p><p>Results of the evaluations show that our optimization approach is expected to have a lower average annual real cost, but with somewhat higher risk, than a set of static comparison strategies in a simulated future. These evaluation results are based on a risk preference set by ourselves, since the government has not expressed its risk preference quantitatively. We also conclude that financial optimization is applicable on the government debt management problem, although some work remains before the method can be incorporated into the strategic work of the SNDO.</p>

De nouvelles architectures de traction (hybride, électrique) entrent en concurrence avec les motorisations thermiques conventionnelles. Des batteries Lithium-ion équipent ces véhicules innovants. La durabilité de ces batteries constitue un enjeu majeur mais dépend de nombreux paramètres environ-nementaux externes. Les outils de prédiction de durée de vie actuellement utilisés sont souvent trop simplificateurs dans leur approche. L'objet de ces travaux consiste à caractériser les conditions d'usage de ces batteries (température, tension, courant, SOC et DOD) afin d'étudier avec précision la durée de vie que l'on peut en attendre en fonction de l'application visée. Différents types de véhicules électrifiés (vélos à assistance élec-trique, voitures électriques, voitures hybrides, et trolleybus) ont été instrumentés afin de documenter les conditions d'usage réel des batteries. De larges volumes de données ont été recueillis puis ana-lysés au moyen d'une méthode innovante qui s'appuie sur la classification d'impulsions de courant par l'algorithme des K-means et la génération de cycles synthétiques par modélisation par chaine de Markov. Les cycles synthétiques ainsi obtenus présentent des caractéristiques très proches de l'échantillon complet de données récoltées et permettent donc de représenter fidèlement l'usage réel. Utilisés lors de campagnes de vieillissement de batteries, ils sont susceptibles de permettre l'obtention d'une juste prédiction de la durée de vie des batteries pour l'application considérée. Plusieurs résultats expérimentaux sont présentés afin d'étayer la pertinence de cette approche.

The Swedish National Debt Office (SNDO) is the Swedish Government’s financial administration. It has several tasks and the main one is to manage the central government’s debt in a way that minimizes the cost with due regard to risk. The debt management problem is to choose currency composition and maturity profile - a problem made difficult because of the many stochastic factors involved. The SNDO has created a simulation model to quantitatively analyze different aspects of this problem by evaluating a set of static strategies in a great number of simulated futures. This approach has a number of drawbacks, which might be handled by using a financial optimization approach based on Stochastic Programming. The objective of this master’s thesis is thus to apply financial optimization on the Swedish government’s strategic debt management problem, using the SNDO’s simulation model to generate scenarios, and to evaluate this approach against a set of static strategies in fictitious future macroeconomic developments. In this report we describe how the SNDO’s simulation model is used along with a clustering algorithm to form future scenarios, which are then used by an optimization model to find an optimal decision regarding the debt management problem. Results of the evaluations show that our optimization approach is expected to have a lower average annual real cost, but with somewhat higher risk, than a set of static comparison strategies in a simulated future. These evaluation results are based on a risk preference set by ourselves, since the government has not expressed its risk preference quantitatively. We also conclude that financial optimization is applicable on the government debt management problem, although some work remains before the method can be incorporated into the strategic work of the SNDO.

Mathematical models of signal transduction pathways are characterized by a large number of proteins and uncertain parameters, yet only a limited amount of quantitative data is available. The dissertation addresses this problem using two different approaches: the first approach deals with a model simplification procedure for signaling pathways that reduces the model size but retains the physical interpretation of the remaining states, while the second approach deals with creating rich data sets by computing transcription factor profiles from fluorescent images of green-fluorescent-protein (GFP) reporter cells. For the first approach a model simplification procedure for signaling pathway models is presented. The technique makes use of sensitivity and observability analysis to select the retained proteins for the simplified model. The presented technique is applied to an IL-6 signaling pathway model. It is found that the model size can be significantly reduced and the simplified model is able to adequately predict the dynamics of key proteins of the signaling pathway. An approach for quantitatively determining transcription factor profiles from GFP reporter data is developed as the second major contribution of this work. The procedure analyzes fluorescent images to determine fluorescence intensity profiles using principal component analysis and K-means clustering, and then computes the transcription factor concentration from the fluorescence intensity profiles by solving an inverse problem involving a model describing transcription, translation, and activation of green fluorescent proteins. Activation profiles of the transcription factors NF-κB, nuclear STAT3, and C/EBPβ are obtained using the presented approach. The data for NF-κB is used to develop a model for TNF-α signal transduction while the data for nuclear STAT3 and C/EBPβ is used to verify the simplified IL-6 model. Finally, an approach is developed to compute the distribution of transcription factor profiles among a population of cells. This approach consists of an algorithm for identifying individual fluorescent cells from fluorescent images, and an algorithm to compute the distribution of transcription factor profiles from the fluorescence intensity distribution by solving an inverse problem. The technique is applied to experimental data to derive the distribution of NF-κB concentrations from fluorescent images of a NF-κB GFP reporter system.

Multiple-centered clustering method and decision making system algorithm on menopause data set depending on multiple-centered clustering are described in this study. This method consists of two stages. At the first stage, fuzzy C-means (FCM) clustering algorithm is applied on the data set under consideration with a high number of cluster centers. As the output of FCM, cluster centers and membership function values for each data member is calculated. At the second stage, original cluster centers obtained in the first stage are merged till the new numbers of clusters are reached. Merging process relies upon a &ldquo / similarity measure&rdquo / between clusters defined in the thesis. During the merging process, the cluster center coordinates do not change but the data members in these clusters are merged in a new cluster. As the output of this method, therefore, one obtains clusters which include many cluster centers. In the final part of this study, an application of the clustering algorithms &ndash / including the multiple centered clustering method &ndash / a decision making system is constructed using a special data on menopause treatment. The decisions are based on the clusterings created by the algorithms already discussed in the previous chapters of the thesis. A verification of the decision making system / v decision aid system is done by a team of experts from the Department of Department of Obstetrics and Gynecology of Hacettepe University under the guidance of Prof. Sinan Beksa&ccedil / .

This research is focused on the extraction of visual set patterns in digital images, using relational properties like nearness and similarity measures, as well as descriptive properties such as texture, colour and image gradient directions. The problem considered in this thesis is application of topology in visual set pattern discovery, and consequently pattern generation. A visual set pattern is a collection of motif patterns generated from different unique points called seed motifs in the set. Each motif pattern is a descriptive neighbourhood of a seed motif. Such a neighbourhood is a set of points that are descriptively near a seed motif. A new similarity distance measure based on dot product between image feature vectors was introduced in this research, for image classification with the generated visual set patterns. An application of this approach to pattern generation can be useful in content based image retrieval and image classification.