A feature selection approach for identification of signature genes from SAGE data

Abstract Background One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements. Results A new framework to select specific genes that distinguish different biological states based on the analysis of SAGE data is proposed. The new framework applies the bolstered error for the identification of strong genes that separate the biological states in a feature space defined by the gene expression of a training set. Credibility intervals defined from a probabilistic model of SAGE measurements are used to identify the genes that distinguish the different states with more reliability among all gene groups selected by the strong genes method. A score taking into account the credibility and the bolstered error values in order to rank the groups of considered genes is proposed. Results obtained using SAGE data from gliomas are presented, thus corroborating the introduced methodology. Conclusion The model representing counting data, such as SAGE, provides additional statistical information that allows a more robust analysis. The additional statistical information provided by the probabilistic model is incorporated in the methodology described in the paper. The introduced method is suitable to identify signature genes that lead to a good separation of the biological states using SAGE and may be adapted for other counting methods such as Massive Parallel Signature Sequencing (MPSS) or the recent Sequencing-By-Synthesis (SBS) technique. Some of such genes identified by the proposed method may be useful to generate classifiers.

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Abstract Background Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

A comparison of face and facial feature detectors based on the viola-jones general object detection framework

[EN]The human face provides useful information during interaction; therefore, any system integrating Vision- BasedHuman Computer Interaction requires fast and reliable face and facial feature detection. Different approaches have focused on this ability but only open source implementations have been extensively used by researchers. A good example is the Viola–Jones object detection framework that particularly in the context of facial processing has been frequently used.

Combining face and facial feature detectors for face detection performance improvement

[EN]In this paper, we experimentally study the combination of face and facial feature detectors to improve face detection performance. The face detection problem, as suggeted by recent face detection challenges, is still not solved. Face detectors traditionally fail in large-scale problems and/or when the face is occluded or di erent head rotations are present. The combination of face and facial feature detectors is evaluated with a public database. The obtained results evidence an improvement in the positive detection rate while reducing the false detection rate. Additionally, we prove that the integration of facial feature detectors provides useful information for pose estimation and face alignment.

Fingerprint Recognition: Enhancement, Feature Extraction and Automatic Evaluation of Algorithms

The identification of people by measuring some traits of individual anatomy or physiology has led to a specific research area called biometric recognition. This thesis is focused on improving fingerprint recognition systems considering three important problems: fingerprint enhancement, fingerprint orientation extraction and automatic evaluation of fingerprint algorithms. An effective extraction of salient fingerprint features depends on the quality of the input fingerprint. If the fingerprint is very noisy, we are not able to detect a reliable set of features. A new fingerprint enhancement method, which is both iterative and contextual, is proposed. This approach detects high-quality regions in fingerprints, selectively applies contextual filtering and iteratively expands like wildfire toward low-quality ones. A precise estimation of the orientation field would greatly simplify the estimation of other fingerprint features (singular points, minutiae) and improve the performance of a fingerprint recognition system. The fingerprint orientation extraction is improved following two directions. First, after the introduction of a new taxonomy of fingerprint orientation extraction methods, several variants of baseline methods are implemented and, pointing out the role of pre- and post- processing, we show how to improve the extraction. Second, the introduction of a new hybrid orientation extraction method, which follows an adaptive scheme, allows to improve significantly the orientation extraction in noisy fingerprints. Scientific papers typically propose recognition systems that integrate many modules and therefore an automatic evaluation of fingerprint algorithms is needed to isolate the contributions that determine an actual progress in the state-of-the-art. The lack of a publicly available framework to compare fingerprint orientation extraction algorithms, motivates the introduction of a new benchmark area called FOE (including fingerprints and manually-marked orientation ground-truth) along with fingerprint matching benchmarks in the FVC-onGoing framework. The success of such framework is discussed by providing relevant statistics: more than 1450 algorithms submitted and two international competitions.

Contour integration and principles of perceptual grouping

Ziel der Arbeit ist die Analyse von Prinzipien der Konturintegration im menschlichen visuellen System. Die perzeptuelle Verbindung benachbarter Teile in einer visuellen Szene zu einem Ganzen wird durch zwei gestalttheoretisch begründete Propositionen gekennzeichnet, die komplementäre lokale Mechanismen der Konturintegration beschreiben. Das erste Prinzip der Konturintegration fordert, dass lokale Ähnlichkeit von Elementen in einem anderen Merkmal als Orientierung nicht hinreicht für die Entdeckung von Konturen, sondern ein zusätzlicher statistischer Merkmalsunterschied von Konturelementen und Umgebung vorliegen muss, um Konturentdeckung zu ermöglichen. Das zweite Prinzip der Konturintegration behauptet, dass eine kollineare Ausrichtung von Konturelementen für Konturintegration hinreicht, und es bei deren Vorliegen zu robuster Konturintegrationsleistung kommt, auch wenn die lokalen merkmalstragenden Elemente in anderen Merkmalen in hohem Maße zufällig variieren und damit keine nachbarschaftliche Ähnlichkeitsbeziehung entlang der Kontur aufweisen. Als empirische Grundlage für die beiden vorgeschlagenen Prinzipien der Konturintegration werden drei Experimente berichtet, die zunächst die untergeordnete Rolle globaler Konturmerkmale wie Geschlossenheit bei der Konturentdeckung aufweisen und daraufhin die Bedeutung lokaler Mechanismen für die Konturintegration anhand der Merkmale Kollinearität, Ortsfrequenz sowie der spezifischen Art der Interaktion zwischen beiden Merkmalen beleuchten. Im ersten Experiment wird das globale Merkmal der Geschlossenheit untersucht und gezeigt, dass geschlossene Konturen nicht effektiver entdeckt werden als offene Konturen. Das zweite Experiment zeigt die Robustheit von über Kollinearität definierten Konturen über die zufällige Variation im Merkmal Ortsfrequenz entlang der Kontur und im Hintergrund, sowie die Unmöglichkeit der Konturintegration bei nachbarschaftlicher Ähnlichkeit der Konturelemente, wenn Ähnlichkeit statt über kollineare Orientierung über gleiche Ortsfrequenzen realisiert ist. Im dritten Experiment wird gezeigt, dass eine redundante Kombination von kollinearer Orientierung mit einem statistischen Unterschied im Merkmal Ortsfrequenz zu erheblichen Sichtbarkeitsgewinnen bei der Konturentdeckung führt. Aufgrund der Stärke der Summationswirkung wird vorgeschlagen, dass durch die Kombination mehrerer Hinweisreize neue kortikale Mechanismen angesprochen werden, die die Konturentdeckung unterstützen. Die Resultate der drei Experimente werden in den Kontext aktueller Forschung zur Objektwahrnehmung gestellt und ihre Bedeutung für die postulierten allgemeinen Prinzipien visueller Gruppierung in der Konturintegration diskutiert. Anhand phänomenologischer Beispiele mit anderen Merkmalen als Orientierung und Ortsfrequenz wird gezeigt, dass die gefundenen Prinzipien Generalisierbarkeit für die Verarbeitung von Konturen im visuellen System beanspruchen können.

Diffusion maps in the Subriemannian motion group and perceptual grouping

Il presente lavoro è motivato dal problema della constituzione di unità percettive a livello della corteccia visiva primaria V1. Si studia dettagliatamente il modello geometrico di Citti-Sarti con particolare attenzione alla modellazione di fenomeni di associazione visiva. Viene studiato nel dettaglio un modello di connettività. Il contributo originale risiede nell'adattamento del metodo delle diffusion maps, recentemente introdotto da Coifman e Lafon, alla geometria subriemanniana della corteccia visiva. Vengono utilizzati strumenti di teoria del potenziale, teoria spettrale, analisi armonica in gruppi di Lie per l'approssimazione delle autofunzioni dell'operatore del calore sul gruppo dei moti rigidi del piano. Le autofunzioni sono utilizzate per l'estrazione di unità percettive nello stimolo visivo. Sono presentate prove sperimentali e originali delle capacità performanti del metodo.

Software tools and efficient algorithms for the feature detection, feature tracking, event localization, and visualization of large sets of atmospheric data

Data sets describing the state of the earth's atmosphere are of great importance in the atmospheric sciences. Over the last decades, the quality and sheer amount of the available data increased significantly, resulting in a rising demand for new tools capable of handling and analysing these large, multidimensional sets of atmospheric data. The interdisciplinary work presented in this thesis covers the development and the application of practical software tools and efficient algorithms from the field of computer science, aiming at the goal of enabling atmospheric scientists to analyse and to gain new insights from these large data sets. For this purpose, our tools combine novel techniques with well-established methods from different areas such as scientific visualization and data segmentation. In this thesis, three practical tools are presented. Two of these tools are software systems (Insight and IWAL) for different types of processing and interactive visualization of data, the third tool is an efficient algorithm for data segmentation implemented as part of Insight.Insight is a toolkit for the interactive, three-dimensional visualization and processing of large sets of atmospheric data, originally developed as a testing environment for the novel segmentation algorithm. It provides a dynamic system for combining at runtime data from different sources, a variety of different data processing algorithms, and several visualization techniques. Its modular architecture and flexible scripting support led to additional applications of the software, from which two examples are presented: the usage of Insight as a WMS (web map service) server, and the automatic production of a sequence of images for the visualization of cyclone simulations. The core application of Insight is the provision of the novel segmentation algorithm for the efficient detection and tracking of 3D features in large sets of atmospheric data, as well as for the precise localization of the occurring genesis, lysis, merging and splitting events. Data segmentation usually leads to a significant reduction of the size of the considered data. This enables a practical visualization of the data, statistical analyses of the features and their events, and the manual or automatic detection of interesting situations for subsequent detailed investigation. The concepts of the novel algorithm, its technical realization, and several extensions for avoiding under- and over-segmentation are discussed. As example applications, this thesis covers the setup and the results of the segmentation of upper-tropospheric jet streams and cyclones as full 3D objects. Finally, IWAL is presented, which is a web application for providing an easy interactive access to meteorological data visualizations, primarily aimed at students. As a web application, the needs to retrieve all input data sets and to install and handle complex visualization tools on a local machine are avoided. The main challenge in the provision of customizable visualizations to large numbers of simultaneous users was to find an acceptable trade-off between the available visualization options and the performance of the application. Besides the implementational details, benchmarks and the results of a user survey are presented.

Effiziente und robuste, feature-basierte Wiedererkennung langer Zeitreihen in großen Datenbanken

Die Materialverfolgung gewinnt in der Metallindustrie immer mehr an Bedeutung:rnEs ist notwendig, dass ein Metallband im Fertigungsprozess ein festgelegtes Programm durchläuft - erst dann ist die Qualität des Endprodukts garantiert. Die bisherige Praxis besteht darin, jedem Metallband eine Nummer zuzuordnen, mit der dieses Band beschriftet wird. Bei einer tagelangen Lagerung der Bänder zwischen zwei Produktionsschritten erweist sich diese Methode als fehleranfällig: Die Beschriftungen können z.B. verloren gehen, verwechselt, falsch ausgelesen oder unleserlich werden. 2007 meldete die iba AG das Patent zur Identifikation der Metallbänder anhand ihres Dickenprofils an (Anhaus [3]) - damit kann die Identität des Metallbandes zweifelsfrei nachgewiesen werden, eine zuverlässige Materialverfolgung wurde möglich.Es stellte sich jedoch heraus, dass die messfehlerbehafteten Dickenprofile, die als lange Zeitreihen aufgefasst werden können, mit Hilfe von bisherigen Verfahren (z.B. L2-Abstandsminimierung oder Dynamic Time Warping) nicht erfolgreich verglichen werden können.Diese Arbeit stellt einen effizienten feature-basierten Algorithmus zum Vergleichrnzweier Zeitreihen vor. Er ist sowohl robust gegenüber Rauschen und Messausfällen als auch invariant gegenüber solchen Koordinatentransformationen der Zeitreihen wie Skalierung und Translation. Des Weiteren sind auch Vergleiche mit Teilzeitreihen möglich. Unser Framework zeichnet sich sowohl durch seine hohe Genauigkeit als auch durch seine hohe Geschwindigkeit aus: Mehr als 99.5% der Anfragen an unsere aus realen Profilen bestehende Testdatenbank werden richtig beantwortet. Mit mehreren hundert Zeitreihen-Vergleichen pro Sekunde ist es etwa um den Faktor 10 schneller als die auf dem Gebiet der Zeitreihenanalyse etablierten Verfahren, die jedoch nicht im Stande sind, mehr als 90% der Anfragen korrekt zu verarbeiten. Der Algorithmus hat sich als industrietauglich erwiesen. Die iba AG setzt ihn in einem weltweit einzigartigen dickenprofilbasierten Überwachungssystemrnzur Materialverfolgung ein, das in ersten Stahl- und Aluminiumwalzwerkenrnbereits erfolgreich zum Einsatz kommt.

Connectivity management and dynamic context grouping in mobile heterogenous systems

In the last 10 years the number of mobile devices has grown rapidly. Each person usually brings at least two personal devices and researchers says that in a near future this number could raise up to ten devices per person. Moreover, all the devices are becoming more integrated to our life than in the past, therefore the amount of data exchanged increases accordingly to the improvement of people's lifestyle. This is what researchers call Internet of Things. Thus, in the future there will be more than 60 billions of nodes and the current infrastructure is not ready to keep track of all the exchanges of data between them. Therefore, infrastructure improvements have been proposed in the last years, like MobileIP and HIP in order to facilitate the exchange of packets in mobility, however none of them have been optimized for the purpose. In the last years, researchers from Mid Sweden University created The MediaSense Framework. Initially, this framework was based on the Chord protocol in order to route packets in a big network, but the most important change has been the introduction of PGrids in order to create the Overlay and the persistence. Thanks to this technology, a lookup in the trie takes up to 0.5*log(N), where N is the total number of nodes in the network. This result could be improved by further optimizations on the management of the nodes, for example by the dynamic creation of groups of nodes. Moreover, since the nodes move, an underlaying support for connectivity management is needed. SCTP has been selected as one of the most promising upcoming standards for simultaneous multiple connection's management.

Costificazione delle matrici per estrusione mediante approccio "feature-based cost".

In questo elaborato viene presentato un nuovo modello di costo per le matrici per estrusione basato su un approccio feature-based. Nel particolare si è cercato di definire il costo di questi prodotti sulla base delle loro caratteristiche geometriche e tecnologiche.

Feature-invariant image registration method for quantification of surgical outcomes in patients with craniosynostosis: a preliminary study

Craniosynostosis consists of a premature fusion of the sutures in an infant skull that restricts skull and brain growth. During the last decades, there has been a rapid increase of fundamentally diverse surgical treatment methods. At present, the surgical outcome has been assessed using global variables such as cephalic index, head circumference, and intracranial volume. However, these variables have failed in describing the local deformations and morphological changes that may have a role in the neurologic disorders observed in the patients. This report describes a rigid image registration-based method to evaluate outcomes of craniosynostosis surgical treatments, local quantification of head growth, and indirect intracranial volume change measurements. The developed semiautomatic analysis method was applied to computed tomography data sets of a 5-month-old boy with sagittal craniosynostosis who underwent expansion of the posterior skull with cranioplasty. Quantification of the local changes between pre- and postoperative images was quantified by mapping the minimum distance of individual points from the preoperative to the postoperative surface meshes, and indirect intracranial volume changes were estimated. The proposed methodology can provide the surgeon a tool for the quantitative evaluation of surgical procedures and detection of abnormalities of the infant skull and its development.

Feature Versus Spatial Strategies by Orangutans (Pongo abelii) and Human Children (Homo sapiens) in a Cross-Dimensional Task

Despite the fact that photographic stimuli are used across experimental contexts with both human and nonhuman subjects, the nature of individuals' perceptions of these stimuli is still not well understood. In the present experiments, we tested whether three orangutans and 36 human children could use photographic information presented on a computer screen to solve a perceptually corresponding problem in the physical domain. Furthermore, we tested the cues that aided in this process by pitting featural information against spatial position in a series of probe trials. We found that many of the children and one orangutan were successfully able to use the information cross-dimensionally; however, the other two orangutans and almost a quarter of the children failed to acquire the task. Species differences emerged with respect to ease of task acquisition. More striking, however, were the differences in cues that participants used to solve the task: Whereas the orangutan used a spatial strategy, the majority of children used a feature one. Possible reasons for these differences are discussed from both evolutionary and developmental perspectives. The novel results found here underscore the need for further testing in this area to design appropriate experimental paradigms in future comparative research settings.