A Monocular SLAM Method to Estimate Relative Pose During Satellite Proximity Operations

Automated satellite proximity operations is an increasingly relevant area of mission operations for the US Air Force with potential to significantly enhance space situational awareness (SSA). Simultaneous localization and mapping (SLAM) is a computer vision method of constructing and updating a 3D map while keeping track of the location and orientation of the imaging agent inside the map. The main objective of this research effort is to design a monocular SLAM method customized for the space environment. The method developed in this research will be implemented in an indoor proximity operations simulation laboratory. A run-time analysis is performed, showing near real-time operation. The method is verified by comparing SLAM results to truth vertical rotation data from a CubeSat air bearing testbed. This work enables control and testing of simulated proximity operations hardware in a laboratory environment. Additionally, this research lays the foundation for autonomous satellite proximity operations with unknown targets and minimal additional size, weight, and power requirements, creating opportunities for numerous mission concepts not previously available

Behaviour modelling with data obtained from the Internet and contributions to cluster validation

[EN]This PhD thesis makes contributions in modelling behaviours found in different types of data acquired from the Internet and in the field of clustering evaluation. Two different types of Internet data were processed, on the one hand, internet traffic with the objective of attack detection and on the other hand, web surfing activity with the objective of web personalization, both data being of sequential nature. To this aim, machine learning techniques were applied, mostly unsupervised techniques. Moreover, contributions were made in cluster evaluation, in order to make easier the selection of the best partition in clustering problems. With regard to network attack detection, first, gureKDDCup database was generated which adds payload data to KDDCup99 connection attributes because it is essential to detect non-flood attacks. Then, by modelling this data a network Intrusion Detection System (nIDS) was proposed where context-independent payload processing was done obtaining satisfying detection rates. In the web mining context web surfing activity was modelled for web personalization. In this context, generic and non-invasive systems to extract knowledge were proposed just using the information stored in webserver log files. Contributions were done in two senses: in problem detection and in link suggestion. In the first application a meaningful list of navigation attributes was proposed for each user session to group and detect different navigation profiles. In the latter, a general and non-invasive link suggestion system was proposed which was evaluated with satisfactory results in a link prediction context. With regard to the analysis of Cluster Validity Indices (CVI), the most extensive CVI comparison found up to a moment was carried out using a partition similarity measure based evaluation methodology. Moreover, we analysed the behaviour of CVIs in a real web mining application with elevated number of clusters in which they tend to be unstable. We proposed a procedure which automatically selects the best partition analysing the slope of different CVI values.[EU]Doktorego-tesi honek internetetik eskuratutako datu mota ezberdinetan aurkitutako portaeren modelugintzan eta multzokatzeen ebaluazioan egiten ditu bere ekarpenak. Zehazki, bi mota ezberdinetako interneteko datuak prozesatu dira: batetik, interneteko trafikoa, erasoak hautemateko helburuarekin; eta bestetik, web nabigazioen jarduera, weba pertsonalizatzeko helburuarekin; bi datu motak izaera sekuentzialekoak direlarik. Helburu hauek lortzeko, ikasketa automatikoko teknikak aplikatu dira, nagusiki gainbegiratu-gabeko teknikak. Testuinguru honetan, multzokatzeen partizio onenaren aukeraketak dakartzan arazoak gutxitzeko multzokatzeen ebaluazioan ere ekarpenak egin dira. Sareko erasoen hautemateari dagokionez, lehenik gureKDDCup datubasea eratu da KDDCup99-ko konexio atributuei payload-ak (sareko paketeen datu eremuak) gehituz, izan ere, ez-flood erasoak (pakete gutxi erabiltzen dituzten erasoak) hautemateko ezinbestekoak baitira. Ondoren, datu hauek modelatuz testuinguruarekiko independenteak diren payload prozesaketak oinarri dituen sareko erasoak hautemateko sistema (network Intrusion Detection System (nIDS)) bat proposatu da maila oneko eraso hautemate-tasak lortuz. Web meatzaritzaren testuinguruan, weba pertsonalizatzeko helburuarekin web nabigazioen jarduera modelatu da. Honetarako, web zerbizarietako lorratz fitxategietan metatutako informazioa soilik erabiliz ezagutza erabilgarria erauziko duen sistema orokor eta ez-inbasiboak proposatu dira. Ekarpenak bi zentzutan eginaz: arazoen hautematean eta esteken iradokitzean. Lehen aplikazioan sesioen nabigazioa adierazteko atributu esanguratsuen zerrenda bat proposatu da, gero nabigazioak multzokatu eta nabigazio profil ezberdinak hautemateko. Bigarren aplikazioan, estekak iradokitzeko sistema orokor eta ez-inbasibo bat proposatu da, eta berau, estekak aurresateko testuinguruan ebaluatu da emaitza onak lortuz. Multzokatzeak balioztatzeko indizeen (Cluster Validity Indices (CVI)) azterketari dagokionez, gaurdaino aurkitu den CVI-en konparaketa zabalena burutu da partizioen antzekotasun neurrian oinarritutako ebaluazio metodologia erabiliz. Gainera, CVI-en portaera aztertu da egiazko web meatzaritza aplikazio batean normalean baino multzo kopuru handiagoak dituena, non CVI-ek ezegonkorrak izateko joera baitute. Arazo honi aurre eginaz, CVI ezberdinek partizio ezberdinetarako lortzen dituzten balioen maldak aztertuz automatikoki partiziorik onena hautatzen duen prozedura proposatu da.[ES]Esta tesis doctoral hace contribuciones en el modelado de comportamientos encontrados en diferentes tipos de datos adquiridos desde internet y en el campo de la evaluación del clustering. Dos tipos de datos de internet han sido procesados: en primer lugar el tráfico de internet con el objetivo de detectar ataques; y en segundo lugar la actividad generada por los usuarios web con el objetivo de personalizar la web; siendo los dos tipos de datos de naturaleza secuencial. Para este fin, se han aplicado técnicas de aprendizaje automático, principalmente técnicas no-supervisadas. Además, se han hecho aportaciones en la evaluación de particiones de clusters para facilitar la selección de la mejor partición de clusters. Respecto a la detección de ataques en la red, primero, se generó la base de datos gureKDDCup que añade el payload (la parte de contenido de los paquetes de la red) a los atributos de la conexión de KDDCup99 porque el payload es esencial para la detección de ataques no-flood (ataques que utilizan pocos paquetes). Después, se propuso un sistema de detección de intrusos (network Intrusion Detection System (IDS)) modelando los datos de gureKDDCup donde se propusieron varios preprocesos del payload independientes del contexto obteniendo resultados satisfactorios. En el contexto de la minerı́a web, se ha modelado la actividad de la navegación web para la personalización web. En este contexto se propondrán sistemas genéricos y no-invasivos para la extracción del conocimiento, utilizando únicamente la información almacenada en los ficheros log de los servidores web. Se han hecho aportaciones en dos sentidos: en la detección de problemas y en la sugerencia de links. En la primera aplicación, se propuso una lista de atributos significativos para representar las sesiones de navegación web para después agruparlos y detectar diferentes perfiles de navegación. En la segunda aplicación, se propuso un sistema general y no-invasivo para sugerir links y se evaluó en el contexto de predicción de links con resultados satisfactorios. Respecto al análisis de ı́ndices de validación de clusters (Cluster Validity Indices (CVI)), se ha realizado la más amplia comparación encontrada hasta el momento que utiliza la metodologı́a de evaluación basada en medidas de similitud de particiones. Además, se ha analizado el comportamiento de los CVIs en una aplicación real de minerı́a web con un número elevado de clusters, contexto en el que los CVIs tienden a ser inestables, ası́ que se propuso un procedimiento para la selección automática de la mejor partición en base a la pendiente de los valores de diferentes CVIs.Grant of the Basque Government (ref.: BFI08.226); Grant of Ministry of Economy and Competitiveness of the Spanish Government (ref.: BES-2011-045989); Research stay grant of Spanish Ministry of Economy and Competitiveness (ref.: EEBB-I-14-08862); University of the Basque Country UPV/EHU (BAILab, grant UFI11/45); Department of Education, Universities and Research of the Basque Government (grant IT-395-10); Ministry of Economy and Competitiveness of the Spanish Government and by the European Regional Development Fund - ERDF (eGovernAbility, grant TIN2014-52665-C2-1-R)

Network and Algebraic Topology of Influenza Evolution

Evolution is a force that has molded human existence since its divergence from chimpanzees about 5.4 million years ago. In that same amount of time, an influenza virus, which replicates every six hours, would have undergone an equivalent number of generations over only a hundred years. The fast replication times of influenza, coupled with its high mutation rate, make the virus a perfect model to study real-time evolution at a mega-Darwin scale, more than a million times faster than human evolution. While recent developments in high-throughput sequencing provide an optimal opportunity to dissect their genetic evolution, a concurrent growth in computational tools is necessary to analyze the large influx of complex genomic data. In my thesis, I present novel computational methods to examine different aspects of influenza evolution. I first focus on seasonal influenza, particularly the problems that hamper public health initiatives to combat the virus. I introduce two new approaches: 1. The q2-coefficient, a method of quantifying pathogen surveillance, and 2. FluGraph, a technique that employs network topology to track the spread of seasonal influenza around the world. The second chapter of my thesis examines how mutations and reassortment combine to alter the course of influenza evolution towards pandemic formation. I highlight inherent deficiencies in the current phylogenetic paradigm for analyzing evolution and offer a novel methodology based on algebraic topology that comprehensively reconstructs both vertical and horizontal evolutionary events. I apply this method to viruses, with emphasis on influenza, but foresee broader application to cancer cells, bacteria, eukaryotes, and other taxa

High-quality, high-throughput measurement of protein-DNA binding using HiTS-FLIP

In order to understand in more depth and on a genome wide scale the behavior of transcription factors (TFs), novel quantitative experiments with high-throughput are needed. Recently, HiTS-FLIP (High-Throughput Sequencing-Fluorescent Ligand Interaction Profiling) was invented by the Burge lab at the MIT (Nutiu et al. (2011)). Based on an Illumina GA-IIx machine for next-generation sequencing, HiTS-FLIP allows to measure the affinity of fluorescent labeled proteins to millions of DNA clusters at equilibrium in an unbiased and untargeted way examining the entire sequence space by Determination of dissociation constants (Kds) for all 12-mer DNA motifs. During my PhD I helped to improve the experimental design of this method to allow measuring the protein-DNA binding events at equilibrium omitting any washing step by utilizing the TIRF (Total Internal Reflection Fluorescence) based optics of the GA-IIx. In addition, I developed the first versions of XML based controlling software that automates the measurement procedure. Meeting the needs for processing the vast amount of data produced by each run, I developed a sophisticated, high performance software pipeline that locates DNA clusters, normalizes and extracts the fluorescent signals. Moreover, cluster contained k-mer motifs are ranked and their DNA binding affinities are quantified with high accuracy. My approach of applying phase-correlation to estimate the relative translative Offset between the observed tile images and the template images omits resequencing and thus allows to reuse the flow cell for several HiTS-FLIP experiments, which greatly reduces cost and time. Instead of using information from the sequencing images like Nutiu et al. (2011) for normalizing the cluster intensities which introduces a nucleotide specific bias, I estimate the cluster related normalization factors directly from the protein Images which captures the non-even illumination bias more accurately and leads to an improved correction for each tile image. My analysis of the ranking algorithm by Nutiu et al. (2011) has revealed that it is unable to rank all measured k-mers. Discarding all the clusters related to previously ranked k-mers has the side effect of eliminating any clusters on which k-mers could be ranked that share submotifs with previously ranked k-mers. This shortcoming affects even strong binding k-mers with only one mutation away from the top ranked k-mer. My findings show that omitting the cluster deletion step in the ranking process overcomes this limitation and allows to rank the full spectrum of all possible k-mers. In addition, the performance of the ranking algorithm is drastically reduced by my insight from a quadratic to a linear run time. The experimental improvements combined with the sophisticated processing of the data has led to a very high accuracy of the HiTS-FLIP dissociation constants (Kds) comparable to the Kds measured by the very sensitive HiP-FA assay (Jung et al. (2015)). However, experimentally HiTS-FLIP is a very challenging assay. In total, eight HiTS-FLIP experiments were performed but only one showed saturation, the others exhibited Protein aggregation occurring at the amplified DNA clusters. This biochemical issue could not be remedied. As example TF for studying the details of HiTS-FLIP, GCN4 was chosen which is a dimeric, basic leucine zipper TF and which acts as the master regulator of the amino acid starvation Response in Saccharomyces cerevisiae (Natarajan et al. (2001)). The fluorescent dye was mOrange. The HiTS-FLIP Kds for the TF GCN4 were validated by the HiP-FA assay and a Pearson correlation coefficient of R=0.99 and a relative error of delta=30.91% was achieved. Thus, a unique and comprehensive data set of utmost quantitative precision was obtained that allowed to study the complex binding behavior of GCN4 in a new way. My Downstream analyses reveal that the known 7-mer consensus motif of GCN4, which is TGACTCA, is modulated by its 2-mer neighboring flanking regions spanning an affinity range over two orders of magnitude from a Kd=1.56 nM to Kd=552.51 nM. These results suggest that the common 9-mer PWM (Position Weight Matrix) for GCN4 is insufficient to describe the binding behavior of GCN4. Rather, an additional left and right flanking nucleotide is required to extend the 9-mer to an 11-mer. My analyses regarding mutations and related delta delta G values suggest long-range interdependencies between nucleotides of the two dimeric half-sites of GCN4. Consequently, models assuming positional independence, such as a PWM, are insufficient to explain these interdependencies. Instead, the full spectrum of affinity values for all k-mers of appropriate size should be measured and applied in further analyses as proposed by Nutiu et al. (2011). Another discovery were new binding motifs of GCN4, which can only be detected with a method like HiTS-FLIP that examines the entire sequence space and allows for unbiased, de-novo motif discovery. All These new motifs contain GTGT as a submotif and the data collected suggests that GCN4 binds as monomer to these new motifs. Therefore, it might be even possible to detect different binding modes with HiTS-FLIP. My results emphasize the binding complexity of GCN4 and demonstrate the advantage of HiTS-FLIP for investigating the complexity of regulative processes

New computational methods and plant models for evolutionary genomics

This thesis is in the service of a greater understanding of the genetic basis of adaptive traits. Chapter 1 introduces background literature relevant to this thesis. Chapters 2, 3, and 4 develop novel methods and software for the analysis of genetic sequencing data. Chapter 5 details a large collaborative project to establish genetic resources in the model cereal Brachypodium, and perform a genome-wide association study for several agriculturally-relevant traits under two climate change scenarios. Chapter 6 investigates the spatial genetic patterns in two species of woodland eucalypt, and determines the landscape process that could be driving these patterns. Finally, Chapter 7 summarises these works, and proposes some areas of further study. In Chapters 2 and 3, I develop methods that enable analysis of Genotyping-by-sequencing analysis. Axe, a short read sequence demultiplexer, demultiplexes samples from multiplexed GBS sequencing datasets. I show Axe has high accuracy, and outperforms previously published software. Axe also tolerates complex indexing schemes such as the variable-length combinatorial indexes used in GBS data. Trimit and libqcpp (Chapter 3) implements several low-level sequence read quality assessment and control methods as a C++ library, and as a command line tool. Both these works have been published in peer-reviewed journals, and are used by numerous groups internationally. In Chapter 4, I develop kWIP, a de novo estimator of genetic distance. kWIP enables rapid estimation of genetic distances directly from sequence reads. We first show kWIP outperforms a competing method at low coverage using simulations that mimic a population resequencing experiment. We propose and demonstrate several use cases for kWIP, including population resequencing, initial assessment of sample identity, and estimating metagenomic similarity. kWIP was published in PLoS Computational Biology. In Chapter 5, I present the results of a large, collaborative project which surveys the global genetic diversity of the model cereal Brachypodium. We amass a collection of over 2000 accessions from the Brachypodium species complex. Using GBS and whole genome sequencing we identify around 800 accessions of the diploid Brachypodium distachyon, within which we find extensive population structure and clonal families. Through population restructuring we create a core collection of 74 accessions containing the majority of genetic diversity in the "A genome" sub-population. Using this core collection, we assay several phenotypes of agricultural interest including early vigour, harvest index and energy use efficiency under two climates, and dissect the genetic basis of these traits using a genome-wide association study (GWAS). This work has been accepted for publication at Genetics; I am co-first author with Pip Wilson and Jared Streich, having lead many genomic analyses. In Chapter 6, I perform a study of landscape genomic variation in two woodland eucalypt species. Using whole genome sequencing of around 200 individuals from around 20 localities of both E. albens and E. sideroxylon, I find incredible genetic diversity and low genome-wide inter-species differentiation.I find no support for strong discrete population structure, but strong support for isolation by (geographic) distance (IBD). Using generalised dissimilarity modelling, I further examine the pattern of IBD, and establish additional isolation by environment (IBE). E. albens shows moderately strong IBD, explaining 26% of deviance in genetic distance using geographic distance, and an additional 6% deviance explained by incorporating environmental predictors (IBE). E. sideroxylon shows much stronger IBD, with 78% of deviance explained by geography, and stronger IBE (12% additional deviance explained). This work will soon be submitted for publication

UAV or Drones for Remote Sensing Applications in GPS/GNSS Enabled and GPS/GNSS Denied Environments

The design of novel UAV systems and the use of UAV platforms integrated with robotic sensing and imaging techniques, as well as the development of processing workflows and the capacity of ultra-high temporal and spatial resolution data, have enabled a rapid uptake of UAVs and drones across several industries and application domains.This book provides a forum for high-quality peer-reviewed papers that broaden awareness and understanding of single- and multiple-UAV developments for remote sensing applications, and associated developments in sensor technology, data processing and communications, and UAV system design and sensing capabilities in GPS-enabled and, more broadly, Global Navigation Satellite System (GNSS)-enabled and GPS/GNSS-denied environments.Contributions include:UAV-based photogrammetry, laser scanning, multispectral imaging, hyperspectral imaging, and thermal imaging;UAV sensor applications; spatial ecology; pest detection; reef; forestry; volcanology; precision agriculture wildlife species tracking; search and rescue; target tracking; atmosphere monitoring; chemical, biological, and natural disaster phenomena; fire prevention, flood prevention; volcanic monitoring; pollution monitoring; microclimates; and land use;Wildlife and target detection and recognition from UAV imagery using deep learning and machine learning techniques;UAV-based change detection

Advances in Character Recognition

This book presents advances in character recognition, and it consists of 12 chapters that cover wide range of topics on different aspects of character recognition. Hopefully, this book will serve as a reference source for academic research, for professionals working in the character recognition field and for all interested in the subject