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HIV/AIDS is widely spread and ranks as the sixth biggest killer all over the world. Moreover, due to the rapid replication rate and the lack of proofreading mechanism of HIV virus, drug resistance is commonly found and is one of the reasons causing the failure of the treatment. Even though the drug resistance tests are provided to the patients and help choose more efficient drugs, such experiments may take up to two weeks to finish and are expensive. Because of the fast development of the computer, drug resistance prediction using machine learning is feasible. In order to accurately predict the HIV drug resistance, two main tasks need to be solved: how to encode the protein structure, extracting the more useful information and feeding it into the machine learning tools; and which kinds of machine learning tools to choose. In our research, we first proposed a new protein encoding algorithm, which could convert various sizes of proteins into a fixed size vector. This algorithm enables feeding the protein structure information to most state of the art machine learning algorithms. In the next step, we also proposed a new classification algorithm based on sparse representation. Following that, mean shift and quantile regression were included to help extract the feature information from the data. Our results show that encoding protein structure using our newly proposed method is very efficient, and has consistently higher accuracy regardless of type of machine learning tools. Furthermore, our new classification algorithm based on sparse representation is the first application of sparse representation performed on biological data, and the result is comparable to other state of the art classification algorithms, for example ANN, SVM and multiple regression. Following that, the mean shift and quantile regression provided us with the potentially most important drug resistant mutants, and such results might help biologists/chemists to determine which mutants are the most representative candidates for further research.

Dans cette thèse, nous cherchons à reconstruire une approximation d'une variété connue seulement à partir d'un nuage de points de grande dimension l'échantillonnant. Nous nous efforçons de trouver des méthodes de reconstructions efficaces et produisant des approximations ayant la même topologie que la variété échantillonnée. Une attention particulière est consacrée aux flag-complexes et particulièrement aux complexes de Rips. Nous montrons que le complexe de Rips capture la topologie d'une variété échantillonnée en supposant de bonnes conditions d'échantillonnage. En tirant avantage de la compacité des flags-complexes qui peuvent être représentés de manière compacte avec un graphe, nous présentons une structure de données appelée squelette/bloqueurs pour complexes simpliciaux. Nous étudions ensuite deux opérations de simplifications, la contraction d'arête et le collapse simplicial, qui s'avèrent utiles pour réduire un complexe simplicial sans en changer sa topologie.

In this thesis, three mesh generation software packages have been developed and implemented. The first two were based on structured mesh generation algorithms and used to solve structured surface and volume mesh generation problems of three-dimensional domains. Structured mesh generation algorithms were based on the concept of isoparametric coordinates. In structured surface mesh generation software, quadrilateral mesh elements were generated for complex three-dimensional surfaces and these elements were then triangulated in order to obtain high-quality triangular mesh elements. Structured volume mesh generation software was used to generate hexahedral mesh elements for volumes. Tetrahedral mesh elements were constructed from hexahedral elements using hexahedral node insertion method. The results, which were produced by the mesh generation algorithms, were converted to a required format in order to be saved in output files. The third software package is an unstructured quality tetrahedral mesh generator and was used to generate exact Delaunay tetrahedralizations, constrained (conforming) Delaunay tetrahedralizations and quality conforming Delaunay tetrahedralizations. Apart from the mesh generation algorithms used and implemented in this thesis, unstructured mesh generation techniques that can be used to generate quadrilateral, triangular, hexahedral and tetrahedral mesh elements were also discussed.

The methods presented in this study are aimed at the identification of subpopulations (clones) of genetically similar cells within tissue samples through measurement of loci-specific Fluorescence in-situ hybridization (FISH) spot signals for each nucleus and analyzing cell spatial distributions by way of Voronoi tessellation and Delaunay triangulation to robustly define cell neighbourhoods. The motivation for the system is to examine lung cancer patient for subpopulations of Non-Small Cell Lung Cancer (NSCLC) cells with biologically meaningful gene copy-number profiles: patterns of genetic alterations statistically associated with resistance to cis-platinum/vinorelbine doublet chemotherapy treatment. Current technologies for gene-copy number profiling rely on large amount of cellular material, which is not always available and suffers from limited sensitivity to only the most dominant clone in often heterogeneous samples. Thus, through the use of FISH, the detection of gene copy-numbers is possible in unprocessed tissues, allowing identification of specific tumour clones with biologically relevant patterns of genetic aberrations. The tissue-wide characterization of multiplexed loci-specific FISH signals, described herein, is achieved through a fully automated, multicolour fluorescence imaging microscope and object segmentation algorithms to identify cell nuclei and FISH spots within. Related tumour clones are identified through analysis of robustly defined cell neighbourhoods and cell-to-cell connections for regions of cells with homogenous and highly interconnected FISH spot signal characteristics. This study presents experiments which demonstrate the system’s ability to accurately quantify FISH spot signals in various tumour tissues and in up to 5 colours simultaneously or more through multiple rounds of FISH staining. Furthermore, the system’s FISH-based cell classification performance is evaluated at a sensitivity of 84% and specificity 81% and clonal identification algorithm results are determined to be comparable to clone delineation by a human-observer. Additionally, guidelines and procedures to perform anticipated, routine analysis experiments are established.

Zugl.: Karlsruhe, Univ., Diss., 2005

Universiẗat, Diss., 2005--Karlsruhe.

Stuttgart, Univ., Diss., 2005.

Μια γρήγορη επίλυση του Delaunay Τριγωνισμός (DT) πρόβληματος αποτελεί ένα από τα βασικά συστατικά σε πολλές θεωριτικές και πρακτικές εφαρμογές. Οι υπάρχουσες μονάδες επεξεργασίας γραφικών (GPU), με βάση τις εφαρμογές των αλγορίθμων DT πάσχουν από δύο σοβαρά μειονεκτήματα. Το πρώτο σχετίζεται με την εξάρτηση του αλγορίθμου καθοδήγηση της GPU από την CPU για τους υπολογισμούς. Το δεύτερο πιο σοβαρό μειονέκτημα είναι η εξάρτησή τους από τη διανομή του σημειοσύνολου εισόδου. Οι περισσότεροι αλγορίθμοι για GPU έχουν καλή απόδοση μόνο με ομοιόμορφες κατανομές σημειοσύνολον. Προτείνουμε ένα καινούριο αλγόριθμο που δεν πάσχουν από τα παραπάνω προβλήματα. / A Fast solver of Delaunay Triangulation (DT) problem constitutes one of the basic ingredients in many practical and sientific applications. Existing Graphics Processing Units (GPU) based implementations of DT algorithms suffer from two serious drawbacks. The first is related to the dependency of the CPU guidance algorithm on GPU calculations. Albeit the modern GPUs have high computational throughput, if the feedback from CPU is necessary for the algorithmic evolution, the overhead caused by CPU-GPU communication can seriously degrade the performance. The second most serious drawback is their dependency on the distribution of the given point-set. Most of the GPU-based implementations can optimally run only on uniformly distributed point-sets, however, in many practical applications this is not the case.

In this thesis, we propose a general computational framework for generating mesh models of single-component (e.g., grayscale) and multi-component (e.g., RGB color) images. This framework builds on ideas from the previously-proposed GPRFSED method for single-component images to produce a framework that can handle images with any arbitrary number of components. The key ideas embodied in our framework are Floyd-Steinberg error diffusion and greedy-point removal. Our framework has several free parameters and the effect of the choices of these parameters is studied. Based on experimentation, we recommend two specific sets of parameter choices, yielding two highly effective single/multi-component mesh-generation methods, known as MED and MGPRFS. These two methods make different trade offs between mesh quality and computational cost. The MGPRFS method is able to produce high quality meshes at a reasonable computational cost, while the MED method trades off some mesh quality for a reduction in computational cost relative to the MGPRFS method. To evaluate the performance of our proposed methods, we compared them to three highly-effective previously-proposed single-component mesh generators for both grayscale and color images. In particular, our evaluation considered the following previously-proposed methods: the error diffusion (ED) method of Yang et al., the greedy-point-removal from-subset (GPRFSED) method of Adams, and the greedy-point removal (GPR) method of Demaret and Iske. Since these methods cannot directly handle color images, color images were handled through conversion to grayscale as a preprocessing step, and then as a postprocessing step after mesh generation, the grayscale sample values in the generated mesh were replaced by their corresponding color values. These color-capable versions of ED, GPRFSED, and GPR are henceforth referred to as CED, CGPRFSED, and CGPR, respectively. Experimental results show that our MGPRFS method yields meshes of higher quality than the CGPRFSED and GPRFSED methods by up to 7.05 dB and 2.88 dB respectively, with nearly the same computational cost. Moreover, the MGPRFS method outperforms the CGPR and GPR methods in mesh quality by up to 7.08 dB and 0.42 dB respectively, with about 5 to 40 times less computational cost. Lastly, our MED method yields meshes of higher quality than the CED and ED methods by up to 7.08 and 4.72 dB respectively, where all three of these methods have a similar computational cost. / Graduate