The existence of new technologies, implemented in efficient platforms and workflows has made massive genotyping available to all fields of biology and medicine. Genetic analyses are no longer dominated by experimental work in laboratories, but rather the interpretation of the resulting data. When billions of data points representing thousands of individuals are available, efficient computational tools are required. The focus of this thesis is on developing models, methods and implementations for such tools. The first theme of the thesis is multi-dimensional scans for quantitative trait loci (QTL) in experimental crosses. By mating individuals from different lines, it is possible to gather data that can be used to pinpoint the genetic variation that influences specific traits to specific genome loci. However, it is natural to expect multiple genes influencing a single trait to interact. The thesis discusses model structure and model selection, giving new insight regarding under what conditions orthogonal models can be devised. The thesis also presents a new optimization method for efficiently and accurately locating QTL, and performing the permuted data searches needed for significance testing. This method has been implemented in a software package that can seamlessly perform the searches on grid computing infrastructures. The other theme in the thesis is the development of adapted optimization schemes for using hidden Markov models in tracing allele inheritance pathways, and specifically inferring haplotypes. The advances presented form the basis for more accurate and non-biased line origin probabilities in experimental crosses, especially multi-generational ones. We show that the new tools are able to reconstruct haplotypes and even genotypes in founder individuals and offspring alike, based on only unordered offspring genotypes. The tools can also handle larger populations than competing methods, resolving inheritance pathways and phase in much larger and more complex populations. Finally, the methods presented are also applicable to datasets where individual relationships are not known, which is frequently the case in human genetics studies. One immediate application for this would be improved accuracy for imputation of SNP markers within genome-wide association studies (GWAS). / eSSENCE

Detecting human actions using a camera has many possible applications in the security industry. When a human performs an action, his/her body goes through a signature sequence of poses. To detect these pose changes and hence the activities performed, a pattern recogniser needs to be built into the video system. Due to the temporal nature of the patterns, Hidden Markov Models (HMM), used extensively in speech recognition, were investigated. Initially a gesture recognition system was built using novel features. These features were obtained by approximating the contour of the foreground object with a polygon and extracting the polygon's vertices. A Gaussian Mixture Model (GMM) was fit to the vertices obtained from a few frames and the parameters of the GMM itself were used as features for the HMM. A more practical activity detection system using a more sophisticated foreground segmentation algorithm immune to varying lighting conditions and permanent changes to the foreground was then built. The foreground segmentation algorithm models each of the pixel values using clusters and continually uses incoming pixels to update the cluster parameters. Cast shadows were identified and removed by assuming that shadow regions were less likely to produce strong edges in the image than real objects and that this likelihood further decreases after colour segmentation. Colour segmentation itself was performed by clustering together pixel values in the feature space using a gradient ascent algorithm called mean shift. More robust features in the form of mesh features were also obtained by dividing the bounding box of the binarised object into grid elements and calculating the ratio of foreground to background pixels in each of the grid elements. These features were vector quantized to reduce their dimensionality and the resulting symbols presented as features to the HMM to achieve a recognition rate of 62% for an event involving a person writing on a white board. The recognition rate increased to 80% for the &quotseen" person sequences, i.e. the sequences of the person used to train the models. With a fixed lighting position, the lack of a shadow removal subsystem improved the detection rate. This is because of the consistent profile of the shadows in both the training and testing sequences due to the fixed lighting positions. Even with a lower recognition rate, the shadow removal subsystem was considered an indispensable part of a practical, generic surveillance system.

Thesis (M.Eng.(Computer Engineering))--University of Pretoria, 2008. / Summaries in Afrikaans and English. Includes bibliographical references (leaves 77-83).

O desafio de encontrar corretamente genes eucarioticos codificadores de proteinas nas sequencias genomicas e um problema em aberto. Neste trabalho, implementamos uma plata- forma, com o objetivo de melhorar a forma com que preditores de genes sao implementados e avaliados. Tres novas ferramentas foram implementadas: ToPS (Toolkit of Probabilistic Models of Sequences) foi o primeiro arcabouco orientado a objetos que fornece ferramentas para implementacao, manipulacao, e combinacao de modelos probabilisticos para representar sequencias de simbolos; MYOP (Make Your Own Predictor) e um sistema que tem como objetivo facilitar a construcao de preditores de genes; e SGEval utiliza grafos de splicing para comparar diferente anotacoes com eventos de splicing alternativos. Utilizamos nossas ferramentas para o desenvolvimentos de preditores de genes em onze genomas distintos: A. thaliana, C. elegans, Z. mays, P. falciparum, D. melanogaster, D. rerio, M. musculus, R. norvegicus, O. sativa, G. max e H. sapiens. Com esse desenvolvimento, estabelecemos um protocolo para implementacao de novos preditores. Alem disso, utilizando a nossa plata- forma, desenvolvemos um fluxo de trabalho para predicao de genes no projeto do genoma da cana de acucar, que ja foi utilizado em 109 sequencias de BAC geradas pelo BIOEN (FAPESP Bioenergy Program). / The challenge of correctly identify eukaryotic protein-coding genes in the genomic se- quences is an open problem. In this work, we implemented a plataform with the aim of improving the way that gene predictors are implemented and evaluated. ToPS (Toolkit of Probabilistic Models of Sequence) was the first object-oriented framework that provides tools for implementation, manipulation, and combination of probabilistic models that represent sequences of symbols. MYOP (Make Your Own Predictor) facilitates the construction of gene predictors. SGEval (Splicing Graph Evaluation) uses splicing graphs to compare dif- ferent annotations with alternative splicing events. We used our plataform to develop gene finders in eleven distinct genomes: A. thaliana, C. elegans, Z. mays, P. falciparum, D. me- lanogaster, D. rerio, M. musculus, R. norvegicus, O. sativa, G. max e H. sapiens. With this development, we established a protocol for implementing new gene predictors. In addi- tion, using our platform, we developed a pipeline to find genes in the 109 sugarcane BAC sequences produced by BIOEN (FAPESP Bioenergy Program).

Les travaux de recherche développés dans cette thèse concernent la mise en oeuvre d'un système de vidéo surveillance intelligente en milieu hospitalier. Dans le contexte d'une application en unité de soins intensifs médicale, nous introduisons la notion originale de Boite Noire Médicale et nous proposons un nouveau système de monitoring visuel de Détection Automatique de Situations à risque et d'Alerte (DASA) basé sur un système de vidéosurveillance multi-caméra intelligent. L'objectif étant d'interpréter les flux d'informations visuelles et de détecter en temps réel les situations à risque afin de prévenir l'équipe médicale et ensuite archiver les évènements dans une base de donnée vidéo qui représente la Boite Noire Médicale. Le système d'interprétation est basé sur des algorithmes de reconnaissance de scénarios qui exploitent les Modèles de Markovs Cachés (MMCs). Une extension du modèle MMC standard est proposé afin de gérer la structure hiérarchique interne des scénarios et de contrôler la durée de chaque état du modèle markovien. La contribution majeure de ce travail repose sur l'intégration d'un raisonnement de type évènementiel, pour gérer la décision de reconnaissance en tenant compte des imperfections des informations disponibles. Les techniques de reconnaissance de scénarios proposées ont été testées et évaluées sur une base de séquences vidéo médicales et comparés aux modèles de Markov cachés probabilistiques classiques. / This thesis focuses on the study and the implementation of an intelligent visual monitoring system in hospitals. In the context of an application for patient monitoring in mediacal intensive care unit, we introduce an original concept of the Medical Black Box and we propose a new system for visual monitoring of Automatic Detection of risk Situations and Alert (DASA) based on a CCTV system with network smart camera. The aim is to interpret the visual information flow and to detect at real-time risk situations to prevent the mediacl team and then archive the events in a video that is based Medical Black Box data. The interpretation system is based on scenario recognition algorithms that exploit the Hidden Markov Models (HMM). An extension of the classic model of HMM is proposed to handle the internal reporting structure of the scenarios and to control the duration of each state of the Markov model. The main contribution of this work relies on the integration of an evidential reasoning, in order to manage the recognition decision taking into account the imperfections of available information. The proposed scenarios recognition method have been tested and assessed on database of medical video sequences and compared to standard probabilistic Hidden Markov Models.

Orientador: Aparecido Nilceu Marana / Banca: Hélio Pedrini / Banca: Aledir Silveira Pereira / Resumo: As técnicas para identificação biométrica têm evoluído cada vez mais devido à necessidade que os seres humanos têm de identificar as pessoas em tempo real e de forma precisa para permitir o acesso a determinados recursos, como por exemplo, as aplicações e serviços WEB. O reconhecimento facial é uma técnica biométrica que apresenta várias vantagens em relação às demais, tais como: uso de equipamentos simples e baratos para a obtenção das amostras e a possibilidade de se realizar o reconhecimento em sigilo e à distância. O reconhecimento de faces a partir de vídeo é uma tendência recente na área de Biometria. Esta dissertação tem por objetivo principal comparar diferentes técnicas de reconhecimento facial a partir de vídeo para determinar as que apresentam um melhor compromisso entre tempo de processamento e precisão. Outro objetivo é a incorporação dessas melhores técnicas no sistema de autenticação biométrica em ambientes de E-Learning, proposto em um trabalho anterior. Foi comparado o classificador vizinho mais próximo usando as medidas de distância Euclidiana e Mahalanobis com os seguintes classificadores: Redes Neurais MLP e SOM, K Vizinhos mais Próximos, Classificador Bayesiano, Máquinas de Vetores de Suporte (SVM) e Floresta de Caminhos Ótimos (OPF). Também foi avaliada a técnica de Modelos Ocultos de Markov (HMM). Nos experimentos realizados com a base Recogna Video Database, criada especialmente para uso neste trabalho, e Honda/UCSD Video Database, os classificadores apresentaram os melhores resultados em termos de precisão, com destaque para o classificador SVM da biblioteca SVM Torch. A técnica HMM, que incorpora informações temporais, apresentou resultados melhores do que as funções de distância, em termos de precisão, mas inferiores aos classificadores / Abstract: The biometric identification techniques have evolved increasingly due to the need that humans have to identify people in real time to allow access to certain resources, such as applications and Web services. Facial recognition is a biometric technique that has several advantages over others. Some of these advantages are the use of simple and cheap equipment to obtain the samples and the ability to perform the recognition in covert mode. The face recognition from video is a recent approach in the area of Biometrics. The work in this dissertation aims at comparing different techniques for face recognition from video in order to find the best rates on processing time and accuracy. Another goal is the incorporation of these techniques in the biometric authentication system for E-Learning environments, proposed in an earlier work. We have compared the nearest neighbor classifier using the Euclidean and Mahalanobis distance measures with some other classifiers, such as neural networks (MLP and SOM), k-nearest neighbor, Bayesian classifier, Support Vector Machines (SVM), and Optimum Path Forest (OPF). We have also evaluated the Hidden Markov Model (HMM) approach, as a way of using the temporal information. In the experiments with Recogna Video Database, created especially for this study, and Honda/UCSD Video Database, the classifiers obtained the best accuracy, especially the SVM classifier from the SVM Torch library. HMM, which takes into account temporal information, presented better performance than the distance metrics, but worse than the classifiers / Mestre

Single molecule experiments study the kinetics of molecular biological systems. Many such studies generate data that can be described by aggregated hidden Markov models, whereby there is a need of doing inference on such data and models. In this study, model selection in aggregated Hidden Markov models was performed with a criterion of maximum Bayesian evidence. Variational Bayes inference was seen to underestimate the evidence for aggregated model fits. Estimation of the evidence integral by brute force Monte Carlo integration theoretically always converges to the correct value, but it converges in far from tractable time. Nested sampling is a promising method for solving this problem by doing faster Monte Carlo integration, but it was here seen to have difficulties generating uncorrelated samples.

Current Ambient Intelligence and Intelligent Environment research focuses on the interpretation of a subject’s behaviour at the activity level by logging the Activity of Daily Living (ADL) such as eating, cooking, etc. In general, the sensors employed (e.g. PIR sensors, contact sensors) provide low resolution information. Meanwhile, the expansion of ubiquitous computing allows researchers to gather additional information from different types of sensor which is possible to improve activity analysis. Based on the previous research about sitting posture detection, this research attempts to further analyses human sitting activity. The aim of this research is to use non-intrusive low cost pressure sensor embedded chair system to recognize a subject’s activity by using their detected postures. There are three steps for this research, the first step is to find a hardware solution for low cost sitting posture detection, second step is to find a suitable strategy of sitting posture detection and the last step is to correlate the time-ordered sitting posture sequences with sitting activity. The author initiated a prototype type of sensing system called IntelliChair for sitting posture detection. Two experiments are proceeded in order to determine the hardware architecture of IntelliChair system. The prototype looks at the sensor selection and integration of various sensor and indicates the best for a low cost, non-intrusive system. Subsequently, this research implements signal process theory to explore the frequency feature of sitting posture, for the purpose of determining a suitable sampling rate for IntelliChair system. For second and third step, ten subjects are recruited for the sitting posture data and sitting activity data collection. The former dataset is collected byasking subjects to perform certain pre-defined sitting postures on IntelliChair and it is used for posture recognition experiment. The latter dataset is collected by asking the subjects to perform their normal sitting activity routine on IntelliChair for four hours, and the dataset is used for activity modelling and recognition experiment. For the posture recognition experiment, two Support Vector Machine (SVM) based classifiers are trained (one for spine postures and the other one for leg postures), and their performance evaluated. Hidden Markov Model is utilized for sitting activity modelling and recognition in order to establish the selected sitting activities from sitting posture sequences.2. After experimenting with possible sensors, Force Sensing Resistor (FSR) is selected as the pressure sensing unit for IntelliChair. Eight FSRs are mounted on the seat and back of a chair to gather haptic (i.e., touch-based) posture information. Furthermore, the research explores the possibility of using alternative non-intrusive sensing technology (i.e. vision based Kinect Sensor from Microsoft) and find out the Kinect sensor is not reliable for sitting posture detection due to the joint drifting problem. A suitable sampling rate for IntelliChair is determined according to the experiment result which is 6 Hz. The posture classification performance shows that the SVM based classifier is robust to “familiar” subject data (accuracy is 99.8% with spine postures and 99.9% with leg postures). When dealing with “unfamiliar” subject data, the accuracy is 80.7% for spine posture classification and 42.3% for leg posture classification. The result of activity recognition achieves 41.27% accuracy among four selected activities (i.e. relax, play game, working with PC and watching video). The result of this thesis shows that different individual body characteristics and sitting habits influence both sitting posture and sitting activity recognition. In this case, it suggests that IntelliChair is suitable for individual usage but a training stage is required.

Magister Scientiae - MSc / Research has shown that five fundamental parameters are required to recognize any sign language gesture: hand shape, hand motion, hand location, hand orientation and facial expressions. The South African Sign Language (SASL) research group at the University of the Western Cape (UWC) has created several systems to recognize sign language gestures using single parameters. These systems are, however, limited to a vocabulary size of 20 – 23 signs, beyond which the recognition accuracy is expected to decrease. The first aim of this research is to investigate the use of two parameters – hand motion and hand shape – to recognise a larger vocabulary of SASL gestures at a high accuracy. Also, the majority of related work in the field of sign language gesture recognition using these two parameters makes use of Hidden Markov Models (HMMs) to classify gestures. Hidden Markov Support Vector Machines (HM-SVMs) are a relatively new technique that make use of Support Vector Machines (SVMs) to simulate the functions of HMMs. Research indicates that HM-SVMs may perform better than HMMs in some applications. To our knowledge, they have not been applied to the field of sign language gesture recognition. This research compares the use of these two techniques in the context of SASL gesture recognition. The results indicate that, using two parameters results in a 15% increase in accuracy over the use of a single parameter. Also, it is shown that HM-SVMs are a more accurate technique than HMMs, generally performing better or at least as good as HMMs.

Philosophiae Doctor - PhD / In this thesis, we explore dynamic signature verification systems. Unlike other signature models, we use genuine signatures in this project as they are more appropriate in real world applications. Signature verification systems are typical examples of biometric devices that use physical and behavioral characteristics to verify that a person really is who he or she claims to be. Other popular biometric examples include fingerprint scanners and hand geometry devices. Hand written signatures have been used for some time to endorse financial transactions and legal contracts although little or no verification of signatures is done. This sets it apart from the other biometrics as it is well accepted method of authentication. Until more recently, only hidden Markov models were used for model construction. Ongoing research on signature verification has revealed that more accurate results can be achieved by combining results of multiple models. We also proposed to use combinations of multiple single variate models instead of single multi variate models which are currently being adapted by many systems. Apart from these, the proposed system is an attractive way for making financial transactions more secure and authenticate electronic documents as it can be easily integrated into existing transaction procedures and electronic communications