With the ever increasing amount of high-throughput molecular profile data, biologists need versatile tools to enable them to quickly and succinctly analyze their data. Furthermore, pathway databases have grown increasingly robust with the KEGG database at the forefront. Previous tools have color-coded the genes on different pathways using differential expression analysis. Unfortunately, they do not adequately capture the relationships of the genes amongst one another. Structure Enrichment Analysis (SEA) thus seeks to take biological analysis to the next level. SEA accomplishes this goal by highlighting for users the sub-pathways of a biological pathways that best correspond to their molecular profile data in an easy to use GUI interface.

In this thesis, the extraction of sparse 3D points from calibrated image sequences is studied. The presented method for sparse 3D reconstruction is examined in two steps, where the first part addresses the problem of two-view reconstruction, and the second part is the extension of the two-view reconstruction algorithm to include multiple views. The examined two-view reconstruction method consists of some basic building blocks, such as feature detection and matching, epipolar geometry estimation, and the reconstruction of cameras and scene structure. Feature detection and matching is achieved by Scale Invariant Feature Transform (SIFT) method. For the estimation of epipolar geometry, the 7-point and 8-point algorithms are examined for Fundamental matrix (F-matrix) computation, while RANSAC and PROSAC are utilized for the robustness and accuracy for model estimation. In the final stage of two-view reconstruction, the camera projection matrices are computed from the F-matrix, and the locations of 3D scene points are estimated by triangulation / hence, determining the scene structure and cameras up to a projective transformation. The extension of the two-view reconstruction to multiple views is achieved by estimating the camera projection matrix of each additional view from the already reconstructed matches, and then adding new points to the scene structure by triangulating the unreconstructed matches. Finally, the reconstruction is upgraded from projective to metric by a rectifying homography computed from the camera calibration information. In order to obtain a refined reconstruction, two different methods are suggested for the removal of erroneous points from the scene structure. In addition to the examination of the solution to the reconstruction problem, experiments have been conducted that compare the performances of competing algorithms used in various stages of reconstruction. In connection with sparse reconstruction, a rate-distortion efficient piecewise planar scene representation algorithm that generates mesh models of scenes from reconstructed point clouds is examined, and its performance is evaluated through experiments.

In this thesis, opti-acoustic stereo imaging, which is the deployment of two-dimensional (2D) high frequency imaging sonar with the electro-optical camera in calibrated stereo configuration, is studied. Optical cameras give detailed images in clear waters. However, in dark or turbid waters, information coming from electro-optical sensor is insufficient for accurate scene perception. Imaging sonars, also known as acoustic cameras, can provide enhanced target details under these scenarios. To illustrate these visibility conditions, a 2D high frequency imaging sonar simulator as well as an underwater optical image simulator is developed. A computationally efficient algorithm is also proposed for the post-processing of the returned sonar signals. Where optical visibility allows, integration of the sonar and optical images effectively provides binocular stereo vision capability and enables the recovery of three-dimensional (3D) structural information. This requires solving the feature correspondence problem for these completely different sensing modalities. Geometrical interpretation of this problem is examined on the simulated optical and sonar images. Matching the features manually, 3D reconstruction performance of opti-acoustic system is also investigated. In addition, motion estimation from opti-acoustic image sequences is studied. Finally, a method is proposed to improve the degraded optical images with the help of sonar images. First, a nonlinear mapping is found to match local the features in opti-acoustical images. Next, features in the sonar image is mapped to the optical image using the transformation. Performance of the mapping is evaluated for different scene geometries.

L’amélioration rapide du nombre de documents stockés électroniquement représente un défi pour la classification automatique de documents. Les systèmes de classification traditionnels traitent les documents en tant que texte plat, mais les documents sont de plus en plus structurés. Par exemple, XML est la norme plus connue et plus utilisée pour la représentation de documents structurés. Ce type des documents comprend des informations complémentaires sur l'organisation du contenu représentées par différents éléments comme les titres, les sections, les légendes etc. Pour tenir compte des informations stockées dans la structure logique, nous proposons une approche de représentation des documents structurés basée à la fois sur la structure logique du document et son contenu textuel. Notre approche étend le modèle traditionnel de représentation du document appelé modèle vectoriel. Nous avons essayé d'utiliser d'information structurelle dans toutes les phases de la représentation du document: -procédure d'extraction de caractéristiques, -La sélection des caractéristiques, -Pondération des caractéristiques. Notre deuxième contribution concerne d’appliquer notre approche générique à un domaine réel : classification des documents techniques. Nous désirons mettre en œuvre notre proposition sur une collection de documents techniques sauvegardés électroniquement dans la société CONTINEW spécialisée dans l'audit de documents techniques. Ces documents sont en format représentations où la structure logique est non accessible. Nous proposons une solution d’interprétation de documents pour détecter la structure logique des documents à partir de leur présentation physique. Ainsi une collection hétérogène en différents formats de stockage est transformée en une collection homogène de documents XML contenant le même schéma logique. Cette contribution est basée sur un apprentissage supervisé. En conclusion, notre proposition prend en charge l'ensemble de flux de traitements des documents partant du format original jusqu’à la détermination de la ses classe Dans notre système l’algorithme de classification utilisé est SVM. / Rapid improvement in the number of documents stored electronically presents a challenge for automatic classification of documents. Traditional classification systems consider documents as a plain text; however documents are becoming more and more structured. For example, XML is the most known and used standard for structured document representation. These documents include supplementary information on content organization represented by different elements such as title, section, caption etc. We propose an approach on structured document classification based on both document logical structure and its content in order to take into account the information present in logical structure. Our approach extends the traditional document representation model called Vector Space Model (VSM). We have tried to integrate structural information in all phases of document representation construction: -Feature extraction procedure, -Feature selection, -Feature weighting. Our second contribution concerns to apply our generic approach to a real domain of technical documentation. We desire to use our proposition for classifying technical documents electronically saved in CONTINEW; society specialized in technical document audit. These documents are in legacy format in which logical structure is inaccessible. Then we propose an approach for document understanding in order to extract documents logical structure from their presentation layout. Thus a collection of heterogeneous documents in different physical presentations and formats is transformed to a homogenous XML collection sharing the same logical structure. Our contribution is based on learning approach where each logical element is described by its physical characteristics. Therefore, our proposal supports whole document transformation workflow from document’s original format to being classified. In our system SVM has been used as classification algorithm.

Die vorliegende Arbeit beschäftigt sich mit der Konzeptionierung und Entwicklung eines neuartigen Fahrerassistenzsystems für Nutzfahrzeuge, welches die lichte Höhe von vor dem Fahrzeug befindlichen Hindernissen berechnet und über einen Abgleich mit der einstellbaren Fahrzeughöhe die Passierbarkeit bestimmt. Dabei werden die von einer Monokamera aufgenommenen Bildsequenzen genutzt, um durch indirekte und direkte Rekonstruktionsverfahren ein 3D-Abbild der Fahrumgebung zu erschaffen. Unter Hinzunahme einer Radodometrie-basierten Eigenbewegungsschätzung wird die erstellte 3D-Repräsentation skaliert und eine Prädiktion der longitudinalen und lateralen Fahrzeugbewegung ermittelt. Basierend auf dem vertikalen Höhenplan der Straßenoberfläche, welcher über die Aneinanderreihung mehrerer Ebenen modelliert wird, erfolgt die Klassifizierung des 3D-Raums in Fahruntergrund, Struktur und potentielle Hindernisse. Die innerhalb des Fahrschlauchs liegenden Hindernisse werden hinsichtlich ihrer Entfernung und Höhe bewertet. Ein daraus abgeleitetes Warnkonzept dient der optisch-akustischen Signalisierung des Hindernisses im Kombiinstrument des Fahrzeugs. Erfolgt keine entsprechende Reaktion durch den Fahrer, so wird bei kritischen Hindernishöhen eine Notbremsung durchgeführt. Die geschätzte Eigenbewegung und berechneten Hindernisparameter werden mithilfe von Referenzsensorik bewertet. Dabei kommt eine dGPS-gestützte Inertialplattform sowie ein terrestrischer und mobiler Laserscanner zum Einsatz. Im Rahmen der Arbeit werden verschiedene Umgebungssituationen und Hindernistypen im urbanen und ländlichen Raum untersucht und Aussagen zur Genauigkeit und Zuverlässigkeit des Verfahrens getroffen. Ein wesentlicher Einflussfaktor auf die Dichte und Genauigkeit der 3D-Rekonstruktion ist eine gleichmäßige Umgebungsbeleuchtung innerhalb der Bildsequenzaufnahme. Es wird in diesem Zusammenhang zwingend auf den Einsatz einer Automotive-tauglichen Kamera verwiesen. Die durch die Radodometrie bestimmte Eigenbewegung eignet sich im langsamen Geschwindigkeitsbereich zur Skalierung des 3D-Punktraums. Dieser wiederum sollte durch eine Kombination aus indirektem und direktem Punktrekonstruktionsverfahren erstellt werden. Der indirekte Anteil stützt dabei die Initialisierung des Verfahrens zum Start der Funktion und ermöglicht eine robuste Kameraschätzung. Das direkte Verfahren ermöglicht die Rekonstruktion einer hohen Anzahl an 3D-Punkten auf den Hindernisumrissen, welche zumeist die Unterkante beinhalten. Die Unterkante kann in einer Entfernung bis zu 20 m detektiert und verfolgt werden. Der größte Einflussfaktor auf die Genauigkeit der Berechnung der lichten Höhe von Hindernissen ist die Modellierung des Fahruntergrunds. Zur Reduktion von Ausreißern in der Höhenberechnung eignet sich die Stabilisierung des Verfahrens durch die Nutzung von zeitlich vorher zur Verfügung stehenden Berechnungen. Als weitere Maßnahme zur Stabilisierung wird zudem empfohlen die Hindernisausgabe an den Fahrer und den automatischen Notbremsassistenten mittels einer Hysterese zu stützen. Das hier vorgestellte System eignet sich für Park- und Rangiervorgänge und ist als kostengünstiges Fahrerassistenzsystem interessant für Pkw mit Aufbauten und leichte Nutzfahrzeuge. / The present work deals with the conception and development of a novel advanced driver assistance system for commercial vehicles, which estimates the clearance height of obstacles in front of the vehicle and determines the passability by comparison with the adjustable vehicle height. The image sequences captured by a mono camera are used to create a 3D representation of the driving environment using indirect and direct reconstruction methods. The 3D representation is scaled and a prediction of the longitudinal and lateral movement of the vehicle is determined with the aid of a wheel odometry-based estimation of the vehicle's own movement. Based on the vertical elevation plan of the road surface, which is modelled by attaching several surfaces together, the 3D space is classified into driving surface, structure and potential obstacles. The obstacles within the predicted driving tube are evaluated with regard to their distance and height. A warning concept derived from this serves to visually and acoustically signal the obstacle in the vehicle's instrument cluster. If the driver does not respond accordingly, emergency braking will be applied at critical obstacle heights. The estimated vehicle movement and calculated obstacle parameters are evaluated with the aid of reference sensors. A dGPS-supported inertial measurement unit and a terrestrial as well as a mobile laser scanner are used. Within the scope of the work, different environmental situations and obstacle types in urban and rural areas are investigated and statements on the accuracy and reliability of the implemented function are made. A major factor influencing the density and accuracy of 3D reconstruction is uniform ambient lighting within the image sequence. In this context, the use of an automotive camera is mandatory. The inherent motion determined by wheel odometry is suitable for scaling the 3D point space in the slow speed range. The 3D representation however, should be created by a combination of indirect and direct point reconstruction methods. The indirect part supports the initialization phase of the function and enables a robust camera estimation. The direct method enables the reconstruction of a large number of 3D points on the obstacle outlines, which usually contain the lower edge. The lower edge can be detected and tracked up to 20 m away. The biggest factor influencing the accuracy of the calculation of the clearance height of obstacles is the modelling of the driving surface. To reduce outliers in the height calculation, the method can be stabilized by using calculations from older time steps. As a further stabilization measure, it is also recommended to support the obstacle output to the driver and the automatic emergency brake assistant by means of hysteresis. The system presented here is suitable for parking and maneuvering operations and is interesting as a cost-effective driver assistance system for cars with superstructures and light commercial vehicles.