Kernel-Based Feature Selection Techniques for Transport Proteins Based on Star Graph Topological Indices

[Abstract] The transport of the molecules inside cells is a very important topic, especially in Drug Metabolism. The experimental testing of the new proteins for the transporter molecular function is expensive and inefficient due to the large amount of new peptides. Therefore, there is a need for cheap and fast theoretical models to predict the transporter proteins. In the current work, the primary structure of a protein is represented as a molecular Star graph, characterized by a series of topological indices. The dataset was made up of 2,503 protein chains, out of which 413 have transporter molecular function and 2,090 have no transporter function. These indices were used as input to several classification techniques to find the best Quantitative Structure Activity Relationship (QSAR) model that can evaluate the transporter function of a new protein chain. Among several feature selection techniques, the Support Vector Machine Recursive Feature Elimination allows us to obtain a classification model based on 20 attributes with a true positive rate of 83% and a false positive rate of 16.7%.Xunta de Galicia; 1OSIN105004P

Digital certificates and threshold cryptography

This dissertation discusses the use of secret sharing cryptographic protocols for distributing and sharing of secret documents, in our case PDF documents. We discuss the advantages and uses of such a system in the context of collaborative environments. Description of the cryptographic protocol involved and the necessary Public Key Infrastructure (PKI) shall be presented. We also provide an implementation of this framework as a “proof of concept” and fundament the use of a certificate extension as the basis for threshold cryptography. Details of the shared secret distribution protocol and shared secret recovery protocol shall be given as well as the associated technical implementation details. The actual secret sharing algorithm implemented at this stage is based on an existing well known secret sharing scheme that uses polynomial interpolation over a finite field. Finally we conclude with a practical assessment of our prototype

SInCom 2015

2nd Baden-Württemberg Center of Applied Research Symposium on Information and Communication Systems, SInCom 2015, 13. November 2015 in Konstan

DESIGN AND IMPLEMENTATION OF PATH FINDING AND VERIFICATION IN THE INTERNET

In the Internet, network traffic between endpoints typically follows one path that is determined by the control plane. Endpoints have little control over the choice of which path their network traffic takes and little ability to verify if the traffic indeed follows a specific path. With the emergence of software-defined networking (SDN), more control over connections can be exercised, and thus the opportunity for novel solutions exists. However, there remain concerns about the attack surface exposed by fine-grained control, which may allow attackers to inject and redirect traffic. To address these opportunities and concerns, we consider two specific challenges: (1) How can the network determine the choices of paths available to connect endpoints, especially when multiple criteria can be considered? And (2) how can endpoints verify the integrity of the path over which network traffic is sent. The latter consists of two subproblems, determining that the source of traffic is authentic and determining that a specified path is traversed without deviation. In this dissertation, we investigate and present solutions for both the network path finding problem and the verification problem. We first address path finding, or routing, which is a core functionality in the Internet. Existing approaches are either based on a single criterion (such as path length, delay, or an artificially defined ``weight’’) or use a combinatorial optimization function when there are multiple criteria. We present a multi-criteria routing algorithm that can search the whole space of all possible paths. To achieve the scalability of our solution, we limit the search to only Pareto-optimal paths, which allows us to prune sub-optimal paths quickly and reduce computational complexity. We show that our approach is tractable on a variety of realistic topologies and the results Pareto-optimal paths can be clustered to present a few alternative options. We then address path verification in the Internet, which consists of source authentication and path validation. Once a path has been selected, we show that an endpoint can validate that traffic indeed traverses along the chosen path. Prior work has relied on cryptographic approaches for such validation, which need significant computational resources. In contrast, we propose a lightweight and scalable technique to address this problem, which uses a set of orthogonal sequences as credentials in the packets. The verification of these orthogonal credentials is based on inner product computations, which can be easily implemented by basic bitwise operations in a processor. We show that the proposed approach can achieve the necessary security properties for both source authentication and path validation. Results from a prototype implementation show that the proposed technique can be implemented efficiently and only add a small computational overhead. The results of our work enable novel uses of networks with fine-grained traffic control, such as enabling more path choices in networks where multiple performance criteria matter. In addition, our work contributes to efforts to make the Internet more secure by presenting techniques that allow endpoints to validate the source and path of network traffic. We believe that these contributions help with improving both the current Internet and also future networks

Blood-Based Gene Expression Profiles Models for Classification of Subsyndromal Symptomatic Depression and Major Depressive Disorder

Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and also lead to significant psychosocial functional impairment as same as major depressive disorder (MDD). Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step. Firstly, we identified 63 differentially expressed SSD signatures in contrast to control (P< = 5.0E-4) and 30 differentially expressed MDD signatures in contrast to control, respectively. Then, 123 gene signatures were identified with significantly differential expression level between SSD and MDD. Secondly, in order to conduct priority selection for biomarkers for SSD and MDD together, we selected top gene signatures from each group of pair-wise comparison results, and merged the signatures together to generate better profiles used for clearly classify SSD and MDD sets in the same time. In details, we tried different combination of signatures from the three pair-wise compartmental results and finally determined 48 gene expression signatures with 100% accuracy. Our finding suggested that SSD and MDD did not exhibit the same expressed genome signature with peripheral blood leukocyte, and blood cell–derived RNA of these 48 gene models may have significant value for performing diagnostic functions and classifying SSD, MDD, and healthy controls

Proceedings of the Doctoral Consortium in Computer Science (JIPII 2021)

Actas de las Jornadas de Investigación Predoctoral en Ingeniería InformáticaThis volume contains the proceedings of the Primeras Jornadas de Investigación Predoctoral en Ingeniería Informática - First Doctoral Consortium in Computer Science, JIPII 2021, which was held online on June 15th, 2021. The aim of JIPII 2021 was to provide a forum for PhD students to present and discuss their research under the guidance of a panel of senior researchers. The advances in their PhD theses under development in the Doctoral Program in Computer Science were presented in the Consortium. This Doctoral Program belongs to the Doctoral School of the University of Cadiz (EDUCA). Different stages of research were covered, from the most incipient phase, such as the PhD Thesis plans (or even a Master’s Thesis), to the most advanced phases in which the defence of the PhD Thesis is imminent. We enjoyed twenty very nice and interesting talks, organized in four sessions. We had a total of fifty participants, including speakers and attendees, with an average of thirty-two people in the morning sessions and an average of twenty people in the afternoon sessions. Several people contributed to the success of JIPII 2021. We are grateful to the Academic Committee of the Doctoral Program in Computer Science and the School of Engineering for their support. We would like also to thank the Program Committee for their work in reviewing the papers, as well as all the students and supervisors for their interest and participation. Finally, the proceedings have been published by the Department of Computer Science and Engineering. We hope that you find the proceedings useful, interesting, and challenging

Automatic Retrieval of Skeletal Structures of Trees from Terrestrial Laser Scanner Data

Research on forest ecosystems receives high attention, especially nowadays with regard to sustainable management of renewable resources and the climate change. In particular, accurate information on the 3D structure of a tree is important for forest science and bioclimatology, but also in the scope of commercial applications. Conventional methods to measure geometric plant features are labor- and time-intensive. For detailed analysis, trees have to be cut down, which is often undesirable. Here, Terrestrial Laser Scanning (TLS) provides a particularly attractive tool because of its contactless measurement technique. The object geometry is reproduced as a 3D point cloud. The objective of this thesis is the automatic retrieval of the spatial structure of trees from TLS data. We focus on forest scenes with comparably high stand density and with many occlusions resulting from it. The varying level of detail of TLS data poses a big challenge. We present two fully automatic methods to obtain skeletal structures from scanned trees that have complementary properties. First, we explain a method that retrieves the entire tree skeleton from 3D data of co-registered scans. The branching structure is obtained from a voxel space representation by searching paths from branch tips to the trunk. The trunk is determined in advance from the 3D points. The skeleton of a tree is generated as a 3D line graph. Besides 3D coordinates and range, a scan provides 2D indices from the intensity image for each measurement. This is exploited in the second method that processes individual scans. Furthermore, we introduce a novel concept to manage TLS data that facilitated the researchwork. Initially, the range image is segmented into connected components. We describe a procedure to retrieve the boundary of a component that is capable of tracing inner depth discontinuities. A 2D skeleton is generated from the boundary information and used to decompose the component into sub components. A Principal Curve is computed from the 3D point set that is associated with a sub component. The skeletal structure of a connected component is summarized as a set of polylines. Objective evaluation of the results remains an open problem because the task itself is ill-defined: There exists no clear definition of what the true skeleton should be w.r.t. a given point set. Consequently, we are not able to assess the correctness of the methods quantitatively, but have to rely on visual assessment of results and provide a thorough discussion of the particularities of both methods. We present experiment results of both methods. The first method efficiently retrieves full skeletons of trees, which approximate the branching structure. The level of detail is mainly governed by the voxel space and therefore, smaller branches are reproduced inadequately. The second method retrieves partial skeletons of a tree with high reproduction accuracy. The method is sensitive to noise in the boundary, but the results are very promising. There are plenty of possibilities to enhance the method’s robustness. The combination of the strengths of both presented methods needs to be investigated further and may lead to a robust way to obtain complete tree skeletons from TLS data automatically.Die Erforschung des ÖkosystemsWald spielt gerade heutzutage im Hinblick auf den nachhaltigen Umgang mit nachwachsenden Rohstoffen und den Klimawandel eine große Rolle. Insbesondere die exakte Beschreibung der dreidimensionalen Struktur eines Baumes ist wichtig für die Forstwissenschaften und Bioklimatologie, aber auch im Rahmen kommerzieller Anwendungen. Die konventionellen Methoden um geometrische Pflanzenmerkmale zu messen sind arbeitsintensiv und zeitaufwändig. Für eine genaue Analyse müssen Bäume gefällt werden, was oft unerwünscht ist. Hierbei bietet sich das Terrestrische Laserscanning (TLS) als besonders attraktives Werkzeug aufgrund seines kontaktlosen Messprinzips an. Die Objektgeometrie wird als 3D-Punktwolke wiedergegeben. Basierend darauf ist das Ziel der Arbeit die automatische Bestimmung der räumlichen Baumstruktur aus TLS-Daten. Der Fokus liegt dabei auf Waldszenen mit vergleichsweise hoher Bestandesdichte und mit zahlreichen daraus resultierenden Verdeckungen. Die Auswertung dieser TLS-Daten, die einen unterschiedlichen Grad an Detailreichtum aufweisen, stellt eine große Herausforderung dar. Zwei vollautomatische Methoden zur Generierung von Skelettstrukturen von gescannten Bäumen, welche komplementäre Eigenschaften besitzen, werden vorgestellt. Bei der ersten Methode wird das Gesamtskelett eines Baumes aus 3D-Daten von registrierten Scans bestimmt. Die Aststruktur wird von einer Voxelraum-Repräsentation abgeleitet indem Pfade von Astspitzen zum Stamm gesucht werden. Der Stamm wird im Voraus aus den 3D-Punkten rekonstruiert. Das Baumskelett wird als 3D-Liniengraph erzeugt. Für jeden gemessenen Punkt stellt ein Scan neben 3D-Koordinaten und Distanzwerten auch 2D-Indizes zur Verfügung, die sich aus dem Intensitätsbild ergeben. Bei der zweiten Methode, die auf Einzelscans arbeitet, wird dies ausgenutzt. Außerdem wird ein neuartiges Konzept zum Management von TLS-Daten beschrieben, welches die Forschungsarbeit erleichtert hat. Zunächst wird das Tiefenbild in Komponenten aufgeteilt. Es wird eine Prozedur zur Bestimmung von Komponentenkonturen vorgestellt, die in der Lage ist innere Tiefendiskontinuitäten zu verfolgen. Von der Konturinformation wird ein 2D-Skelett generiert, welches benutzt wird um die Komponente in Teilkomponenten zu zerlegen. Von der 3D-Punktmenge, die mit einer Teilkomponente assoziiert ist, wird eine Principal Curve berechnet. Die Skelettstruktur einer Komponente im Tiefenbild wird als Menge von Polylinien zusammengefasst. Die objektive Evaluation der Resultate stellt weiterhin ein ungelöstes Problem dar, weil die Aufgabe selbst nicht klar erfassbar ist: Es existiert keine eindeutige Definition davon was das wahre Skelett in Bezug auf eine gegebene Punktmenge sein sollte. Die Korrektheit der Methoden kann daher nicht quantitativ beschrieben werden. Aus diesem Grund, können die Ergebnisse nur visuell beurteiltwerden. Weiterhinwerden die Charakteristiken beider Methoden eingehend diskutiert. Es werden Experimentresultate beider Methoden vorgestellt. Die erste Methode bestimmt effizient das Skelett eines Baumes, welches die Aststruktur approximiert. Der Detaillierungsgrad wird hauptsächlich durch den Voxelraum bestimmt, weshalb kleinere Äste nicht angemessen reproduziert werden. Die zweite Methode rekonstruiert Teilskelette eines Baums mit hoher Detailtreue. Die Methode reagiert sensibel auf Rauschen in der Kontur, dennoch sind die Ergebnisse vielversprechend. Es gibt eine Vielzahl von Möglichkeiten die Robustheit der Methode zu verbessern. Die Kombination der Stärken von beiden präsentierten Methoden sollte weiter untersucht werden und kann zu einem robusteren Ansatz führen um vollständige Baumskelette automatisch aus TLS-Daten zu generieren

Iterative restricted space search : a solving approach based on hybridization

Face à la complexité qui caractérise les problèmes d'optimisation de grande taille l'exploration complète de l'espace des solutions devient rapidement un objectif inaccessible. En effet, à mesure que la taille des problèmes augmente, des méthodes de solution de plus en plus sophistiquées sont exigées afin d'assurer un certain niveau d 'efficacité. Ceci a amené une grande partie de la communauté scientifique vers le développement d'outils spécifiques pour la résolution de problèmes de grande taille tels que les méthodes hybrides. Cependant, malgré les efforts consentis dans le développement d'approches hybrides, la majorité des travaux se sont concentrés sur l'adaptation de deux ou plusieurs méthodes spécifiques, en compensant les points faibles des unes par les points forts des autres ou bien en les adaptant afin de collaborer ensemble. Au meilleur de notre connaissance, aucun travail à date n'à été effectué pour développer un cadre conceptuel pour la résolution efficace de problèmes d'optimisation de grande taille, qui soit à la fois flexible, basé sur l'échange d'information et indépendant des méthodes qui le composent. L'objectif de cette thèse est d'explorer cette avenue de recherche en proposant un cadre conceptuel pour les méthodes hybrides, intitulé la recherche itérative de l'espace restreint, ±Iterative Restricted Space Search (IRSS)>>, dont, la principale idée est la définition et l'exploration successives de régions restreintes de l'espace de solutions. Ces régions, qui contiennent de bonnes solutions et qui sont assez petites pour être complètement explorées, sont appelées espaces restreints "Restricted Spaces (RS)". Ainsi, l'IRSS est une approche de solution générique, basée sur l'interaction de deux phases algorithmiques ayant des objectifs complémentaires. La première phase consiste à identifier une région restreinte intéressante et la deuxième phase consiste à l'explorer. Le schéma hybride de l'approche de solution permet d'alterner entre les deux phases pour un nombre fixe d'itérations ou jusqu'à l'atteinte d'une certaine limite de temps. Les concepts clés associées au développement de ce cadre conceptuel et leur validation seront introduits et validés graduellement dans cette thèse. Ils sont présentés de manière à permettre au lecteur de comprendre les problèmes que nous avons rencontrés en cours de développement et comment les solutions ont été conçues et implémentées. À cette fin, la thèse a été divisée en quatre parties. La première est consacrée à la synthèse de l'état de l'art dans le domaine de recherche sur les méthodes hybrides. Elle présente les principales approches hybrides développées et leurs applications. Une brève description des approches utilisant le concept de restriction d'espace est aussi présentée dans cette partie. La deuxième partie présente les concepts clés de ce cadre conceptuel. Il s'agit du processus d'identification des régions restreintes et des deux phases de recherche. Ces concepts sont mis en oeuvre dans un schéma hybride heuristique et méthode exacte. L'approche a été appliquée à un problème d'ordonnancement avec deux niveaux de décision, relié au contexte des pâtes et papier: "Pulp Production Scheduling Problem". La troisième partie a permit d'approfondir les concepts développés et ajuster les limitations identifiées dans la deuxième partie, en proposant une recherche itérative appliquée pour l'exploration de RS de grande taille et une structure en arbre binaire pour l'exploration de plusieurs RS. Cette structure a l'avantage d'éviter l'exploration d 'un espace déjà exploré précédemment tout en assurant une diversification naturelle à la méthode. Cette extension de la méthode a été testée sur un problème de localisation et d'allocation en utilisant un schéma d'hybridation heuristique-exact de manière itérative. La quatrième partie généralise les concepts préalablement développés et conçoit un cadre général qui est flexible, indépendant des méthodes utilisées et basé sur un échange d'informations entre les phases. Ce cadre a l'avantage d'être général et pourrait être appliqué à une large gamme de problèmes