004 Datenverarbeitung; Informatik
Refine
Has Fulltext
- yes (285)
Year of publication
Document Type
- Journal article (127)
- Doctoral Thesis (80)
- Working Paper (37)
- Preprint (19)
- Conference Proceeding (9)
- Jahresbericht (5)
- Master Thesis (4)
- Report (3)
- Other (1)
Language
- English (257)
- German (27)
- Multiple languages (1)
Keywords
- virtual reality (16)
- Datennetz (14)
- Leistungsbewertung (13)
- Quran (8)
- Robotik (8)
- Koran (7)
- Mobiler Roboter (7)
- Text Mining (7)
- Autonomer Roboter (6)
- Simulation (6)
Institute
- Institut für Informatik (203)
- Theodor-Boveri-Institut für Biowissenschaften (29)
- Institut Mensch - Computer - Medien (17)
- Institut für deutsche Philologie (17)
- Institut für Klinische Epidemiologie und Biometrie (7)
- Rechenzentrum (7)
- Center for Computational and Theoretical Biology (4)
- Graduate School of Science and Technology (3)
- Medizinische Klinik und Poliklinik II (3)
- Institut für Funktionsmaterialien und Biofabrikation (2)
Schriftenreihe
Sonstige beteiligte Institutionen
- Cologne Game Lab (2)
- Birmingham City University (1)
- DATE Lab, KITE Research Insititute, University Health Network, Toronto, Canada (1)
- EMBL Heidelberg (1)
- INAF Padova, Italy (1)
- Jacobs University Bremen, Germany (1)
- Open University of the Netherlands (1)
- Servicezentrum Medizin-Informatik (Universitätsklinikum) (1)
- Social and Technological Systems (SaTS) lab, School of Art, Media, Performance and Design, York University, Toronto, Canada (1)
- TH Köln (1)
Background
The actin cytoskeleton is a hallmark of eukaryotic cells. Its regulation as well as its interaction with other proteins is carefully orchestrated by actin interaction domains. One of the key players is the WH2 motif, which enables binding to actin monomers and filaments and is involved in the regulation of actin nucleation. Contrasting conserved domains, the identification of this motif in protein sequences is challenging, as it is short and poorly conserved.
Findings
To identify divergent members, we combined Hidden-Markov-Model (HMM) to HMM alignments with orthology predictions. Thereby, we identified nearly 500 proteins containing so far not annotated WH2 motifs. This included shootin-1, an actin binding protein involved in neuron polarization. Among others, WH2 motifs of ‘proximal to raf’ (ptr)-orthologs, which are described in the literature, but not annotated in genome databases, were identified.
Conclusion
In summary, we increased the number of WH2 motif containing proteins substantially. This identification of candidate regions for actin interaction could steer their experimental characterization. Furthermore, the approach outlined here can easily be adapted to the identification of divergent members of further domain families.
Background
Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These methods typically rely on standardized terminologies that guide this process. Many languages and clinical domains, however, lack appropriate resources and tools, as well as evaluations of their applications, especially if detailed conceptualizations of the domain are required. For instance, German transthoracic echocardiography reports have not been targeted sufficiently before, despite of their importance for clinical trials. This work therefore aimed at development and evaluation of an information extraction component with a fine-grained terminology that enables to recognize almost all relevant information stated in German transthoracic echocardiography reports at the University Hospital of Würzburg.
Methods
A domain expert validated and iteratively refined an automatically inferred base terminology. The terminology was used by an ontology-driven information extraction system that outputs attribute value pairs. The final component has been mapped to the central elements of a standardized terminology, and it has been evaluated according to documents with different layouts.
Results
The final system achieved state-of-the-art precision (micro average.996) and recall (micro average.961) on 100 test documents that represent more than 90 % of all reports. In particular, principal aspects as defined in a standardized external terminology were recognized with f 1=.989 (micro average) and f 1=.963 (macro average). As a result of keyword matching and restraint concept extraction, the system obtained high precision also on unstructured or exceptionally short documents, and documents with uncommon layout.
Conclusions
The developed terminology and the proposed information extraction system allow to extract fine-grained information from German semi-structured transthoracic echocardiography reports with very high precision and high recall on the majority of documents at the University Hospital of Würzburg. Extracted results populate a clinical data warehouse which supports clinical research.
Introduction The fast, precise, and accurate measurement of the new generation of oral anticoagulants such as dabigatran and rivaroxaban in patients' plasma my provide important information in different clinical circumstances such as in the case of suspicion of overdose, when patients switch from existing oral anticoagulant, in patients with hepatic or renal impairment, by concomitant use of interaction drugs, or to assess anticoagulant concentration in patients' blood before major surgery. Methods Here, we describe a quick and precise method to measure the coagulation inhibitors dabigatran and rivaroxaban using ultra-performance liquid chromatography electrospray ionization-tandem mass spectrometry in multiple reactions monitoring (MRM) mode (UPLC-MRM MS). Internal standards (ISs) were added to the sample and after protein precipitation; the sample was separated on a reverse phase column. After ionization of the analytes the ions were detected using electrospray ionization-tandem mass spectrometry. Run time was 2.5 minutes per injection. Ion suppression was characterized by means of post-column infusion. Results The calibration curves of dabigatran and rivaroxaban were linear over the working range between 0.8 and 800 mu g/L (r > 0.99). Limits of detection (LOD) in the plasma matrix were 0.21 mu g/L for dabigatran and 0.34 mu g/L for rivaroxaban, and lower limits of quantification (LLOQ) in the plasma matrix were 0.46 mu g/L for dabigatran and 0.54 mu g/L for rivaroxaban. The intraassay coefficients of variation (CVs) for dabigatran and rivaroxaban were < 4% and 6%; respectively, the interassay CVs were < 6% for dabigatran and < 9% for rivaroxaban. Inaccuracy was < 5% for both substances. The mean recovery was 104.5% (range 83.8-113.0%) for dabigatran and 87.0%(range 73.6-105.4%) for rivaroxaban. No significant ion suppressions were detected at the elution times of dabigatran or rivaroxaban. Both coagulation inhibitors were stable in citrate plasma at -20 degrees C, 4 degrees C and even at RT for at least one week. A method comparison between our UPLC-MRM MS method, the commercially available automated Direct Thrombin Inhibitor assay (DTI assay) for dabigatran measurement from CoaChrom Diagnostica, as well as the automated anti-Xa assay for rivaroxaban measurement from Chromogenix both performed by ACL-TOP showed a high degree of correlation. However, UPLC-MRM MS measurement of dabigatran and rivaroxaban has a much better selectivity than classical functional assays measuring activities of various coagulation factors which are susceptible to interference by other coagulant drugs. Conclusions Overall, we developed and validated a sensitive and specific UPLC-MRM MS assay for the quick and specific measurement of dabigatran and rivaroxaban in human plasma.
Studies investigating the correlates of immune protection against Yersinia infection have established that both humoral and cell mediated immune responses are required for the comprehensive protection. In our previous study, we established that the bivalent fusion protein (rVE) comprising immunologically active regions of Y pestis LcrV (100-270 aa) and YopE (50-213 aa) proteins conferred complete passive and active protection against lethal Y enterocolitica 8081 challenge. In the present study, cohort of BALB/c mice immunized with rVE or its component proteins rV, rE were assessed for cell mediated immune responses and memory immune protection against Y enterocolitica 8081 rVE immunization resulted in extensive proliferation of both CD4 and CD8 T cell subsets; significantly high antibody titer with balanced IgG1: IgG2a/IgG2b isotypes (1:1 ratio) and up regulation of both Th1 (INF-\(\alpha\), IFN-\(\gamma\), IL 2, and IL 12) and Th2 (IL 4) cytokines. On the other hand, rV immunization resulted in Th2 biased IgG response (11:1 ratio) and proliferation of CD4+ T-cell; rE group of mice exhibited considerably lower serum antibody titer with predominant Th1 response (1:3 ratio) and CD8+ T-cell proliferation. Comprehensive protection with superior survival (100%) was observed among rVE immunized mice when compared to the significantly lower survival rates among rE (37.5%) and rV (25%) groups when IP challenged with Y enterocolitica 8081 after 120 days of immunization. Findings in this and our earlier studies define the bivalent fusion protein rVE as a potent candidate vaccine molecule with the capability to concurrently stimulate humoral and cell mediated immune responses and a proof of concept for developing efficient subunit vaccines against Gram negative facultative intracellular bacterial pathogens.
The ecosystem of the high northern latitudes is affected by the recently changing environmental conditions. The Arctic has undergone a significant climatic change over the last decades. The land coverage is changing and a phenological response to the warming is apparent. Remotely sensed data can assist the monitoring and quantification of these changes. The remote sensing of the Arctic was predominantly carried out by the usage of optical sensors but these encounter problems in the Arctic environment, e.g. the frequent cloud cover or the solar geometry. In contrast, the imaging of Synthetic Aperture Radar is not affected by the cloud cover and the acquisition of radar imagery is independent of the solar illumination. The objective of this work was to explore how polarimetric Synthetic Aperture Radar (PolSAR) data of TerraSAR-X, TanDEM-X, Radarsat-2 and ALOS PALSAR and interferometric-derived digital elevation model data of the TanDEM-X Mission can contribute to collect meaningful information on the actual state of the Arctic Environment. The study was conducted for Canadian sites of the Mackenzie Delta Region and Banks Island and in situ reference data were available for the assessment. The up-to-date analysis of the PolSAR data made the application of the Non-Local Means filtering and of the decomposition of co-polarized data necessary.
The Non-Local Means filter showed a high capability to preserve the image values, to keep the edges and to reduce the speckle. This supported not only the suitability for the interpretation but also for the classification. The classification accuracies of Non-Local Means filtered data were in average +10% higher compared to unfiltered images. The correlation of the co- and quad-polarized decomposition features was high for classes with distinct surface or double bounce scattering and a usage of the co-polarized data is beneficial for regions of natural land coverage and for low vegetation formations with little volume scattering. The evaluation further revealed that the X- and C-Band were most sensitive to the generalized land cover classes. It was found that the X-Band data were sensitive to low vegetation formations with low shrub density, the C-Band data were sensitive to the shrub density and the shrub dominated tundra. In contrast, the L-Band data were less sensitive to the land cover. Among the different dual-polarized data the HH/VV-polarized data were identified to be most meaningful for the characterization and classification, followed by the HH/HV-polarized and the VV/VH-polarized data. The quad-polarized data showed highest sensitivity to the land cover but differences to the co-polarized data were small. The accuracy assessment showed that spectral information was required for accurate land cover classification. The best results were obtained when spectral and radar information was combined. The benefit of including radar data in the classification was up to +15% accuracy and most significant for the classes wetland and sparse vegetated tundra. The best classifications were realized with quad-polarized C-Band and multispectral data and with co-polarized X-Band and multispectral data. The overall accuracy was up to 80% for unsupervised and up to 90% for supervised classifications. The results indicated that the shortwave co-polarized data show promise for the classification of tundra land cover since the polarimetric information is sensitive to low vegetation and the wetlands. Furthermore, co-polarized data provide a higher spatial resolution than the quad-polarized data.
The analysis of the intermediate digital elevation model data of the TanDEM-X showed a high potential for the characterization of the surface morphology. The basic and relative topographic features were shown to be of high relevance for the quantification of the surface morphology and an area-wide application is feasible. In addition, these data were of value for the classification and delineation of landforms. Such classifications will assist the delineation of geomorphological units and have potential to identify locations of actual and future morphologic activity.
In the course of the growth of the Internet and due to increasing availability of data, over the last two decades, the field of network science has established itself as an own area of research. With quantitative scientists from computer science, mathematics, and physics working on datasets from biology, economics, sociology, political sciences, and many others, network science serves as a paradigm for interdisciplinary research.
One of the major goals in network science is to unravel the relationship between topological graph structure and a network’s function. As evidence suggests, systems from the same fields, i.e. with similar function, tend to exhibit similar structure. However, it is still vague whether a similar graph structure automatically implies likewise function. This dissertation aims at helping to bridge this gap, while particularly focusing on the role of triadic structures.
After a general introduction to the main concepts of network science, existing work devoted to the relevance of triadic substructures is reviewed. A major challenge in modeling triadic structure is the fact that not all three-node subgraphs can be specified independently
of each other, as pairs of nodes may participate in multiple of those triadic subgraphs.
In order to overcome this obstacle, we suggest a novel class of generative network models based on so called Steiner triple systems. The latter are partitions of a graph’s vertices into pair-disjoint triples (Steiner triples). Thus, the configurations on Steiner triples can be specified independently of each other without overdetermining the network’s link
structure.
Subsequently, we investigate the most basic realization of this new class of models. We call it the triadic random graph model (TRGM). The TRGM is parametrized by a probability distribution over all possible triadic subgraph patterns. In order to generate a network instantiation of the model, for all Steiner triples in the system, a pattern is drawn from the distribution and adjusted randomly on the Steiner triple. We calculate the degree distribution of the TRGM analytically and find it to be similar to a Poissonian distribution. Furthermore, it is shown that TRGMs possess non-trivial triadic structure. We discover inevitable correlations in the abundance of certain triadic subgraph
patterns which should be taken into account when attributing functional relevance to particular motifs – patterns which occur significantly more frequently than expected at random. Beyond, the strong impact of the probability distributions on the Steiner triples on the occurrence of triadic subgraphs over the whole network is demonstrated. This interdependence allows us to design ensembles of networks with predefined triadic substructure. Hence, TRGMs help to overcome the lack of generative models needed for assessing the relevance of triadic structure.
We further investigate whether motifs occur homogeneously or heterogeneously distributed over a graph. Therefore, we study triadic subgraph structures in each node’s neighborhood individually. In order to quantitatively measure structure from an individual node’s perspective, we introduce an algorithm for node-specific pattern mining for both directed unsigned, and undirected signed networks. Analyzing real-world datasets, we find that there are networks in which motifs are distributed highly heterogeneously, bound to the proximity of only very few nodes. Moreover, we observe indication for the potential sensitivity of biological systems to a targeted removal of these critical vertices. In addition, we study whole graphs with respect to the homogeneity and homophily of their node-specific triadic structure. The former describes the similarity of subgraph distributions in the neighborhoods of individual vertices. The latter quantifies whether connected vertices
are structurally more similar than non-connected ones. We discover these features to be characteristic for the networks’ origins. Moreover, clustering the vertices of graphs regarding their triadic structure, we investigate structural groups in the neural network of C. elegans, the international airport-connection network, and the global network of diplomatic sentiments between countries. For the latter we find evidence for the instability of triangles considered socially unbalanced according to sociological theories.
Finally, we utilize our TRGM to explore ensembles of networks with similar triadic substructure in terms of the evolution of dynamical processes acting on their nodes. Focusing on oscillators, coupled along the graphs’ edges, we observe that certain triad motifs impose a clear signature on the systems’ dynamics, even when embedded in a larger
network structure.
A simple test setup has been developed at Institute of Aerospace Information Technology, University of Würzburg, Germany to realize basic functionalities for formation flight of quadrocopters. The test environment is planned to be utilized for developing and validating the algorithms for formation flying capability in real environment as well as for education purpose. An already existing test bed for single quadrocopter was extended with necessary inter-communication and distributed control mechanism to test the algorithms for formation flights in 2 degrees of freedom (roll / pitch). This study encompasses the domain of communication, control engineering and embedded systems programming. Bluetooth protocol has been used for inter-communication between two quadrocopters. A simple approach of PID control in combination with Kalman filter has been exploited. MATLAB Instrument Control Toolbox has been used for data display, plotting and analysis. Plots can be drawn in real-time and received information can also be stored in the form of files for later use and analysis. The test setup has been developed indigenously and at considerably low cost. Emphasis has been placed on simplicity to facilitate students learning process. Several lessons have been learnt during the course of development of this setup. Proposed setup is quite flexible that can be modified as per changing requirements.
At the center of the Internet’s protocol stack stands the Internet Protocol (IP) as a common denominator that enables all communication. To make routing efficient, resilient, and scalable, several aspects must be considered. Care must be taken that traffic is well balanced to make efficient use of the existing network resources, both in failure free operation and in failure scenarios.
Finding the optimal routing in a network is an NP-complete problem. Therefore, routing optimization is usually performed using heuristics. This dissertation shows that a routing optimized with one objective function is often not good when looking at other objective functions. It can even be worse than unoptimized routing with respect to that objective function. After looking at failure-free routing and traffic distribution in different failure scenarios, the analysis is extended to include the loop-free alternate (LFA) IP fast reroute mechanism. Different application scenarios of LFAs are examined and a special focus is set on the fact that LFAs usually cannot protect all traffic in a network even against single link failures. Thus, the routing optimization for LFAs is targeted on both link utilization and failure coverage. Finally, the pre-congestion notification mechanism PCN for network admission control and overload protection is analyzed and optimized. Different design options for implementing the protocol are compared, before algorithms are developed for the calculation and optimization of protocol parameters and PCN-based routing.
The second part of the thesis tackles a routing problem that can only be resolved on a global scale. The scalability of the Internet is at risk since a major and intensifying growth of the interdomain routing tables has been observed. Several protocols and architectures are analyzed that can be used to make interdomain routing more scalable. The most promising approach is the locator/identifier (Loc/ID) split architecture which separates routing from host identification. This way, changes in connectivity, mobility of end hosts, or traffic-engineering activities are hidden from the routing in the core of the Internet and the routing tables can be kept much smaller. All of the currently proposed Loc/ID split approaches have their downsides. In particular, the fact that most architectures use the ID for routing outside the Internet’s core is a poor design, which inhibits many of the possible features of a new routing architecture. To better understand the problems and to provide a solution for a scalable routing design that implements a true Loc/ID split, the new GLI-Split protocol is developed in this thesis, which provides separation of global and local routing and uses an ID that is independent from any routing decisions.
Besides GLI-Split, several other new routing architectures implementing Loc/ID split have been proposed for the Internet. Most of them assume that a mapping system is queried for EID-to-RLOC mappings by an intermediate node at the border of an edge network. When the mapping system is queried by an intermediate node, packets are already on their way towards their destination, and therefore, the mapping system must be fast, scalable, secure, resilient, and should be able to relay packets without locators to nodes that can forward them to the correct destination. The dissertation develops a classification for all proposed mapping system architectures and shows their similarities and differences. Finally, the fast two-level mapping system FIRMS is developed. It includes security and resilience features as well as a relay service for initial packets of a flow when intermediate nodes encounter a cache miss for the EID-to-RLOC mapping.
Knowledge-based systems (KBS) face an ever-increasing interest in various disciplines and contexts. Yet, the former aim to construct the ’perfect intelligent software’ continuously shifts to user-centered, participative solutions. Such systems enable users to contribute their personal knowledge to the problem solving process for increased efficiency and an ameliorated user experience. More precisely, we define non-functional key requirements of participative KBS as: Transparency (encompassing KBS status mediation), configurability (user adaptability, degree of user control/exploration), quality of the KB and UI, and evolvability (enabling the KBS to grow mature with their users). Many of those requirements depend on the respective target users, thus calling for a more user-centered development. Often, also highly expertise domains are targeted — inducing highly complex KBs — which requires a more careful and considerate UI/interaction design. Still, current KBS engineering (KBSE) approaches mostly focus on knowledge acquisition (KA) This often leads to non-optimal, little reusable, and non/little evaluated KBS front-end solutions.
In this thesis we propose a more encompassing KBSE approach. Due to the strong mutual influences between KB and UI, we suggest a novel form of intertwined UI and KB development. We base the approach on three core components for encompassing KBSE:
(1) Extensible prototyping, a tailored form of evolutionary prototyping; this builds on mature UI prototypes and offers two extension steps for the anytime creation of core KBS prototypes (KB + core UI) and fully productive KBS (core KBS prototype + common framing functionality). (2) KBS UI patterns, that define reusable solutions for the core KBS UI/interaction; we provide a basic collection of such patterns in this work. (3) Suitable usability instruments for the assessment of the KBS artifacts. Therewith, we do not strive for ’yet another’ self-contained KBS engineering methodology. Rather, we motivate to extend existing approaches by the proposed key components. We demonstrate this based on an agile KBSE model.
For practical support, we introduce the tailored KBSE tool ProKEt. ProKEt offers a basic selection of KBS core UI patterns and corresponding configuration options out of the box; their further adaption/extension is possible on various levels of expertise. For practical usability support, ProKEt offers facilities for quantitative and qualitative data collection. ProKEt explicitly fosters the suggested, intertwined development of UI and KB. For seamlessly integrating KA activities, it provides extension points for two selected external KA tools: For KnowOF, a standard office based KA environment. And for KnowWE, a semantic wiki for collaborative KA. Therewith, ProKEt offers powerful support for encompassing, user-centered KBSE.
Finally, based on the approach and the tool, we also developed a novel KBS type: Clarification KBS as a mashup of consultation and justification KBS modules. Those denote a specifically suitable realization for participative KBS in highly expertise contexts and consequently require a specific design. In this thesis, apart from more common UI solutions, we particularly also introduce KBS UI patterns especially tailored towards Clarification KBS.
The issue of sustainability is at the top of the political and societal agenda, being considered of extreme importance and urgency. Human individual action impacts the environment both locally (e.g., local air/water quality, noise disturbance) and globally (e.g., climate change, resource use). Urban environments represent a crucial example, with an increasing realization that the most effective way of producing a change is involving the citizens themselves in monitoring campaigns (a citizen science bottom-up approach). This is possible by developing novel technologies and IT infrastructures enabling large citizen participation. Here, in the wider framework of one of the first such projects, we show results from an international competition where citizens were involved in mobile air pollution monitoring using low cost sensing devices, combined with a web-based game to monitor perceived levels of pollution. Measures of shift in perceptions over the course of the campaign are provided, together with insights into participatory patterns emerging from this study. Interesting effects related to inertia and to direct involvement in measurement activities rather than indirect information exposure are also highlighted, indicating that direct involvement can enhance learning and environmental awareness. In the future, this could result in better adoption of policies towards decreasing pollution.
Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/or sequences covaried with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance- associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hairlike organs distributed across the fly's body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms.
Object six Degrees of Freedom (6DOF) pose estimation is a fundamental problem in many practical robotic applications, where the target or an obstacle with a simple or complex shape can move fast in cluttered environments. In this thesis, a 6DOF pose estimation algorithm is developed based on the fused data from a time-of-flight camera and a color camera. The algorithm is divided into two stages, an annealed particle filter based coarse pose estimation stage and a gradient decent based accurate pose optimization stage. In the first stage, each particle is evaluated with sparse representation. In this stage, the large inter-frame motion of the target can be well handled. In the second stage, the range data based conventional Iterative Closest Point is extended by incorporating the target appearance information and used for calculating the accurate pose by refining the coarse estimate from the first stage. For dealing with significant illumination variations during the tracking, spherical harmonic illumination modeling is investigated and integrated into both stages. The robustness and accuracy of the proposed algorithm are demonstrated through experiments on various objects in both indoor and outdoor environments. Moreover, real-time performance can be achieved with graphics processing unit acceleration.
This technical report introduces the Descartes Modeling Language (DML), a new architecture-level modeling language for modeling Quality-of-Service (QoS) and resource management related aspects of modern dynamic IT systems, infrastructures and services. DML is designed to serve as a basis for self-aware resource management during operation ensuring that system QoS requirements are continuously satisfied while infrastructure resources are utilized as efficiently as possible.
Today’s Internet architecture was not designed from scratch but was driven by new services that emerged during its development. Hence, it is often described as patchwork where additional patches are applied in case new services require modifications to the existing architecture. This process however is rather slow and hinders the development of innovative network services with certain architecture or network requirements. Currently discussed technologies like Software-Defined Networking (SDN) or Network Virtualization (NV) are seen as key enabling technologies to overcome this rigid best effort legacy of the Internet. Both technologies offer the possibility to create virtual networks that accommodate the specific needs of certain services. These logical networks are operated on top of a physical substrate and facilitate flexible network resource allocation as physical resources can be added and removed depending on the current network and load situation. In addition, the clear separation and isolation of networks foster the development of application-aware networks that fulfill the special requirements of emerging applications. A prominent use case that benefits from these extended capabilities of the network is denoted with service component mobility. Services hosted on Virtual Machines (VMs) follow their consuming mobile endpoints, so that access latency as well as consumed network resources are reduced. Especially for applications like video streaming, which consume a large fraction of the available resources, is this an important means to relieve the resource constraints and eventually provide better service quality. Service and endpoint mobility both allow an adaptation of the used paths between an offered service, i.e., video streaming and the consuming users in case the service quality drops due to network problems. To make evidence-based adaptations in case of quality drops, a scalable monitoring component is required that is able to monitor the service quality for video streaming applications with reliable accuracy. This monograph details challenges that arise when deploying a certain service, i.e., video streaming, in a future virtualized network architecture and discusses possible solutions. In particular, this work evaluates the performance of mechanisms enabling service mobility and presents an optimized architecture for service mobility. Concerning endpoint mobility, improvements are developed that reduce the latency between endpoints and consumed services and ensure connectivity regardless of the used mobile access network. In the last part, a network-based video quality monitoring solution is developed and its accuracy is evaluated.
In many cases, problems, data, or information can be modeled as graphs. Graphs can be used as a tool for modeling in any case where connections between distinguishable objects occur. Any graph consists of a set of objects, called vertices, and a set of connections, called edges, such that any edge connects a pair of vertices. For example, a social network can be modeled by a graph by
transforming the users of the network into vertices and friendship relations between users into edges. Also physical networks like computer networks or transportation networks, for example, the metro network of a city, can be seen as graphs.
For making graphs and, thereby, the data that is modeled, well-understandable for users, we need a visualization. Graph drawing deals with algorithms for visualizing graphs. In this thesis, especially the use of crossings and curves is investigated for graph drawing problems under additional constraints. The constraints that occur in the problems investigated in this thesis especially restrict the positions of (a part of) the vertices; this is done either as a hard constraint or as an optimization criterion.
With the introduction of OpenFlow by the Stanford University in 2008, a process began in the area of network research, which questions the predominant approach of fully distributed network control. OpenFlow is a communication protocol that allows the externalization of the network control plane from the network devices, such as a router, and to realize it as a logically-centralized entity in software. For this concept, the term "Software Defined Networking" (SDN) was coined during scientific discourse.
For the network operators, this concept has several advantages. The two most important can be summarized under the points cost savings and flexibility. Firstly, it is possible through the uniform interface for network hardware ("Southbound API"), as implemented by OpenFlow, to combine devices and software from different manufacturers, which increases the innovation and price pressure on them. Secondly, the realization of the network control plane as a freely programmable software with open interfaces ("Northbound API") provides the opportunity to adapt it to the individual circumstances of the operator's network and to exchange information with the applications it serves. This allows the network to be more flexible and to react more quickly to changing circumstances as well as transport the traffic more effectively and tailored to the user’s "Quality of Experience" (QoE).
The approach of a separate network control layer for packet-based networks is not new and has already been proposed several times in the past. Therefore, the SDN approach has raised many questions about its feasibility in terms of efficiency and applicability. These questions are caused to some extent by the fact that there is no generally accepted definition of the SDN concept to date. It is therefore a part of this thesis to derive such a definition. In addition, several of the open issues are investigated. This Investigations follow the three aspects: Performance Evaluation of Software Defined Networking, applications on the SDN control layer, and the usability of SDN Northbound-API for creation application-awareness in network operation.
Performance Evaluation of Software Defined Networking: The question of the efficiency of an SDN-based system was from the beginning one of the most important. In this thesis, experimental measurements of the performance of OpenFlow-enabled switch hardware and control software were conducted for the purpose of answering this question. The results of these measurements were used as input parameters for establishing an analytical model of the reactive SDN approach. Through the model it could be determined that the performance of the software control layer, often called "Controller", is crucial for the overall performance of the system, but that the approach is generally viable. Based on this finding a software for analyzing the performance of SDN controllers was developed. This software allows the emulation of the forwarding layer of an SDN network towards the control software and can thus determine its performance in different situations and configurations. The measurements with this software showed that there are quite significant differences in the behavior of different control software implementations. Among other things it has been shown that some show different characteristics for various switches, in particular in terms of message processing speed. Under certain circumstances this can lead to network failures.
Applications on the SDN control layer: The core piece of software defined networking are the intelligent network applications that operate on the control layer. However, their development is still in its infancy and little is known about the technical possibilities and their limitations. Therefore, the relationship between an SDN-based and classical implementation of a network function is investigated in this thesis. This function is the monitoring of network links and the traffic they carry. A typical approach for this task has been built based on Wiretapping and specialized measurement hardware and compared with an implementation based on OpenFlow switches and a special SDN control application. The results of the comparison show that the SDN version can compete in terms of measurement accuracy for bandwidth and delay estimation with the traditional measurement set-up. However, a compromise has to be found for measurements below the millisecond range.
Another question regarding the SDN control applications is whether and how well they can solve existing problems in networks. Two programs have been developed based on SDN in this thesis to solve two typical network issues. Firstly, the tool "IPOM", which enables considerably more flexibility in the study of effects of network structures for a researcher, who is confined to a fixed physical test network topology.
The second software provides an interface between the Cloud Orchestration Software "OpenNebula" and an OpenFlow controller. The purpose of this software was to investigate experimentally whether a pre-notification of the network of an impending relocation of a virtual service in a data center is sufficient to ensure the continuous operation of that service. This was demonstrated on the example of a video service.
Usability of the SDN Northbound API for creating application-awareness in network operation: Currently, the fact that the network and the applications that run on it are developed and operated separately leads to problems in network operation. SDN offers with the Northbound-API an open interface that enables the exchange between information of both worlds during operation. One aim of this thesis was to investigate whether this interface can be exploited so that the QoE experienced by the user can be maintained on high level. For this purpose, the QoE influence factors were determined on a challenging application by means of a subjective survey study. The application is cloud gaming, in which the calculation of video game environments takes place in the cloud and is transported via video over the network to the user. It was shown that apart from the most important factor influencing QoS, i.e., packet loss on the downlink, also the type of game type and its speed play a role. This demonstrates that in addition to QoS the application state is important and should be communicated to the network. Since an implementation of such a state conscious SDN for the example of Cloud Gaming was not possible due to its proprietary implementation, in this thesis the application “YouTube video streaming” was chosen as an alternative. For this application, status information is retrievable via the "Yomo" tool and can be used for network control. It was shown that an SDN-based implementation of an application-aware network has distinct advantages over traditional network management methods and the user quality can be obtained in spite of disturbances.
Routing is one of the most important issues in any communication network. It defines on which path packets are transmitted from the source of a connection to the destination. It allows to control the distribution of flows between different locations in the network and thereby is a means to influence the load distribution or to reach certain constraints imposed by particular applications. As failures in communication networks appear regularly and cannot be completely avoided, routing is required to be resilient against such outages, i.e., routing still has to be able to forward packets on backup paths even if primary paths are not working any more.
Throughout the years, various routing technologies have been introduced that are very different in their control structure, in their way of working, and in their ability to handle certain failure cases. Each of the different routing approaches opens up their own specific questions regarding configuration, optimization, and inclusion of resilience issues. This monograph investigates, with the example of three particular routing technologies, some concrete issues regarding the analysis and optimization of resilience. It thereby contributes to a better general, technology-independent understanding of these approaches and of their diverse potential for the use in future network architectures.
The first considered routing type, is decentralized intra-domain routing based on administrative IP link costs and the shortest path principle. Typical examples are common today's intra-domain routing protocols OSPF and IS-IS. This type of routing includes automatic restoration abilities in case of failures what makes it in general very robust even in the case of severe network outages including several failed components. Furthermore, special IP-Fast Reroute mechanisms allow for a faster reaction on outages. For routing based on link costs, traffic engineering, e.g. the optimization of the maximum relative link load in the network, can be done indirectly by changing the administrative link costs to adequate values.
The second considered routing type, MPLS-based routing, is based on the a priori configuration of primary and backup paths, so-called Label Switched Paths. The routing layout of MPLS paths offers more freedom compared to IP-based routing as it is not restricted by any shortest path constraints but any paths can be setup. However, this in general involves a higher configuration effort.
Finally, in the third considered routing type, typically centralized routing using a Software Defined Networking (SDN) architecture, simple switches only forward packets according to routing decisions made by centralized controller units. SDN-based routing layouts offer the same freedom as for explicit paths configured using MPLS. In case of a failure, new rules can be setup by the controllers to continue the routing in the reduced topology. However, new resilience issues arise caused by the centralized architecture. If controllers are not reachable anymore, the forwarding rules in the single nodes cannot be adapted anymore. This might render a rerouting in case of connection problems in severe failure scenarios infeasible.
Two studies are reported that investigate how readily accessible and applicable ten force-dynamic categories are to novices in describing short episodes of human-technology interaction (Study 1) and that establish a measure of inter-coder reliability when re-classifying these episodes into force-dynamic categories (Study 2). The results of the first study show that people can easily and confidently relate their experiences with technology to the definitions of force-dynamic events (e.g. “The driver released the handbrake” as an example of restraint removal). The results of the second study show moderate agreement between four expert coders across all ten force-dynamic categories (Cohen’s kappa = .59) when re-classifying these episodes. Agreement values for single force-dynamic categories ranged between ‘fair’ and ‘almost perfect’, i.e. between kappa = .30 and .95. Agreement with the originally intended classifications of study 1 was higher than the pure inter-coder reliabilities. Single coders achieved an average kappa of .71, indicating substantial agreement. Using more than one coder increased kappas to almost perfect: up to .87 for four coders. A qualitative analysis of the predicted versus the observed number of category confusions revealed that about half of the category disagreement could be predicted from strong overlaps in the definitions of force-dynamic categories. From the quantitative and qualitative results, guidelines are derived to aid the better training of coders in order to increase inter-coder reliability.
The work presents a performance evaluation and optimization of so-called overlay networks for content distribution in the Internet. Chapter 1 describes the importance which have such networks in today's Internet, for example, for the transmission of video content. The focus of this work is on overlay networks based on the peer-to-peer principle. These are characterized by the fact that users who download content, also contribute to the distribution process by sharing parts of the data to other users. This enables efficient content distribution because each user not only consumes resources in the system, but also provides its own resources. Chapter 2 of the monograph contains a detailed description of the functionality of today's most popular overlay network BitTorrent. It explains the various components and their interaction. This is followed by an illustration of why such overlay networks for Internet service providers (ISPs) are problematic. The reason lies in the large amount of inter-ISP traffic that is produced by these overlay networks. Since this inter-ISP traffic leads to high costs for ISPs, they try to reduce it by improved mechanisms for overlay networks. One optimization approach is the use of topology awareness within the overlay networks. It provides users of the overlay networks with information about the underlying physical network topology. This allows them to avoid inter-ISP traffic by exchanging data preferrentially with other users that are connected to the same ISP. Another approach to save inter-ISP traffic is caching. In this case the ISP provides additional computers in its network, called caches, which store copies of popular content. The users of this ISP can then obtain such content from the cache. This prevents that the content must be retrieved from locations outside of the ISP's network, and saves costly inter-ISP traffic in this way. In the third chapter of the thesis, the results of a comprehensive measurement study of overlay networks, which can be found in today's Internet, are presented. After a short description of the measurement methodology, the results of the measurements are described. These results contain data on a variety of characteristics of current P2P overlay networks in the Internet. These include the popularity of content, i.e., how many users are interested in specific content, the evolution of the popularity and the size of the files. The distribution of users within the Internet is investigated in detail. Special attention is given to the number of users that exchange a particular file within the same ISP. On the basis of these measurement results, an estimation of the traffic savings that can achieved by topology awareness is derived. This new estimation is of scientific and practical importance, since it is not limited to individual ISPs and files, but considers the whole Internet and the total amount of data exchanged in overlay networks. Finally, the characteristics of regional content are considered, in which the popularity is limited to certain parts of the Internet. This is for example the case of videos in German, Italian or French language. Chapter 4 of the thesis is devoted to the optimization of overlay networks for content distribution through caching. It presents a deterministic flow model that describes the influence of caches. On the basis of this model, it derives an estimate of the inter-ISP traffic that is generated by an overlay network, and which part can be saved by caches. The results show that the influence of the cache depends on the structure of the overlay networks, and that caches can also lead to an increase in inter-ISP traffic under certain circumstances. The described model is thus an important tool for ISPs to decide for which overlay networks caches are useful and to dimension them. Chapter 5 summarizes the content of the work and emphasizes the importance of the findings. In addition, it explains how the findings can be applied to the optimization of future overlay networks. Special attention is given to the growing importance of video-on-demand and real-time video transmissions.
The development of ICT infrastructures has facilitated the emergence of new paradigms for looking at society and the environment over the last few years. Participatory environmental sensing, i.e. directly involving citizens in environmental monitoring, is one example, which is hoped to encourage learning and enhance awareness of environmental issues. In this paper, an analysis of the behaviour of individuals involved in noise sensing is presented. Citizens have been involved in noise measuring activities through the WideNoise smartphone application. This application has been designed to record both objective (noise samples) and subjective (opinions, feelings) data. The application has been open to be used freely by anyone and has been widely employed worldwide. In addition, several test cases have been organised in European countries. Based on the information submitted by users, an analysis of emerging awareness and learning is performed. The data show that changes in the way the environment is perceived after repeated usage of the application do appear. Specifically, users learn how to recognise different noise levels they are exposed to. Additionally, the subjective data collected indicate an increased user involvement in time and a categorisation effect between pleasant and less pleasant environments.
Background: Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed.
Results: (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones).
Conclusions: Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior.
The present paper compares the effect of different waypoint parameters on the flight performance of a special autonomous indoor UAV (unmanned aerial vehicle) fusing ultrasonic, inertial, pressure and optical sensors for 3D positioning and controlling. The investigated parameters are the acceptance threshold for reaching a waypoint as well as the maximal waypoint step size or block size. The effect of these parameters on the flight time and accuracy of the flight path is investigated. Therefore the paper addresses how the acceptance threshold and step size influence the speed and accuracy of the autonomous flight and thus influence the performance of the presented autonomous quadrocopter under real indoor navigation circumstances.
Furthermore the paper demonstrates a drawback of the standard potential field method for navigation of such autonomous quadrocopters and points to an improvement.
A procedure to control all six DOF (degrees of freedom) of a UAV (unmanned aerial vehicle) without an external reference system and to enable fully autonomous flight is presented here. For 2D positioning the principle of optical flow is used. Together with the output of height estimation, fusing ultrasonic, infrared and inertial and pressure sensor data, the 3D position of the UAV can be computed, controlled and steered. All data processing is done on the UAV. An external computer with a pathway planning interface is for commanding purposes only. The presented system is part of the AQopterI8 project, which aims to develop an autonomous flying quadrocopter for indoor application. The focus of this paper is 2D positioning using an optical flow sensor. As a result of the performed evaluation, it can be concluded that for position hold, the standard deviation of the position error is 10cm and after landing the position error is about 30cm.
Radiation therapy today, on account of improvements in treatment procedures over the last 60 years, allows precise treatment of static tumors inside the human body. However, irradiation of moving tumors is still a challenging task as moving tumors often leave the treatment beam and the radiation dose delivered to the tumor reduces simultaneously increasing that on healthy tissue. This research work aims to push the frontiers of radiation therapy in order to enable precise treatment of moving tumors with focus on research and development of a unique real-time system enabling active motion compensation through robotic means to compensate tumor motion. During treatment, patients lie on a treatment couch which is normally used for static position corrections of patient set-up errors prior to radiation treatment. The treatment couch used, called HexaPOD, is a parallel manipulator with six degrees of freedom which can precisely position heavy loads inside a small region. Despite the HexaPOD not initially built with dynamics in mind, it is used in this work for sustained motion compensation by moving patients such that tumors stay precisely located at the center of the treatment beam during the complete course of treatment. In order to realize real-time tumor motion compensation by means of the HexaPOD, several challanges need to be addressed. Real-time aspects are covered by the adoption of a hard real-time operation system in combination with measurement and estimation of latencies of all physical quantities in the compensation system such as tumor or breathing position measurements. Accurate timing information is respected consistently in the whole system and all software-induced latencies are adaptively compensated for. This requires knowledge of future tumor positions from predictors. Several predictors for breathing and tumor motion predictions are proposed and evaluated in terms of a variety of different performance metrics. Extensions to prediction algorithms are introduced fusing both breathing and tumor position information to allow for predictions without the need of an explicit correlation model. Predictions determine the future motion path of the HexaPOD in order to compensate for tumor motion. Several control schemes are developed to enable reference tracking for the HexaPOD. Based on linear and non-linear dynamic modelling of the HexaPOD with system identification methods, a first controller is derived in the form of a model predictive controller. A second controller is proposed based on an assumption of the working principle of the HexaPOD's internal controller. Finally, a third controller is derived as combination of the first and second one. For each of these controllers, comparative results with real hardware experiments and humans in the loop as well as choices of free parameters are presented and discussed. Apart from precise tracking, emphasis is placed on patient comfort which is of crucial importance for acceptance of the system. It is demonstrated that smooth trajectories can be realized by the controllers to guarantee that patients feel comfortable while their tumor motion is compensated at sub-millimeter accuracies. Overall errors of the system are analyzed by relating them to tracking and prediction errors. By exploiting the properties of different predictors, it is shown that the startup time until tracking is reached can be reduced to only a few seconds, even in the case of an initially at-rest HexaPOD and with no initial knowledge of tumor motion. This makes the system especially suitable for the relatively short-fractionated treatment sessions for lung tumors. The tumor motion compensation system has been developed solely based on standard clinical hardware, found in most treatment rooms. With a simple and flexible design, existing treatment can be updated in a cost-efficient way to introduce motion compensation capabilities. Simultaneously, the system does not impose any constraints on state-of-the-art treatment types such as intensity modulated radiotherapy or volumetric modulated arc therapy. Supporting different compensation modes, the system can be applied to any moving tumor whether its motion is predictable (lung tumors) or unpredictable (prostate tumors). By integration of adequate tumor position determination methods, the system can be easily extended to other tumors as well.
This work takes a close look at several quite different research areas related to the design of networked embedded sensor/actuator systems. The variety of the topics illustrates the potential complexity of current sensor network applications; especially when enriched with actuators for proactivity and environmental interaction. Besides their conception, development, installation and long-term operation, we'll mainly focus on more "low-level" aspects: Compositional hardware and software design, task cooperation and collaboration, memory management, and real-time operation will be addressed from a local node perspective. In contrast, inter-node synchronization, communication, as well as sensor data acquisition, aggregation, and fusion will be discussed from a rather global network view. The diversity in the concepts was intentionally accepted to finally facilitate the reliable implementation of truly complex systems. In particular, these should go beyond the usual "sense and transmit of sensor data", but show how powerful today's networked sensor/actuator systems can be despite of their low computational performance and constrained hardware: If their resources are only coordinated efficiently!
Die Entwicklung eines wissensbasierten Systems, speziell eines Diagnosesystems, ist eine Teildisziplin der künstlichen Intelligenz und angewandten Informatik. Im Laufe der Forschung auf diesem Gebiet wurden verschiedene Lösungsansätze mit unterschiedlichem Erfolg bei der Anwendung in der Kraftfahrzeugdiagnose entwickelt. Diagnosesysteme in Vertragswerkstätten, das heißt in Fahrzeughersteller gebundenen Werkstätten, wenden hauptsächlich die fallbasierte Diagnostik an. Zum einen hält sich hier die Fahrzeugvielfalt in Grenzen und zum anderen besteht eine Meldepflicht bei neuen, nicht im System vorhandenen Fällen. Die freien Werkstätten verfügen nicht über eine solche Datenbank. Somit ist der fallbasierte Ansatz schwer umsetzbar. In freien Werkstätten - Fahrzeughersteller unabhängigen Werkstätten - basiert die Fehlersuche hauptsächlich auf Fehlerbäumen. Wegen der wachsenden Fahrzeugkomplexität, welche wesentlich durch die stark zunehmende Anzahl der durch mechatronische Systeme realisierten Funktionen bedingt ist, und der steigenden Typenvielfalt ist die geführte Fehlersuche in freien Werkstätten nicht immer zielführend. Um die Unterstützung des Personals von freien Werkstätten bei der zukünftigen Fehlersuche zu gewährleisten, werden neue Generationen von herstellerunabhängigen Diagnosetools benötigt, die die Probleme der Variantenvielfalt und Komplexität lösen. In der vorliegenden Arbeit wird ein Lösungsansatz vorgestellt, der einen qualitativen, modellbasierten Diagnoseansatz mit einem auf heuristischem Diagnosewissen basierenden Ansatz vereint. Neben der Grundlage zur Wissenserhebung werden in dieser Arbeit die theoretische Grundlage zur Beherrschung der Variantenvielfalt sowie die Tests für die erstellten Diagnosemodelle behandelt. Die Diagnose ist symptombasiert und die Inferenzmechanismen zur Verarbeitung des Diagnosewissens sind eine Kombination aus Propagierung der abweichenden physikalischen Größen im Modell und der Auswertung des heuristischen Wissens. Des Weiteren werden in dieser Arbeit verschiedene Aspekte der Realisierung der entwickelten theoretischen Grundlagen dargestellt, zum Beispiel: Systemarchitektur, Wissenserhebungsprozess, Ablauf des Diagnosevorgangs in den Werkstätten. Die Evaluierung der entwickelten Lösung bei der Wissenserhebung in Form von Modellerstellungen und Modellierungsworkshops sowie Feldtests dient nicht nur zur Bestätigung des entwickelten Ansatzes, sondern auch zur Ideenfindung für die Integration der entwickelten Tools in die existierende IT-Infrastruktur.
Internet applications are becoming more and more flexible to support diverge user demands and network conditions. This is reflected by technical concepts, which provide new adaptation mechanisms to allow fine grained adjustment of the application quality and the corresponding bandwidth requirements. For the case of video streaming, the scalable video codec H.264/SVC allows the flexible adaptation of frame rate, video resolution and image quality with respect to the available network resources. In order to guarantee a good user-perceived quality (Quality of Experience, QoE) it is necessary to adjust and optimize the video quality accurately. But not only have the applications of the current Internet changed. Within network and transport, new technologies evolved during the last years providing a more flexible and efficient usage of data transport and network resources. One of the most promising technologies is Network Virtualization (NV) which is seen as an enabler to overcome the ossification of the Internet stack. It provides means to simultaneously operate multiple logical networks which allow for example application-specific addressing, naming and routing, or their individual resource management. New transport mechanisms like multipath transmission on the network and transport layer aim at an efficient usage of available transport resources. However, the simultaneous transmission of data via heterogeneous transport paths and communication technologies inevitably introduces packet reordering. Additional mechanisms and buffers are required to restore the correct packet order and thus to prevent a disturbance of the data transport. A proper buffer dimensioning as well as the classification of the impact of varying path characteristics like bandwidth and delay require appropriate evaluation methods. Additionally, for a path selection mechanism real time evaluation mechanisms are needed. A better application-network interaction and the corresponding exchange of information enable an efficient adaptation of the application to the network conditions and vice versa. This PhD thesis analyzes a video streaming architecture utilizing multipath transmission and scalable video coding and develops the following optimization possibilities and results: Analysis and dimensioning methods for multipath transmission, quantification of the adaptation possibilities to the current network conditions with respect to the QoE for H.264/SVC, and evaluation and optimization of a future video streaming architecture, which allows a better interaction of application and network.
Consider the situation where two or more images are taken from the same object. After taking the first image, the object is moved or rotated so that the second recording depicts it in a different manner. Additionally, take heed of the possibility that the imaging techniques may have also been changed. One of the main problems in image processing is to determine the spatial relation between such images. The corresponding process of finding the spatial alignment is called “registration”. In this work, we study the optimization problem which corresponds to the registration task. Especially, we exploit the Lie group structure of the set of transformations to construct efficient, intrinsic algorithms. We also apply the algorithms to medical registration tasks. However, the methods developed are not restricted to the field of medical image processing. We also have a closer look at more general forms of optimization problems and show connections to related tasks.
In this research, an attempt to create a knowledge-based learning system for the Quranic text has been performed. The knowledge base is made up of the Quranic text along with detailed information about each chapter and verse, and some rules. The system offers the possibility to study the Quran through web-based interfaces, implementing novel visualization techniques for browsing, querying, consulting, and testing the acquired knowledge. Additionally the system possesses knowledge acquisition facilities for maintaining the knowledge base.
To jointly provide different services/technologies, like IP and Ethernet or IP and SDH/SONET, in a single network, equipment of multiple technologies needs to be deployed to the sites/Points of Presence (PoP) and interconnected with each other. Therein, a technology may provide transport functionality to other technologies and increase the number of available resources by using multiplexing techniques. By providing its own switching functionality, each technology creates connections in a logical layer which leads to the notion of multi-layer networks. The design of such networks comprises the deployment and interconnection of components to suit to given traffic demands. To prevent traffic loss due to failures of networking equipment, protection mechanisms need to be established. In multi-layer networks, protection usually can be applied in any of the considered layers. In turn, the hierarchical structure of multi-layer networks also bears shared risk groups (SRG). To achieve a cost-optimal resilient network, an appropriate combination of multiplexing techniques, technologies, and their interconnections needs to be found. Thus, network design is a combinatorial problem with a large parameter and solution space. After the design stage, the resources of a multi-layer network can be provided to traffic demands. Especially, dynamic capacity provisioning requires interaction of sites and layers, as well as accurate retrieval of constraint information. In recent years, generalized multiprotocol label switching (GMPLS) and path computation elements (PCE) have emerged as possible approaches for these challenges. Like the design, the provisioning of multi-layer networks comprises a variety of optimization parameters, like blocking probability, resilience, and energy efficiency. In this work, we introduce several efficient heuristics to approach the considered optimization problems. We perform capital expenditure (CAPEX)-aware design of multi-layer networks from scratch, based on IST NOBEL phase 2 project's cost and equipment data. We comprise traffic and resilience requirements in different and multiple layers as well as different network architectures. On top of the designed networks, we consider the dynamic provisioning of multi-layer traffic based on the GMPLS and PCE architecture. We evaluate different PCE deployments, information retrieval strategies, and re-optimization. Finally, we show how information about provisioning utilization can be used to provide a feedback for network design.
BACKGROUND: In the face of growing resistance in malaria parasites to drugs, pharmacological combination therapies are important. There is accumulating evidence that methylene blue (MB) is an effective drug against malaria. Here we explore the biological effects of both MB alone and in combination therapy using modeling and experimental data.
RESULTS: We built a model of the central metabolic pathways in P. falciparum. Metabolic flux modes and their changes under MB were calculated by integrating experimental data (RT-PCR data on mRNAs for redox enzymes) as constraints and results from the YANA software package for metabolic pathway calculations. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, chloroquine resistance based on pfmdr/and pfcrt transporters, as well as pyrimethamine/sulfadoxine resistance (by mutations in DHF/DHPS), were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs.
CONCLUSIONS: Theoretical and experimental results support that methylene blue should, because of its resistance-breaking potential, be further tested as a key component in drug combination therapy efforts in holoendemic areas.
Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases.
The ITS2 Database
(2012)
The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation.
The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold.
The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure.
In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.
A binary tanglegram is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential that both trees are drawn without edge crossings and that the inter-tree edges have as few crossings as possible. It is known that finding a tanglegram with the minimum number of crossings is NP-hard and that the problem is fixed-parameter tractable with respect to that number.
We prove that under the Unique Games Conjecture there is no constant-factor approximation for binary trees. We show that the problem is NP-hard even if both trees are complete binary trees. For this case we give an O(n 3)-time 2-approximation and a new, simple fixed-parameter algorithm. We show that the maximization version of the dual problem for binary trees can be reduced to a version of MaxCut for which the algorithm of Goemans and Williamson yields a 0.878-approximation.
Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer.
Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
Background: Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions.
Methodology/Principal Findings: We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. Overall, the pattern of gene expression strongly suggests that the response of the aged rat brain is qualitatively rather than quantitatively different from the young, i.e. the total number of regulated genes is comparable in the two age groups, but the aged rats had great difficulty in mounting a timely response to stroke. Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. New therapeutic options in aged rats may also include Calcrl, Cyp11b1, Prcp, Cebpa, Cfd, Gpnmb, Fcgr2b, Fcgr3a, Tnfrsf26, Adam 17 and Mmp14. An unexpected target is the enzyme 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 in aged rats, a key enzyme in the cholesterol synthesis pathway. Post-stroke axonal growth was compromised in both age groups.
Conclusion/Significance: We suggest that a multi-stage, multimodal treatment in aged animals may be more likely to produce positive results. Such a therapeutic approach should be focused on tissue restoration but should also address other aspects of patient post-stroke therapy such as neuropathic syndrome, stress, anxiety disorders, depression, neurotransmission and blood pressure.
Cover contact graphs
(2012)
We study problems that arise in the context of covering certain geometric objects called seeds (e.g., points or disks) by a set of other geometric objects called cover (e.g., a set of disks or homothetic triangles). We insist that the interiors of the seeds and the cover elements are pairwise disjoint, respectively, but they can touch. We call the contact graph of a cover a cover contact graph (CCG). We are interested in three types of tasks, both in the general case and in the special case of seeds on a line: (a) deciding whether a given seed set has a connected CCG, (b) deciding whether a given graph has a realization as a CCG on a given seed set, and (c) bounding the sizes of certain classes of CCG’s. Concerning (a) we give efficient algorithms for the case that seeds are points and show that the problem becomes hard if seeds and covers are disks. Concerning (b) we show that this problem is hard even for point seeds and disk covers (given a fixed correspondence between graph vertices and seeds). Concerning (c) we obtain upper and lower bounds on the number of CCG’s for point seeds.
In this paper we study connectivity augmentation problems. Given a connected graph G with some desirable property, we want to make G 2-vertex connected (or 2-edge connected) by adding edges such that the resulting graph keeps the property. The aim is to add as few edges as possible. The property that we consider is planarity, both in an abstract graph-theoretic and in a geometric setting, where vertices correspond to points in the plane and edges to straight-line segments.
We show that it is NP-hard to nd a minimum-cardinality augmentation that makes a planar graph 2-edge connected. For making a planar graph 2-vertex connected this was known. We further show that both problems are hard in the geometric setting, even when restricted to trees. The problems remain hard for higher degrees of connectivity. On the other hand we give polynomial-time algorithms for the special case of convex geometric graphs.
We also study the following related problem. Given a planar (plane geometric) graph G, two vertices s and t of G, and an integer c, how many edges have to be added to G such that G is still planar (plane geometric) and contains c edge- (or vertex-) disjoint s{t paths? For the planar case we give a linear-time algorithm for c = 2. For the plane geometric case we give optimal worst-case bounds for c = 2; for c = 3 we characterize the cases that have a solution.
Background:
Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.
Methodology/Principal Findings:
Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.
Conclusions/Significance:
Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.
Practical optimization problems often comprise several incomparable and conflicting objectives. When booking a trip using several means of transport, for instance, it should be fast and at the same time not too expensive. The first part of this thesis is concerned with the algorithmic solvability of such multiobjective optimization problems. Several solution notions are discussed and compared with respect to their difficulty. Interestingly, these solution notions are always equally difficulty for a single-objective problem and they differ considerably already for two objectives (unless P = NP). In this context, the difference between search and decision problems is also investigated in general. Furthermore, new and improved approximation algorithms for several variants of the traveling salesperson problem are presented. Using tools from discrepancy theory, a general technique is developed that helps to avoid an obstacle that is often hindering in multiobjective approximation: The problem of combining two solutions such that the new solution is balanced in all objectives and also mostly retains the structure of the original solutions. The second part of this thesis is dedicated to several aspects of systems of equations for (formal) languages. Firstly, conjunctive and Boolean grammars are studied, which are extensions of context-free grammars by explicit intersection and complementation operations, respectively. Among other results, it is shown that one can considerably restrict the union operation on conjunctive grammars without changing the generated language. Secondly, certain circuits are investigated whose gates do not compute Boolean values but sets of natural numbers. For these circuits, the equivalence problem is studied, i.\,e.\ the problem of deciding whether two given circuits compute the same set or not. It is shown that, depending on the allowed types of gates, this problem is complete for several different complexity classes and can thus be seen as a parametrized) representative for all those classes.
In the future Internet, the people-centric communication paradigm will be complemented by a ubiquitous communication among people and devices, or even a communication between devices. This comes along with the need for a more flexible, cheap, widely available Internet access. Two types of wireless networks are considered most appropriate for attaining those goals. While wireless sensor networks (WSNs) enhance the Internet’s reach by providing data about the properties of the environment, wireless mesh networks (WMNs) extend the Internet access possibilities beyond the wired backbone. This monograph contains four chapters which present modeling and optimization methods for WSNs and WMNs. Minimizing energy consumptions is the most important goal of WSN optimization and the literature consequently provides countless energy consumption models. The first part of the monograph studies to what extent the used energy consumption model influences the outcome of analytical WSN optimizations. These considerations enable the second contribution, namely overcoming the problems on the way to a standardized energy-efficient WSN communication stack based on IEEE 802.15.4 and ZigBee. For WMNs both problems are of minor interest whereas the network performance has a higher weight. The third part of the work, therefore, presents algorithms for calculating the max-min fair network throughput in WMNs with multiple link rates and Internet gateway. The last contribution of the monograph investigates the impact of the LRA concept which proposes to systematically assign more robust link rates than actually necessary, thereby allowing to exploit the trade-off between spatial reuse and per-link throughput. A systematical study shows that a network-wide slightly more conservative LRA than necessary increases the throughput of a WMN where max-min fairness is guaranteed. It moreover turns out that LRA is suitable for increasing the performance of a contention-based WMN and is a valuable optimization tool.
The field of small satellite formations and constellations attracted growing attention, based on recent advances in small satellite engineering. The utilization of distributed space systems allows the realization of innovative applications and will enable improved temporal and spatial resolution in observation scenarios. On the other side, this new paradigm imposes a variety of research challenges. In this monograph new networking concepts for space missions are presented, using networks of ground stations. The developed approaches combine ground station resources in a coordinated way to achieve more robust and efficient communication links. Within this thesis, the following topics were elaborated to improve the performance in distributed space missions: Appropriate scheduling of contact windows in a distributed ground system is a necessary process to avoid low utilization of ground stations. The theoretical basis for the novel concept of redundant scheduling was elaborated in detail. Additionally to the presented algorithm was a scheduling system implemented, its performance was tested extensively with real world scheduling problems. In the scope of data management, a system was developed which autonomously synchronizes data frames in ground station networks and uses this information to detect and correct transmission errors. The system was validated with hardware in the loop experiments, demonstrating the benefits of the developed approach.
Given a collection of diverging documents about some lost original text, any person interested in the text would try reconstructing it from the diverging documents. Whether it is eclecticism, stemmatics, or copy-text, one is expected to explicitly or indirectly select one of the documents as a starting point or as a base text, which could be emended through comparison with remaining documents, so that a text that could be designated as the original document is generated. Unfortunately the process of giving priority to one of the documents also known as witnesses is a subjective approach. In fact even Cladistics, which could be considered as a computer-based approach of implementing stemmatics, does not present or recommend users to select a certain witness as a starting point for the process of reconstructing the original document. In this study, a computational method using a rule-based Bayesian classifier is used, to assist text scholars in their attempts of reconstructing a non-existing document from some available witnesses. The method developed in this study consists of selecting a base text successively and collating it with remaining documents. Each completed collation cycle stores the selected base text and its closest witness, along with a weighted score of their similarities and differences. At the end of the collation process, a witness selected more often by majority of base texts is considered as the probable base text of the collection. Witnesses’ scores are weighted using a weighting system, based on effects of types of textual modifications on the process of reconstructing original documents. Users have the possibility to select between baseless and base text collation. If a base text is selected, the task is reduced to ranking the witnesses with respect to the base text, otherwise a base text as well as ranking of the witnesses with respect to the base text are computed and displayed on a histogram.
Learning a book in general involves reading it, underlining important words, adding comments, summarizing some passages, and marking up some text or concepts. Once deeper understanding is achieved, one would like to organize and manage her/his knowledge in such a way that, it could be easily remembered and efficiently transmitted to others. In this paper, books organized in terms of chapters consisting of verses, are considered as the source of knowledge to be modeled. The knowledge model consists of verses with their metadata and semantic annotations. The metadata represent the multiple perspectives of knowledge modeling. Verses with their metadata and annotations form a meta-model, which will be published on a web Mashup. The meta-model with linking between its elements constitute a knowledge base. An XML-based annotation system breaking down the learning process into specific tasks, helps constructing the desired meta-model. The system is made up of user interfaces for creating metadata, annotating chapters’ contents according to user selected semantics, and templates for publishing the generated knowledge on the Internet. The proposed software system improves comprehension and retention of knowledge contained in religious texts through modeling and visualization. The system has been applied to the Quran, and the result obtained shows that multiple perspectives of information modeling can be successfully applied to religious texts. It is expected that this short ongoing study would motivate others to engage in devising and offering software systems for cross-religions learning.
Design and Implementation of Architectures for Interactive Textual Documents Collation Systems
(2011)
One of the main purposes of textual documents collation is to identify a base text or closest witness to the base text, by analyzing and interpreting differences also known as types of changes that might exist between those documents. Based on this fact, it is reasonable to argue that, explicit identification of types of changes such as deletions, additions, transpositions, and mutations should be part of the collation process. The identification could be carried out by an interpretation module after alignment has taken place. Unfortunately existing collation software such as CollateX1 and Juxta2’s collation engine do not have interpretation modules. In fact they implement the Gothenburg model [1] for collation process which does not include an interpretation unit. Currently both CollateX and Juxta’s collation engine do not distinguish in their critical apparatus between the types of changes, and do not offer statistics about those changes. This paper presents a model for both integrated and distributed collation processes that improves the Gothenburg model. The model introduces an interpretation component for computing and distinguishing between the types of changes that documents could have undergone. Moreover two architectures implementing the model in order to solve the problem of interactive collation are discussed as well. Each architecture uses CollateX library, and provides on the one hand preprocessing functions for transforming input documents into CollateX input format, and on the other hand a post-processing module for enabling interactive collation. Finally simple algorithms for distinguishing between types of changes, and linking collated source documents with the collation results are also introduced.
The Quran is the holy book of Islam consisting of 6236 verses divided into 114 chapters called suras. Many verses are similar and even identical. Searching for similar texts (e.g verses) could return thousands of verses, that when displayed completely or partly as textual list would make analysis and understanding difficult and confusing. Moreover it would be visually impossible to instantly figure out the overall distribution of the retrieved verses in the Quran. As consequence reading and analyzing the verses would be tedious and unintuitive. In this study a combination of interactive scatter plots and tables has been developed to assist analysis and understanding of the search result. Retrieved verses are clustered by chapters, and a weight is assigned to each cluster according to number of verses it contains, so that users could visually identify most relevant areas, and figure out the places of revelation of the verses. Users visualize the complete result and can select a region of the plot to zoom in, click on a marker to display a table containing verses with English translation side by side.
A Knowledge-based Hybrid Statistical Classifier for Reconstructing the Chronology of the Quran
(2011)
Computationally categorizing Quran’s chapters has been mainly confined to the determination of chapters’ revelation places. However this broad classification is not sufficient to effectively and thoroughly understand and interpret the Quran. The chronology of revelation would not only improve comprehending the philosophy of Islam, but also the easiness of implementing and memorizing its laws and recommendations. This paper attempts estimating possible chapters’ dates of revelation through their lexical frequency profiles. A hybrid statistical classifier consisting of stemming and clustering algorithms for comparing lexical frequency profiles of chapters, and deriving dates of revelation has been developed. The classifier is trained using some chapters with known dates of revelation. Then it classifies chapters with uncertain dates of revelation by computing their proximity to the training ones. The results reported here indicate that the proposed methodology yields usable results in estimating dates of revelation of the Quran’s chapters based on their lexical contents.
This paper discusses the categorization of Quranic chapters by major phases of Prophet Mohammad’s messengership using machine learning algorithms. First, the chapters were categorized by places of revelation using Support Vector Machine and naïve Bayesian classifiers separately, and their results were compared to each other, as well as to the existing traditional Islamic and western orientalists classifications. The chapters were categorized into Meccan (revealed in Mecca) and Medinan (revealed in Medina). After that, chapters of each category were clustered using a kind of fuzzy-single linkage clustering approach, in order to correspond to the major phases of Prophet Mohammad’s life. The major phases of the Prophet’s life were manually derived from the Quranic text, as well as from the secondary Islamic literature e.g hadiths, exegesis. Previous studies on computing the places of revelation of Quranic chapters relied heavily on features extracted from existing background knowledge of the chapters. For instance, it is known that Meccan chapters contain mostly verses about faith and related problems, while Medinan ones encompass verses dealing with social issues, battles…etc. These features are by themselves insufficient as a basis for assigning the chapters to their respective places of revelation. In fact, there are exceptions, since some chapters do contain both Meccan and Medinan features. In this study, features of each category were automatically created from very few chapters, whose places of revelation have been determined through identification of historical facts and events such as battles, migration to Medina…etc. Chapters having unanimously agreed places of revelation were used as the initial training set, while the remaining chapters formed the testing set. The classification process was made recursive by regularly augmenting the training set with correctly classified chapters, in order to classify the whole testing set. Each chapter was preprocessed by removing unimportant words, stemming, and representation with vector space model. The result of this study shows that, the two classifiers have produced useable results, with an outperformance of the support vector machine classifier. This study indicates that, the proposed methodology yields encouraging results for arranging Quranic chapters by phases of Prophet Mohammad’s messengership.
Currently, we observe a strong growth of services and applications, which use the Internet for data transport. However, the network requirements of these applications differ significantly. This makes network management difficult, since it complicated to separate network flows into application classes without inspecting application layer data. Network virtualization is a promising solution to this problem. It enables running different virtual network on the same physical substrate. Separating networks based on the service supported within allows controlling each network according to the specific needs of the application. The aim of such a network control is to optimize the user perceived quality as well as the cost efficiency of the data transport. Furthermore, network virtualization abstracts the network functionality from the underlying implementation and facilitates the split of the currently tightly integrated roles of Internet Service Provider and network owner. Additionally, network virtualization guarantees that different virtual networks run on the same physical substrate do not interfere with each other. This thesis discusses different aspects of the network virtualization topic. It is focused on how to manage and control a virtual network to guarantee the best Quality of Experience for the user. Therefore, a top-down approach is chosen. Starting with use cases of virtual networks, a possible architecture is derived and current implementation options based on hardware virtualization are explored. In the following, this thesis focuses on assessing the Quality of Experience perceived by the user and how it can be optimized on application layer. Furthermore, options for measuring and monitoring significant network parameters of virtual networks are considered.
Computing Generic Causes of Revelation of the Quranic Verses Using Machine Learning Techniques
(2011)
Because many verses of the holy Quran are similar, there is high probability that, similar verses addressing same issues share same generic causes of revelation. In this study, machine learning techniques have been employed in order to automatically derive causes of revelation of Quranic verses. The derivation of the causes of revelation is viewed as a classification problem. Initially the categories are based on the verses with known causes of revelation, and the testing set consists of the remaining verses. Based on a computed threshold value, a naïve Bayesian classifier is used to categorize some verses. After that, using a decision tree classifier the remaining uncategorized verses are separated into verses that contain indicators (resultative connectors, causative expressions…), and those that do not. As for those verses having indicators, each one is segmented into its constituent clauses by identification of the linking indicators. Then a dominant clause is extracted and considered either as the cause of revelation, or post-processed by adding or subtracting some terms to form a causal clause that constitutes the cause of revelation. Concerning remaining unclassified verses without indicators, a naive Bayesian classifier is again used to assign each one of them to one of the existing classes based on features and topics similarity. As for verses that could not be classified so far, manual classification was made by considering each verse as a category on its own. The result obtained in this study is encouraging, and shows that automatic derivation of Quranic verses’ generic causes of revelation is achievable, and reasonably reliable for understanding and implementing the teachings of the Quran.
Learning a book in general involves reading it, underlining important words, adding comments, summarizing some passages, and marking up some text or concepts. Once deeper understanding is achieved, one would like to organize and manage her/his knowledge in such a way that, it could be easily remembered and efficiently transmitted to others. This paper discusses about modeling religious texts using semantic XML markup based on frame-based knowledge representation, with the purpose of assisting understanding, retention, and sharing of knowledge they contain. In this study, books organized in terms of chapters made up of verses are considered as the source of knowledge to model. Some metadata representing the multiple perspectives of knowledge modeling are assigned to each chapter and verse. Chapters and verses with their metadata form a meta-model, which is represented using frames, and published on a web mashup. An XML-based annotation and visualization system equipped with user interfaces for creating static and dynamic metadata, annotating chapters’ contents according to user selected semantics, and templates for publishing generated knowledge on the Internet, has been developed. The system has been applied to the Quran, and the result obtained shows that multiple perspectives of information modeling can be successfully applied to religious texts, in order to support analysis, understanding, and retention of the texts.
Given a collection of diverging documents about some lost original text, any person interested in the text would try reconstructing it from the diverging documents. Whether it is eclecticism, stemmatics, or copy-text, one is expected to explicitly or indirectly select one of the documents as a starting point or as a base text, which could be emended through comparison with remaining documents, so that a text that could be designated as the original document is generated. Unfortunately the process of giving priority to one of the documents also known as witnesses is a subjective approach. In fact even Cladistics, which could be considered as a computer-based approach of implementing stemmatics, does not present or recommend users to select a certain witness as a starting point for the process of reconstructing the original document. In this study, a computational method using a rule-based Bayesian classifier is used, to assist text scholars in their attempts of reconstructing a non-existing document from some available witnesses. The method developed in this study consists of selecting a base text successively and collating it with remaining documents. Each completed collation cycle stores the selected base text and its closest witness, along with a weighted score of their similarities and differences. At the end of the collation process, a witness selected more often by majority of base texts is considered as the probable base text of the collection. Witnesses’ scores are weighted using a weighting system, based on effects of types of textual modifications on the process of reconstructing original documents. Users have the possibility to select between baseless and base text collation. If a base text is selected, the task is reduced to ranking the witnesses with respect to the base text, otherwise a base text as well as ranking of the witnesses with respect to the base text are computed and displayed on a bar diagram. Additionally this study includes a recursive algorithm for automatically reconstructing the original text from the identified base text and ranked witnesses.
The question of why the Quran structure does not follow its chronology of revelation is a recurring one. Some Islamic scholars such as [1] have answered the question using hadiths, as well as other philosophical reasons based on internal evidences of the Quran itself. Unfortunately till today many are still wondering about this issue. Muslims believe that the Quran is a summary and a copy of the content of a preserved tablet called Lawhul-Mahfuz located in the heaven. Logically speaking, this suggests that the arrangement of the verses and chapters is expected to be similar to that of the Lawhul-Mahfuz. As for the arrangement of the verses in each chapter, there is unanimity that it was carried out by the Prophet himself under the guidance of Angel Gabriel with the recommendation of God. But concerning the ordering of the chapters, there are reports about some divergences [3] among the Prophet’s companions as to which chapter should precede which one. This paper argues that Quranic chapters might have been arranged according to months and seasons of revelation. In fact, based on some verses of the Quran, it is defendable that the Lawhul-Mahfuz itself is understood to have been structured in terms of the months of the year. In this study, philosophical and mathematical arguments for computing chapters’ months of revelation are discussed, and the result is displayed on an interactive scatter plot.
Der große Vorteil eines q-Gramm Indexes liegt darin, dass es möglich ist beliebige Zeichenketten in einer Dokumentensammlung zu suchen. Ein Nachteil jedoch liegt darin, dass bei größer werdenden Datenmengen dieser Index dazu neigt, sehr groß zu werden, was mit einem deutlichem Leistungsabfall verbunden ist. In dieser Arbeit wird eine neuartige Technik vorgestellt, die die Leistung eines q-Gramm Indexes mithilfe zusätzlicher M-Matrizen für jedes q-Gramm und durch die Kombination mit einem invertierten Index erhöht. Eine M-Matrix ist eine Bit-Matrix, die Informationen über die Positionen eines q-Gramms enthält. Auch bei der Kombination von zwei oder mehreren Q-Grammen bieten diese M-Matrizen Informationen über die Positionen der Kombination. Dies kann verwendet werden, um die Komplexität der Zusammenführung der q-Gramm Trefferlisten für eine gegebene Suchanfrage zu reduzieren und verbessert die Leistung des n-Gramm-invertierten Index. Die Kombination mit einem termbasierten invertierten Index beschleunigt die durchschnittliche Suchzeit zusätzlich und vereint die Vorteile beider Index-Formate. Redundante Informationen werden in dem q-Gramm Index reduziert und weitere Funktionalität hinzugefügt, wie z.B. die Bewertung von Treffern nach Relevanz, die Möglichkeit, nach Konzepten zu suchen oder Indexpartitionierungen nach Wichtigkeit der enthaltenen Terme zu erstellen.
Einleitung:
Multiple-Choice-Klausuren spielen immer noch eine herausragende Rolle für fakultätsinterne medizinische Prüfungen. Neben inhaltlichen Arbeiten stellt sich die Frage, wie die technische Abwicklung optimiert werden kann. Für Dozenten in der Medizin gibt es zunehmend drei Optionen zur Durchführung von MC-Klausuren: Papierklausuren mit oder ohne Computerunterstützung oder vollständig elektronische Klausuren. Kritische Faktoren sind der Aufwand für die Formatierung der Klausur, der logistische Aufwand bei der Klausurdurchführung, die Qualität, Schnelligkeit und der Aufwand der Klausurkorrektur, die Bereitstellung der Dokumente für die Einsichtnahme, und die statistische Analyse der Klausurergebnisse.
Methoden:
An der Universität Würzburg wird seit drei Semestern ein Computerprogramm zur Eingabe und Formatierung der MC-Fragen in medizinischen und anderen Papierklausuren verwendet und optimiert, mit dem im Wintersemester (WS) 2009/2010 elf, im Sommersemester (SS) 2010 zwölf und im WS 2010/11 dreizehn medizinische Klausuren erstellt und anschließend die eingescannten Antwortblätter automatisch ausgewertet wurden. In den letzten beiden Semestern wurden die Aufwände protokolliert.
Ergebnisse:
Der Aufwand der Formatierung und der Auswertung einschl. nachträglicher Anpassung der Auswertung einer Durchschnittsklausur mit ca. 140 Teilnehmern und ca. 35 Fragen ist von 5-7 Stunden für Klausuren ohne Komplikation im WS 2009/2010 über ca. 2 Stunden im SS 2010 auf ca. 1,5 Stunden im WS 2010/11 gefallen. Einschließlich der Klausuren mit Komplikationen bei der Auswertung betrug die durchschnittliche Zeit im SS 2010 ca. 3 Stunden und im WS 10/11 ca. 2,67 Stunden pro Klausur.
Diskussion:
Für konventionelle Multiple-Choice-Klausuren bietet die computergestützte Formatierung und Auswertung von Papierklausuren einen beträchtlichen Zeitvorteil für die Dozenten im Vergleich zur manuellen Korrektur von Papierklausuren und benötigt im Vergleich zu rein elektronischen Klausuren eine deutlich einfachere technische Infrastruktur und weniger Personal bei der Klausurdurchführung.
This article is about a measurement analysis based approach to help software practitioners in managing the additional level complexities and variabilities in software product line applications. The architecture of the proposed approach i.e. ZAC is designed and implemented to perform preprocessesed source code analysis, calculate traditional and product line metrics and visualize results in two and three dimensional diagrams. Experiments using real time data sets are performed which concluded with the results that the ZAC can be very helpful for the software practitioners in understanding the overall structure and complexity of product line applications. Moreover the obtained results prove strong positive correlation between calculated traditional and product line measures.
In today's Internet, building overlay structures to provide a service is becoming more and more common. This approach allows for the utilization of client resources, thus being more scalable than a client-server model in this respect. However, in these architectures the quality of the provided service depends on the clients and is therefore more complex to manage. Resource utilization, both at the clients themselves and in the underlying network, determine the efficiency of the overlay application. Here, a trade-off exists between the resource providers and the end users that can be tuned via overlay mechanisms. Thus, resource management and traffic management is always quality-of-service management as well. In this monograph, the three currently significant and most widely used overlay types in the Internet are considered. These overlays are implemented in popular applications which only recently have gained importance. Thus, these overlay networks still face real-world technical challenges which are of high practical relevance. We identify the specific issues for each of the considered overlays, and show how their optimization affects the trade-offs between resource efficiency and service quality. Thus, we supply new insights and system knowledge that is not provided by previous work.
While developing modern applications, it is necessary to ensure an efficient and performant communication between different applications. In current environments, a middleware software is used, which supports the publish/subscribe communication pattern. Using this communication pattern, a publisher sends information encapsulated in messages to the middleware. A subscriber registers its interests at the middleware. The monograph describes three different steps to determine the performance of such a system. In a first step, the message throughput performance of a publish/subscribe in different scenarios is measured using a Java Message Service (JMS) based implementation. In the second step the maximum achievable message throughput is described by adapted models depending on the filter complexity and the replication grade. Using the model, the performance characteristics of a specific system in a given scenario can be determined. These numbers are used for the queuing model described in the third part of the thesis, which supports the dimensioning of a system in realistic scenarios. Additionally, we introduce a method to approximate an M/G/1 system numerically in an efficient way, which can be used for real time analysis to predict the expected performance in a certain scenario. Finally, the analytical model is used to investigate different possibilities to ensure the scalability of the maximum achievable message throughput of the overall system.
Jährliches Fachgespräch zu Sensornetzen der GI/ITG Fachgruppe Kommunikation und Verteilte Systeme, 16. - 17. September 2010, Universität Würzburg
This work is composed of three main parts: remote control of mobile systems via Internet, ad-hoc networks of mobile robots, and remote control of mobile robots via 3G telecommunication technologies. The first part gives a detailed state of the art and a discussion of the problems to be solved in order to teleoperate mobile robots via the Internet. The focus of the application to be realized is set on a distributed tele-laboratory with remote experiments on mobile robots which can be accessed world-wide via the Internet. Therefore, analyses of the communication link are used in order to realize a robust system. The developed and implemented architecture of this distributed tele-laboratory allows for a smooth access also with a variable or low link quality. The second part covers the application of ad-hoc networks for mobile robots. The networking of mobile robots via mobile ad-hoc networks is a very promising approach to realize integrated telematic systems without relying on preexisting communication infrastructure. Relevant civilian application scenarios are for example in the area of search and rescue operations where first responders are supported by multi-robot systems. Here, mobile robots, humans, and also existing stationary sensors can be connected very fast and efficient. Therefore, this work investigates and analyses the performance of different ad-hoc routing protocols for IEEE 802.11 based wireless networks in relevant scenarios. The analysis of the different protocols allows for an optimization of the parameter settings in order to use these ad-hoc routing protocols for mobile robot teleoperation. Also guidelines for the realization of such telematics systems are given. Also traffic shaping mechanisms of application layer are presented which allow for a more efficient use of the communication link. An additional application scenario, the integration of a small size helicopter into an IP based ad-hoc network, is presented. The teleoperation of mobile robots via 3G telecommunication technologies is addressed in the third part of this work. The high availability, high mobility, and the high bandwidth provide a very interesting opportunity to realize scenarios for the teleoperation of mobile robots or industrial remote maintenance. This work analyses important parameters of the UMTS communication link and investigates also the characteristics for different data streams. These analyses are used to give guidelines which are necessary for the realization of or industrial remote maintenance or mobile robot teleoperation scenarios. All the results and guidelines for the design of telematic systems in this work were derived from analyses and experiments with real hardware.
With the progress in robotics research the human machine interfaces reach more and more the status of being the major limiting factor for the overall system performance of a system for remote navigation and coordination of robots. In this monograph it is elaborated how mixed reality technologies can be applied for the user interfaces in order to increase the overall system performance. Concepts, technologies, and frameworks are developed and evaluated in user studies which enable for novel user-centered approaches to the design of mixed-reality user interfaces for remote robot operation. Both the technological requirements and the human factors are considered to achieve a consistent system design. Novel technologies like 3D time-of-flight cameras are investigated for the application in the navigation tasks and for the application in the developed concept of a generic mixed reality user interface. In addition it is shown how the network traffic of a video stream can be shaped on application layer in order to reach a stable frame rate in dynamic networks. The elaborated generic mixed reality framework enables an integrated 3D graphical user interface. The realized spatial integration and visualization of available information reduces the demand for mental transformations for the human operator and supports the use of immersive stereo devices. The developed concepts make also use of the fact that local robust autonomy components can be realized and thus can be incorporated as assistance systems for the human operators. A sliding autonomy concept is introduced combining force and visual augmented reality feedback. The force feedback component allows rendering the robot's current navigation intention to the human operator, such that a real sliding autonomy with seamless transitions is achieved. The user-studies prove the significant increase in navigation performance by application of this concept. The generic mixed reality user interface together with robust local autonomy enables a further extension of the teleoperation system to a short-term predictive mixed reality user interface. With the presented concept of operation, it is possible to significantly reduce the visibility of system delays for the human operator. In addition, both advantageous characteristics of a 3D graphical user interface for robot teleoperation- an exocentric view and an augmented reality view – can be combined.
Overlapping is a common word used to describe documents whose structural dimensions cannot be adequately represented using tree structure. For instance a quotation that starts in one verse and ends in another verse. The problem of overlapping hierarchies is a recurring one, which has been addressed by a variety of approaches. There are XML based solutions as well as Non-XML ones. The XML-based solutions are: multiple documents, empty elements, fragmentation, out-of-line markup, JITT and BUVH. And the Non-XML approaches comprise CONCUR/XCONCUR, MECS, LMNL ...etc. This paper presents shortly state-of-the-art in overlapping hierarchies, and introduces two variations on the TEI fragmentation markup that have several advantages.
The focus of this work lies on the communication issues of Medium Access Control (MAC) and routing protocols in the context of WSNs. The communication challenges in these networks mainly result from high node density, low bandwidth, low energy constraints and the hardware limitations in terms of memory, computational power and sensing capabilities of low-power transceivers. For this reason, the structure of WSNs is always kept as simple as possible to minimize the impact of communication issues. Thus, the majority of WSNs apply a simple one hop star topology since multi-hop communication has high demands on the routing protocol since it increases the bandwidth requirements of the network. Moreover, medium access becomes a challenging problem due to the fact that low-power transceivers are very limited in their sensing capabilities. The first contribution is represented by the Backoff Preamble-based MAC Protocol with Sequential Contention Resolution (BPS-MAC) which is designed to overcome the limitations of low-power transceivers. Two communication issues, namely the Clear Channel Assessment (CCA) delay and the turnaround time, are directly addressed by the protocol. The CCA delay represents the period of time which is required by the transceiver to detect a busy radio channel while the turnaround time specifies the period of time which is required to switch between receive and transmit mode. Standard Carrier Sense Multiple Access (CSMA) protocols do not achieve high performance in terms of packet loss if the traffic is highly correlated due to the fact that the transceiver is not able to sense the medium during the switching phase. Therefore, a node may start to transmit data while another node is already transmitting since it has sensed an idle medium right before it started to switch its transceiver from receive to transmit mode. The BPS-MAC protocol uses a new sequential preamble-based medium access strategy which can be adapted to the hardware capabilities of the transceivers. The protocol achieves a very low packet loss rate even in wireless networks with high node density and event-driven traffic without the need of synchronization. This makes the protocol attractive to applications such as structural health monitoring, where event suppression is not an option. Moreover, acknowledgments or complex retransmission strategies become almost unnecessary since the sequential preamble-based contention resolution mechanism minimizes the collision probability. However, packets can still be lost as a consequence of interference or other issues which affect signal propagation. The second contribution consists of a new routing protocol which is able to quickly detect topology changes without generating a large amount of overhead. The key characteristics of the Statistic-Based Routing (SBR) protocol are high end-to-end reliability (in fixed and mobile networks), load balancing capabilities, a smooth continuous routing metric, quick adaptation to changing network conditions, low processing and memory requirements, low overhead, support of unidirectional links and simplicity. The protocol can establish routes in a hybrid or a proactive mode and uses an adaptive continuous routing metric which makes it very flexible in terms of scalability while maintaining stable routes. The hybrid mode is optimized for low-power WSNs since routes are only established on demand. The difference of the hybrid mode to reactive routing strategies is that routing messages are periodically transmitted to maintain already established routes. However, the protocol stops the transmission of routing messages if no data packets are transmitted for a certain time period in order to minimize the routing overhead and the energy consumption. The proactive mode is designed for high data rate networks which have less energy constraints. In this mode, the protocol periodically transmits routing messages to establish routes in a proactive way even in the absence of data traffic. Thus, nodes in the network can immediately transmit data since the route to the destination is already established in advance. In addition, a new delay-based routing message forwarding strategy is introduced. The forwarding strategy is part of SBR but can also be applied to many routing protocols in order to modify the established topology. The strategy can be used, e.g. in mobile networks, to decrease the packet loss by deferring routing messages with respect to the neighbor change rate. Thus, nodes with a stable neighborhood forward messages faster than nodes within a fast changing neighborhood. As a result, routes are established through nodes with correlated movement which results in fewer topology changes due to higher link durations.
The Visual Editor for XML (Vex)[1] used by TextGrid [2]and other applications has got rendering and layout engines. The layout engine is well documented but the rendering engine is not. This lack of documenting the rendering engine has made refactoring and extending the editor hard and tedious. For instance many CSS2.1 and upcoming CSS3 properties have not been implemented. Software developers in different projects such as TextGrid using Vex would like to update its CSS rendering engine in order to provide advanced user interfaces as well as support different document types. In order to minimize the effort of extending Vex functionality, I found it beneficial to write a basic documentation about Vex software architecture in general and its CSS rendering engine in particular. The documentation is mainly based on the idea of architectural layered diagrams. In fact layered diagrams can help developers understand software’s source code faster and easier in order to alter it, and fix errors. This paper is written for the purpose of providing direct support for exploration in the comprehension process of Vex source code. It discusses Vex software architecture. The organization of packages that make up the software, the architecture of its CSS rendering engine, an algorithm explaining the working principle of its rendering engine are described.
The technique of using Cascading Style Sheets (CSS) to format and present structured data is called CSS processing model. For instance a CSS processing model for XML documents describes steps involved in formatting and presenting XML documents on screens or papers. Many software applications such as browsers and XML editors have their own CSS processing models which are part of their rendering engines. For instance each browser based on its CSS processing model renders CSS layout differently, as a result an inconsistency in the support of CSS features arises. Some browsers support more CSS features than others, and the rendering itself varies. Moreover the W3C standards are not even adhered by some browsers such as Internet Explorer. Test suites and other hacks and filters cannot definitely solve these problems, because these solutions are temporary and fragile. To palliate this inconsistency and browser compatibility issues with respect to CSS, a reference CSS processing model is needed. By extension it could even allow interoperability across CSS rendering engines. A reference architecture would provide common software architecture and interfaces, and facilitate refactoring, reuse, and automated unit testing. In [2] a reference architecture for browsers has been proposed. However this reference architecture is a macro reference model which does not consider separately individual components of rendering and layout engines. In this paper an attempt to develop a reference architecture for CSS processing models is discussed. In addition the Vex editor [3] rendering and layout engines, as well as an extended version of the editor used in TextGrid project [5] are also presented in order to validate the proposed reference architecture.
Empirical Study on Screen Scraping Web Service Creation: Case of Rhein-Main-Verkehrsverbund (RMV)
(2010)
Internet is the biggest database that science and technology have ever produced. The world wide web is a large repository of information that cannot be used for automation by many applications due to its limited target audience. One of the solutions to the automation problem is to develop wrappers. Wrapping is a process whereby unstructured extracted information is transformed into a more structured one such as XML, which could be provided as webservice to other applications. A web service is a web page whose content is well structured so that a computer program can consume it automatically. This paper describes steps involved in constructing wrappers manually in order to automatically generate web services.
This article discusses web frameworks that are available to a software developer in Java language. It introduces MVC paradigm and some frameworks that implement it. The article presents an overview of Struts, Spring MVC, JSF Frameworks, as well as guidelines for selecting one of them as development environment.
Webservices composition is traditionally carried out using composition technologies such as Business Process Execution Language (BPEL) [1] and Web Service Choreography Interface (WSCI) [2]. The composition technology involves the process of web service discovery, invocation, and composition. However these technologies are not easy and flexible enough because they are mainly developer-centric. Moreover majority of websites have not yet embarked into the world of web service, although they have very important and useful information to offer. Is it because they have not understood the usefulness of web services or is it because of the costs? Whatever might be the answers to these questions, time and money are definitely required in order to create and offer web services. To avoid these expenditures, wrappers [7] to automatically generate webservices from websites would be a cheaper and easier solution. Mashups offer a different way of doing webservices composition. In web environment a Mashup is a web application that brings together data from several sources using webservices, APIs, wrappers and so on, in order to create entirely a new application that was not provided before. This paper presents first an overview of Mashups and the process of web service invocation and composition based on Mashup, then describes an example of a web-based simulator for navigation system in Germany.
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
(2010)
Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see “Additional Files” section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/
Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.
In der vorliegenden Arbeit wird das Problem der Kalibrierung Agenten-basierter Simulationen (ABS) behandelt, also das Problem, die Parameterwerte eines Agenten-basierten Simulationsmodells so einzustellen, dass valides Simulationsverhalten erreicht wird. Das Kalibrierungsproblem für Simulationen an sich ist nicht neu und ist im Rahmen klassischer Simulationsparadigmen, wie z.B. der Makro-Simulation, fester Bestandteil der Forschung. Im Vergleich zu den dort betrachteten Kalibrierungsproblemen zeichnet sich das Kalibrierungsproblem für ABS jedoch durch eine Reihe zusätzlicher Herausforderungen aus, welche die direkte Anwendung existierender Kalibrierungsverfahren in begrenzter Zeit erschweren, bzw. nicht mehr sinnvoll zulassen. Die Lösung dieser Probleme steht im Zentrum dieser Dissertation: Das Ziel besteht darin, den Nutzer bei der Kalibrierung von ABS auf der Basis von unzureichenden, potentiell fehlerhaften Daten und Wissen zu unterstützen. Dabei sollen drei Hauptprobleme gelöst werden: 1)Vereinfachung der Kalibrierung großer Agenten-Parametermengen auf der Mikro- Ebene in Agenten-basierten Simulationen durch Ausnutzung der spezifischen Struktur von ABS (nämlich dem Aufbau aus einer Menge von Agentenmodellen). 2)Kalibrierung Agenten-basierter Simulationen, so dass auf allen relevanten Beobachtungsebenen valides Simulationsverhalten erzeugt wird (mindestens Mikro und Makro-Ebene). Als erschwerende Randbedingung muss die Kalibrierung unter der Voraussetzung einer Makro-Mikro-Wissenslücke durchgeführt werden. 3)Kalibrierung Agenten-basierter Simulationen auf der Mikro-Ebene unter der Voraussetzung, dass zur Kalibrierung einzelner Agentenmodelle nicht ausreichend und potentiell verfälschte Daten zur Verhaltensvalidierung zur Verfügung stehen. Hierzu wird in dieser Arbeit das sogenannte Makro-Mikro-Verfahren zur Kalibrierung von Agenten-basierten Simulationen entwickelt. Das Verfahren besteht aus einem Basisverfahren, das im Verlauf der Arbeit um verschiedene Zusatzverfahren erweitert wird. Das Makro-Mikro-Verfahren und seine Erweiterungen sollen dazu dienen, die Modellkalibrierung trotz stark verrauschter Daten und eingeschränktem Wissen über die Wirkungszusammenhänge im Originalsystem geeignet zu ermöglichen und dabei den Kalibrierungsprozess zu beschleunigen: 1) Makro-Mikro-Kalibrierungsverfahren: Das in dieser Arbeit entwickelte Makro- Mikro-Verfahren unterstützt den Nutzer durch eine kombinierte Kalibrierung auf der Mikro- und der Makro-Beobachtungsebene, die gegebenenfalls durch Zwischenebenen erweitert werden kann. Der Grundgedanke des Verfahrens besteht darin, das Kalibrierungsproblem in eines auf aggregierter Verhaltensebene und eines auf der Ebene des Mikro-Agentenverhaltens aufzuteilen. Auf der Makro-Ebene wird nach validen idealen aggregierten Verhaltensmodellen (IVM) der Agenten gesucht. Auf der Mikro-Ebene wird versucht die individuellen Modelle der Agenten auf Basis des erwünschten Gesamtverhaltens und der ermittelten IVM so zu kalibrieren, das insgesamt Simulationsverhalten entsteht, das sowohl auf Mikro- als auch auf Makro-Ebene valide ist. 2) Erweiterung 1: Robuste Kalibrierung: Um den Umgang mit potentiell verrauschten Validierungskriterien (d.h. mit verrauschten Daten über ein Originalsystem, auf denen die Validierungskriterien der Simulation beruhen) und Modellteilen während der Kalibrierung von ABS zu ermöglichen, wird eine robuste Kalibrierungstechnik zur Anwendung im Makro-Mikro-Verfahren entwickelt. 3) Erweiterung 2: Kalibrierung mit Heterogenitätssuche: Als zweite Erweiterung des Makro-Mikro-Verfahrens wird ein Verfahren entwickelt, das das Problem des unklaren Detaillierungsgrades von ABS auf der Ebene der Parameterwerte adressiert. Prinzipiell kann zwar jeder Agent unterschiedliche Parameterwerte verwenden, obwohl eine geringere Heterogenität zur Erzeugung validen Verhaltens ausreichend wäre. Die entwickelte Erweiterung versucht, während der Kalibrierung, eine geeignete Heterogenitätsausprägung für die Parameterwerte der Agenten zu ermitteln. Unter einer Heterogenitätsausprägung wird dabei eine Einteilung der simulierten Agenten in Gruppen mit jeweils gleichen Parameterwerten verstanden. Die Heterogenitätssuche dient dazu, einen Kompromiss zu finden zwischen der Notwendigkeit, sehr große Parametersuchräume durchsuchen zu müssen und gleichzeitig den Suchraum so klein wie möglich halten zu wollen.
Future broadband wireless networks should be able to support not only best effort traffic but also real-time traffic with strict Quality of Service (QoS) constraints. In addition, their available resources are scare and limit the number of users. To facilitate QoS guarantees and increase the maximum number of concurrent users, wireless networks require careful planning and optimization. In this monograph, we studied three aspects of performance optimization in wireless networks: resource optimization in WLAN infrastructure networks, quality of experience control in wireless mesh networks, and planning and optimization of wireless mesh networks. An adaptive resource management system is required to effectively utilize the limited resources on the air interface and to guarantee QoS for real-time applications. Thereby, both WLAN infrastructure and WLAN mesh networks have to be considered. An a-priori setting of the access parameters is not meaningful due to the contention-based medium access and the high dynamics of the system. Thus, a management system is required which dynamically adjusts the channel access parameters based on the network load. While this is sufficient for wireless infrastructure networks, interferences on neighboring paths and self-interferences have to be considered for wireless mesh networks. In addition, a careful channel allocation and route assignment is needed. Due to the large parameter space, standard optimization techniques fail for optimizing large wireless mesh networks. In this monograph, we reveal that biology-inspired optimization techniques, namely genetic algorithms, are well-suitable for the planning and optimization of wireless mesh networks. Although genetic algorithms generally do not always find the optimal solution, we show that with a good parameter set for the genetic algorithm, the overall throughput of the wireless mesh network can be significantly improved while still sharing the resources fairly among the users.
In today's Internet, services are very different in their requirements on the underlying transport network. In the future, this diversity will increase and it will be more difficult to accommodate all services in a single network. A possible approach to cope with this diversity within future networks is the introduction of support for running isolated networks for different services on top of a single shared physical substrate. This would also enable easy network management and ensure an economically sound operation. End-customers will readily adopt this approach as it enables new and innovative services without being expensive. In order to arrive at a concept that enables this kind of network, it needs to be designed around and constantly checked against realistic use cases. In this contribution, we present three use cases for future networks. We describe functional blocks of a virtual network architecture, which are necessary to support these use cases within the network. Furthermore, we discuss the interfaces needed between the functional blocks and consider standardization issues that arise in order to achieve a global consistent control and management structure of virtual networks.
We consider competitive location problems where two competing providers place their facilities sequentially and users can decide between the competitors. We assume that both competitors act non-cooperatively and aim at maximizing their own benefits. We investigate the complexity and approximability of such problems on graphs, in particular on simple graph classes such as trees and paths. We also develop fast algorithms for single competitive location problems where each provider places a single facilty. Voting location, in contrast, aims at identifying locations that meet social criteria. The provider wants to satisfy the users (customers) of the facility to be opened. In general, there is no location that is favored by all users. Therefore, a satisfactory compromise has to be found. To this end, criteria arising from voting theory are considered. The solution of the location problem is understood as the winner of a virtual election among the users of the facilities, in which the potential locations play the role of the candidates and the users represent the voters. Competitive and voting location problems turn out to be closely related.
In this thesis, we present novel approaches for formation driving of nonholonomic robots and optimal trajectory planning to reach a target region. The methods consider a static known map of the environment as well as unknown and dynamic obstacles detected by sensors of the formation. The algorithms are based on leader following techniques, where the formation of car-like robots is maintained in a shape determined by curvilinear coordinates. Beyond this, the general methods of formation driving are specialized and extended for an application of airport snow shoveling. Detailed descriptions of the algorithms complemented by relevant stability and convergence studies will be provided in the following chapters. Furthermore, discussions of the applicability will be verified by various simulations in existing robotic environments and also by a hardware experiment.
In future telecommunication systems, we observe an increasing diversity of access networks. The separation of transport services and applications or services leads to multi-network services, i.e., a future service has to work transparently to the underlying network infrastructure. Multi-network services with edge-based intelligence, like P2P file sharing or the Skype VoIP service, impose new traffic control paradigms on the future Internet. Such services adapt the amount of consumed bandwidth to reach different goals. A selfish behavior tries to keep the QoE of a single user above a certain level. Skype, for instance, repeats voice samples depending on the perceived end-to-end loss. From the viewpoint of a single user, the replication of voice data overcomes the degradation caused by packet loss and enables to maintain a certain QoE. The cost for this achievement is a higher amount of consumed bandwidth. However, if the packet loss is caused by congestion in the network, this additionally required bandwidth even worsens the network situation. Altruistic behavior, on the other side, would reduce the bandwidth consumption in such a way that the pressure on the network is released and thus the overall network performance is improved. In this monograph, we analyzed the impact of the overlay, P2P, and QoE paradigms in future Internet applications and the interactions from the observing user behavior. The shift of intelligence toward the edge is accompanied by a change in the emerging user behavior and traffic profile, as well as a change from multi-service networks to multi-networks services. In addition, edge-based intelligence may lead to a higher dynamics in the network topology, since the applications are often controlled by an overlay network, which can rapidly change in size and structure as new nodes can leave or join the overlay network in an entirely distributed manner. As a result, we found that the performance evaluation of such services provides new challenges, since novel key performance factors have to be first identified, like pollution of P2P systems, and appropriate models of the emerging user behavior are required, e.g. taking into account user impatience. As common denominator of the presented studies in this work, we focus on a user-centric view when evaluating the performance of future Internet applications. For a subscriber of a certain application or service, the perceived quality expressed as QoE will be the major criterion of the user's satisfaction with the network and service providers. We selected three different case studies and characterized the application's performance from the end user's point of view. Those are (1) cooperation in mobile P2P file sharing networks, (2) modeling of online TV recording services, and (3) QoE of edge-based VoIP applications. The user-centric approach facilitates the development of new mechanisms to overcome problems arising from the changing user behavior. An example is the proposed CycPriM cooperation strategy, which copes with selfish user behavior in mobile P2P file sharing system. An adequate mechanism has also been shown to be efficient in a heterogeneous B3G network with mobile users conducting vertical handovers between different wireless access technologies. The consideration of the user behavior and the user perceived quality guides to an appropriate modeling of future Internet applications. In the case of the online TV recording service, this enables the comparison between different technical realizations of the system, e.g. using server clusters or P2P technology, to properly dimension the installed network elements and to assess the costs for service providers. Technologies like P2P help to overcome phenomena like flash crowds and improve scalability compared to server clusters, which may get overloaded in such situations. Nevertheless, P2P technology invokes additional challenges and different user behavior to that seen in traditional client/server systems. Beside the willingness to share files and the churn of users, peers may be malicious and offer fake contents to disturb the data dissemination. Finally, the understanding and the quantification of QoE with respect to QoS degradations permits designing sophisticated edge-based applications. To this end, we identified and formulated the IQX hypothesis as an exponential interdependency between QoE and QoS parameters, which we validated for different examples. The appropriate modeling of the emerging user behavior taking into account the user's perceived quality and its interactions with the overlay and P2P paradigm will finally help to design future Internet applications.
This work focuses on coordination methods and the control of motion in groups of nonholonomic wheeled mobile robots, in particular of the car-like type. These kind of vehicles are particularly restricted in their mobility. In the main part of this work the two problems of formation motion coordination and of rendezvous in distributed multi-vehicle systems are considered. We introduce several enhancements to an existing motion planning approach for formations of nonholonomic mobile robots. Compared to the original method, the extended approach is able to handle time-varying reference speeds as well as adjustments of the formation's shape during reference trajectory segments with continuously differentiable curvature. Additionally, undesired discontinuities in the speed and steering profiles of the vehicles are avoided. Further, the scenario of snow shoveling on an airfield by utilizing multiple formations of autonomous snowplows is discussed. We propose solutions to the subproblems of motion planning for the formations and tracking control for the individual vehicles. While all situations that might occur have been tested in a simulation environment, we also verified the developed tracking controller in real robot hardware experiments. The task of the rendezvous problem in groups of car-like robots is to drive all vehicles to a common position by means of decentralized control laws. Typically there exists no direct interaction link between all of the vehicles. In this work we present decentralized rendezvous control laws for vehicles with free and with bounded steering. The convergence properties of the approaches are analyzed by utilizing Lyapunov based techniques. Furthermore, they are evaluated within various simulation experiments, while the bounded steering case is also verified within laboratory hardware experiments. Finally we introduce a modification to the bounded steering system that increases the convergence speed at the expense of a higher traveled distance of the vehicles.
Das Potenzial der Wissensentdeckung in Daten wird häufig nicht ausgenutzt, was hauptsächlich auf Barrieren zwischen dem Entwicklerteam und dem Endnutzer des Data-Mining zurückzuführen ist. In dieser Arbeit wird ein transparenter Ansatz zum Beschreiben und Erklären von Daten für Entscheidungsträger vorgestellt. In Entscheidungsträger-zentrierten Aufgaben werden die Projektanforderungen definiert und die Ergebnisse zu einer Geschichte zusammengestellt. Eine Anforderung besteht dabei aus einem tabellarischen Bericht und ggf. Mustern in seinem Inhalt, jeweils verständlich für einen Entscheidungsträger. Die technischen Aufgaben bestehen aus einer Datenprüfung, der Integration der Daten in einem Data-Warehouse sowie dem Generieren von Berichten und dem Entdecken von Mustern wie in den Anforderungen beschrieben. Mehrere Data-Mining-Projekte können durch Wissensmanagement sowie eine geeignete Infrastruktur voneinander profitieren. Der Ansatz wurde in zwei Projekten unter Verwendung von ausschließlich Open-Source-Software angewendet.
This thesis deals with the management and analysis of source code, which is represented in XML. Using the elementary methods of the XML repository, the XML source code representation is accessed, changed, updated, and saved. We reason about the source code, refactor source code and we visualize dependency graphs for call analysis. The visualized dependencies between files, modules, or packages are used to structure the source code in order to get a system, which is easily to comprehend, to modify and to complete. Sophisticated methods have been developed to slice the source code in order to obtain a working package of a large system, containing only a specific functionality. The basic methods, on which the visualizations and analyses are built on can be changed like changing a plug-in. The visualization methods can be reused in order to handle arbitrary source code representations, e.g., JAML, PHPML, PROLOGML. Dependencies of other context can be visualized, too, e.g., ER diagrams, or website references. The tool SCAV supports source code visualization and analyzing methods.
No abstract available
Mobile telecommunication systems of the 3.5th generation (3.5G) constitute a first step towards the requirements of an all-IP world. As the denotation suggests, 3.5G systems are not completely new designed from scratch. Instead, they are evolved from existing 3G systems like UMTS or cdma2000. 3.5G systems are primarily designed and optimized for packet-switched best-effort traffic, but they are also intended to increase system capacity by exploiting available radio resources more efficiently. Systems based on cdma2000 are enhanced with 1xEV-DO (EV-DO: evolution, data-optimized). In the UMTS domain, the 3G partnership project (3GPP) specified the High Speed Packet Access (HSPA) family, consisting of High Speed Downlink Packet Access (HSDPA) and its counterpart High Speed Uplink Packet Access (HSUPA) or Enhanced Uplink. The focus of this monograph is on HSPA systems, although the operation principles of other 3.5G systems are similar. One of the main contributions of our work are performance models which allow a holistic view on the system. The models consider user traffic on flow-level, such that only on significant changes of the system state a recalculation of parameters like bandwidth is necessary. The impact of lower layers is captured by stochastic models. This approach combines accurate modeling and the ability to cope with computational complexity. Adopting this approach to HSDPA, we develop a new physical layer abstraction model that takes radio resources, scheduling discipline, radio propagation and mobile device capabilities into account. Together with models for the calculation of network-wide interference and transmit powers, a discrete-event simulation and an analytical model based on a queuing-theoretical approach are proposed. For the Enhanced Uplink, we develop analytical models considering independent and correlated other-cell interference.
Parametric weighted finite automata (PWFA) are a multi-dimensional generalization of weighted finite automata. The expressiveness of PWFA contains the expressiveness of weighted finite automata as well as the expressiveness of affine iterated function system. The thesis discusses theory and applications of PWFA. The properties of PWFA definable sets are studied and it is shown that some fractal generator systems can be simulated using PWFA and that various real and complex functions can be represented by PWFA. Furthermore, the decoding of PWFA and the interpretation of PWFA definable sets is discussed.
The Internet sees an ongoing transformation process from a single best-effort service network into a multi-service network. In addition to traditional applications like e-mail,WWW-traffic, or file transfer, future generation networks (FGNs) will carry services with real-time constraints and stringent availability and reliability requirements like Voice over IP (VoIP), video conferencing, virtual private networks (VPNs) for finance, other real-time business applications, tele-medicine, or tele-robotics. Hence, quality of service (QoS) guarantees and resilience to failures are crucial characteristics of an FGN architecture. At the same time, network operations must be efficient. This necessitates sophisticated mechanisms for the provisioning and the control of future communication infrastructures. In this work we investigate such echanisms for resilient FGNs. There are many aspects of the provisioning and control of resilient FGNs such as traffic matrix estimation, traffic characterization, traffic forecasting, mechanisms for QoS enforcement also during failure cases, resilient routing, or calability concerns for future routing and addressing mechanisms. In this work we focus on three important aspects for which performance analysis can deliver substantial insights: load balancing for multipath Internet routing, fast resilience concepts, and advanced dimensioning techniques for resilient networks. Routing in modern communication networks is often based on multipath structures, e.g., equal-cost multipath routing (ECMP) in IP networks, to facilitate traffic engineering and resiliency. When multipath routing is applied, load balancing algorithms distribute the traffic over available paths towards the destination according to pre-configured distribution values. State-of-the-art load balancing algorithms operate either on the packet or the flow level. Packet level mechanisms achieve highly accurate traffic distributions, but are known to have negative effects on the performance of transport protocols and should not be applied. Flow level mechanisms avoid performance degradations, but at the expense of reduced accuracy. These inaccuracies may have unpredictable effects on link capacity requirements and complicate resource management. Thus, it is important to exactly understand the accuracy and dynamics of load balancing algorithms in order to be able to exercise better network control. Knowing about their weaknesses, it is also important to look for alternatives and to assess their applicability in different networking scenarios. This is the first aspect of this work. Component failures are inevitable during the operation of communication networks and lead to routing disruptions if no special precautions are taken. In case of a failure, the robust shortest-path routing of the Internet reconverges after some time to a state where all nodes are again reachable – provided physical connectivity still exists. But stringent availability and reliability criteria of new services make a fast reaction to failures obligatory for resilient FGNs. This led to the development of fast reroute (FRR) concepts for MPLS and IP routing. The operations of MPLS-FRR have already been standardized. Still, the standards leave some degrees of freedom for the resilient path layout and it is important to understand the tradeoffs between different options for the path layout to efficiently provision resilient FGNs. In contrast, the standardization for IP-FRR is an ongoing process. The applicability and possible combinations of different concepts still are open issues. IP-FRR also facilitates a comprehensive resilience framework for IP routing covering all steps of the failure recovery cycle. These points constitute another aspect of this work. Finally, communication networks are usually over-provisioned, i.e., they have much more capacity installed than actually required during normal operation. This is a precaution for various challenges such as network element failures. An alternative to this capacity overprovisioning (CO) approach is admission control (AC). AC blocks new flows in case of imminent overload due to unanticipated events to protect the QoS for already admitted flows. On the one hand, CO is generally viewed as a simple mechanism, AC as a more complex mechanism that complicates the network control plane and raises interoperability issues. On the other hand, AC appears more cost-efficient than CO. To obtain advanced provisioning methods for resilient FGNs, it is important to find suitable models for irregular events, such as failures and different sources of overload, and to incorporate them into capacity dimensioning methods. This allows for a fair comparison between CO and AC in various situations and yields a better understanding of the strengths and weaknesses of both concepts. Such an advanced capacity dimensioning method for resilient FGNs represents the third aspect of this work.
This work deals with teams in teleoperation scenarios, where one human team partner (supervisor) guides and controls multiple remote entities (either robotic or human) and coordinates their tasks. Such a team needs an appropriate infrastructure for sharing information and commands. The robots need to have a level of autonomy, which matches the assigned task. The humans in the team have to be provided with autonomous support, e.g. for information integration. Design and capabilities of the human-robot interfaces will strongly influence the performance of the team as well as the subjective feeling of the human team partners. Here, it is important to elaborate the information demand as well as how information is presented. Such human-robot systems need to allow the supervisor to gain an understanding of what is going on in the remote environment (situation awareness) by providing the necessary information. This includes achieving fast assessment of the robot´s or remote human´s state. Processing, integration and organization of data as well as suitable autonomous functions support decision making and task allocation and help to decrease the workload in this multi-entity teleoperation task. Interaction between humans and robots is improved by a common world model and a responsive system and robots. The remote human profits from a simplified user interface providing exactly the information needed for the actual task at hand. The topic of this thesis is the investigation of such teleoperation interfaces in human-robot teams, especially for high-risk, time-critical, and dangerous tasks. The aim is to provide a suitable human-robot team structure as well as analyze the demands on the user interfaces. On one side, it will be looked on the theoretical background (model, interactions, and information demand). On the other side, real implementations for system, robots, and user interfaces are presented and evaluated as testbeds for the claimed requirements. Rescue operations, more precisely fire-fighting, was chosen as an exemplary application scenario for this work. The challenges in such scenarios are high (highly dynamic environments, high risk, time criticality etc.) and it can be expected that results can be transferred to other applications, which have less strict requirements. The present work contributes to the introduction of human-robot teams in task-oriented scenarios, such as working in high risk domains, e.g. fire-fighting. It covers the theoretical background of the required system, the analysis of related human factors concepts, as well as discussions on implementation. An emphasis is placed on user interfaces, their design, requirements and user testing, as well as on the used techniques (three-dimensional sensor data representation, mixed reality, and user interface design guidelines). Further, the potential integration of 3D sensor data as well as the visualization on stereo visualization systems is introduced.
Overlay networks establish logical connections between users on top of the physical network. While randomly connected overlay networks provide only a best effort service, a new generation of structured overlay systems based on Distributed Hash Tables (DHTs) was proposed by the research community. However, there is still a lack of understanding the performance of such DHTs. Additionally, those architectures are highly distributed and therefore appear as a black box to the operator. Yet an operator does not want to lose control over his system and needs to be able to continuously observe and examine its current state at runtime. This work addresses both problems and shows how the solutions can be combined into a more self-organizing overlay concept. At first, we evaluate the performance of structured overlay networks under different aspects and thereby illuminate in how far such architectures are able to support carrier-grade applications. Secondly, to enable operators to monitor and understand their deployed system in more detail, we introduce both active as well as passive methods to gather information about the current state of the overlay network.
Verteilte dynamische Systeme unter lokalen und globalen Gesichtspunkten zu optimieren ist eine schwierige Aufgabe. Zwar sind grundsätzliche Auswirkungen einzelner Maßnahmen häufig bekannt, durch widerstrebende Ziele, Wechselwirkungen zwischen Prozessen und Nebenwirkungen von Maßnahmen ist ein analytisches Vorgehen bei der Optimierung nicht möglich. Besonders schwierig wird es, wenn lokale Einheiten einerseits ihre Ziele und Autonomie behalten sollen, aber durch zentrale Vorgaben bzw. Anreize so gesteuert werden sollen, dass ein übergeordnetes Ziel erreicht wird. Ein praktisches Beispiel dieses allgemeinen Optimierungsproblems findet sich im Gesundheitswesen. Das Management von modernen Kliniken ist stets mit dem Problem konfrontiert, die Qualität der Pflege zu gewährleisten und gleichzeitig kosteneffizient zu arbeiten. Hier gilt es unter gegeben Rahmenbedingungen und bei Respektierung der Autonomie der Funktionseinheiten, Optimierungsmaßnahmen zu finden und durchzuführen. Vorhandene Werkzeuge zur Simulation und Modellierung bieten für diese Aufgabe keine ausreichend guten Vorgehensmodelle und Modellierungsmechanismen. Die agentenbasierte Simulation ermöglicht die Abbildung solcher Systeme und die Durchführung von Simulationsexperimenten zur Bewertung einzelner Maßnahmen. Es werden Lösungswege und Werkzeuge vorgestellt und evaluiert, die den Benutzer bei der Formalisierung des Wissens und der Modellierung solch komplexer Szenarien unterstützen und ein systematisches Vorgehen zur Optimierung ermöglichen.
Performance Evaluation of Efficient Resource Management Concepts for Next Generation IP Networks
(2007)
Next generation networks (NGNs) must integrate the services of current circuit-switched telephone networks and packet-switched data networks. This convergence towards a unified communication infrastructure necessitates from the high capital expenditures (CAPEX) and operational expenditures (OPEX) due to the coexistence of separate networks for voice and data. In the end, NGNs must offer the same services as these legacy networks and, therefore, they must provide a low-cost packet-switched solution with real-time transport capabilities for telephony and multimedia applications. In addition, NGNs must be fault-tolerant to guarantee user satisfaction and to support business-critical processes also in case of network failures. A key technology for the operation of NGNs is the Internet Protocol (IP) which evolved to a common and well accepted standard for networking in the Internet during the last 25 years. There are two basically different approaches to achieve QoS in IP networks. With capacity overprovisioning (CO), an IP network is equipped with sufficient bandwidth such that network congestion becomes very unlikely and QoS is maintained most of the time. The second option to achieve QoS in IP networks is admission control (AC). AC represents a network-inherent intelligence that admits real-time traffic flows to a single link or an entire network only if enough resources are available such that the requirements on packet loss and delay can be met. Otherwise, the request of a new flow is blocked. This work focuses on resource management and control mechanisms for NGNs, in particular on AC and associated bandwidth allocation methods. The first contribution consists of a new link-oriented AC method called experience-based admission control (EBAC) which is a hybrid approach dealing with the problems inherent to conventional AC mechanisms like parameter-based or measurement-based AC (PBAC/MBAC). PBAC provides good QoS but suffers from poor resource utilization and, vice versa, MBAC uses resources efficiently but is susceptible to QoS violations. Hence, EBAC aims at increasing the resource efficiency while maintaining the QoS which increases the revenues of ISPs and postpones their CAPEX for infrastructure upgrades. To show the advantages of EBAC, we first review today’s AC approaches and then develop the concept of EBAC. EBAC is a simple mechanism that safely overbooks the capacity of a single link to increase its resource utilization. We evaluate the performance of EBAC by its simulation under various traffic conditions. The second contribution concerns dynamic resource allocation in transport networks which implement a specific network admission control (NAC) architecture. In general, the performance of different NAC systems may be evaluated by conventional methods such as call blocking analysis which has often been applied in the context of multi-service asynchronous transfer mode (ATM) networks. However, to yield more practical results than abstract blocking probabilities, we propose a new method to compare different AC approaches by their respective bandwidth requirements. To present our new method for comparing different AC systems, we first give an overview of network resource management (NRM) in general. Then we present the concept of adaptive bandwidth allocation (ABA) in capacity tunnels and illustrate the analytical performance evaluation framework to compare different AC systems by their capacity requirements. Different network characteristics influence the performance of ABA. Therefore, the impact of various traffic demand models and tunnel implementations, and the influence of resilience requirements is investigated. In conclusion, the resources in NGNs must be exclusively dedicated to admitted traffic to guarantee QoS. For that purpose, robust and efficient concepts for NRM are required to control the requested bandwidth with regard to the available transmission capacity. Sophisticated AC will be a key function for NRM in NGNs and, therefore, efficient resource management concepts like experience-based admission control and adaptive bandwidth allocation for admission-controlled capacity tunnels, as presented in this work are appealing for NGN solutions.
This thesis is devoted to the study of computational complexity theory, a branch of theoretical computer science. Computational complexity theory investigates the inherent difficulty in designing efficient algorithms for computational problems. By doing so, it analyses the scalability of computational problems and algorithms and places practical limits on what computers can actually accomplish. Computational problems are categorised into complexity classes. Among the most important complexity classes are the class NP and the subclass of NP-complete problems, which comprises many important optimisation problems in the field of operations research. Moreover, with the P-NP-problem, the class NP represents the most important unsolved question in computer science. The first part of this thesis is devoted to the study of NP-complete-, and more generally, NP-hard problems. It aims at improving our understanding of this important complexity class by systematically studying how altering NP-hard sets affects their NP-hardness. This research is related to longstanding open questions concerning the complexity of unions of disjoint NP-complete sets, and the existence of sparse NP-hard sets. The second part of the thesis is also dedicated to complexity classes but takes a different perspective: In a sense, after investigating the interior of complexity classes in the first part, the focus shifts to the description of complexity classes and thereby to the exterior in the second part. It deals with the description of complexity classes through leaf languages, a uniform framework which allows us to characterise a great variety of important complexity classes. The known concepts are complemented by a new leaf-language model. To a certain extent, this new approach combines the advantages of the known models. The presented results give evidence that the connection between the theory of formal languages and computational complexity theory might be closer than formerly known.
Das stochastische Denken, die Bernoullische Stochastik und dessen informationstechnologische Umsetzung, namens Stochastikon stellen die Grundlage für das Verständnis und die erfolgreiche Nutzung einer stochastischen Wissenschaft dar. Im Rahmen dieser Arbeit erfolgt eine Klärung des Begriffs des stochastischen Denkens, eine anschauliche Darstellung der von Elart von Collani entwickelten Bernoullischen Stochastik und eine Beschreibung von Stochastikon. Dabei werden sowohl das Gesamtkonzept von Stochastikon, sowie die Ziele, Aufgaben und die Realisierung der beiden Teilsysteme namens Mentor und Encyclopedia vorgestellt. Das stochastische Denken erlaubt eine realitätsnahe Sichtweise der Dinge, d.h. eine Sichtweise, die mit den menschlichen Beobachtungen und Erfahrungen im Einklang steht und somit die Unsicherheit über zukünftige Entwicklungen berücksichtigt. Der in diesem Kontext verwendete Begriff der Unsicherheit bezieht sich ausschließlich auf zukünftige Entwicklungen und äußert sich in Variabilität. Quellen der Unsicherheit sind einerseits die menschliche Ignoranz und andererseits der Zufall. Unter Ignoranz wird hierbei die Unwissenheit des Menschen über die unbekannten, aber feststehenden Fakten verstanden, die die Anfangsbedingungen der zukünftigen Entwicklung repräsentieren. Die Bernoullische Stochastik liefert ein Regelwerk und ermöglicht die Entwicklung eines quantitativen Modells zur Beschreibung der Unsicherheit und expliziter Einbeziehung der beiden Quellen Ignoranz und Zufall. Das Modell trägt den Namen Bernoulli-Raum und bildet die Grundlage für die Herleitung quantitativer Verfahren, um zuverlässige und genaue Aussagen sowohl über die nicht-existente zufällige Zukunft (Vorhersageverfahren), als auch über die unbekannte feststehende Vergangenheit (Messverfahren). Das Softwaresystem Stochastikon implementiert die Bernoullische Stochastik in Form einer Reihe autarker, miteinander kommunizierender Teilsysteme. Ziel des Teilsystems Encyclopedia ist die Bereitstellung und Bewertung stochastischen Wissens. Das Teilsystem Mentor dient der Unterstützung des Anwenders bei der Problemlösungsfindung durch Identifikation eines richtigen Modells bzw. eines korrekten Bernoulli-Raums. Der Lösungsfindungsprozess selber enthält keinerlei Unsicherheit. Die ganze Unsicherheit steckt in der Lösung, d.h. im Bernoulli-Raum, der explizit die vorhandene Unwissenheit (Ignoranz) und den vorliegenden Zufall abdeckend enthält.
No abstract available
Data mining has proved its significance in various domains and applications. As an important subfield of the general data mining task, subgroup mining can be used, e.g., for marketing purposes in business domains, or for quality profiling and analysis in medical domains. The goal is to efficiently discover novel, potentially useful and ultimately interesting knowledge. However, in real-world situations these requirements often cannot be fulfilled, e.g., if the applied methods do not scale for large data sets, if too many results are presented to the user, or if many of the discovered patterns are already known to the user. This thesis proposes a combination of several techniques in order to cope with the sketched problems: We discuss automatic methods, including heuristic and exhaustive approaches, and especially present the novel SD-Map algorithm for exhaustive subgroup discovery that is fast and effective. For an interactive approach we describe techniques for subgroup introspection and analysis, and we present advanced visualization methods, e.g., the zoomtable that directly shows the most important parameters of a subgroup and that can be used for optimization and exploration. We also describe various visualizations for subgroup comparison and evaluation in order to support the user during these essential steps. Furthermore, we propose to include possibly available background knowledge that is easy to formalize into the mining process. We can utilize the knowledge in many ways: To focus the search process, to restrict the search space, and ultimately to increase the efficiency of the discovery method. We especially present background knowledge to be applied for filtering the elements of the problem domain, for constructing abstractions, for aggregating values of attributes, and for the post-processing of the discovered set of patterns. Finally, the techniques are combined into a knowledge-intensive process supporting both automatic and interactive methods for subgroup mining. The practical significance of the proposed approach strongly depends on the available tools. We introduce the VIKAMINE system as a highly-integrated environment for knowledge-intensive active subgroup mining. Also, we present an evaluation consisting of two parts: With respect to objective evaluation criteria, i.e., comparing the efficiency and the effectiveness of the subgroup discovery methods, we provide an experimental evaluation using generated data. For that task we present a novel data generator that allows a simple and intuitive specification of the data characteristics. The results of the experimental evaluation indicate that the novel SD-Map method outperforms the other described algorithms using data sets similar to the intended application concerning the efficiency, and also with respect to precision and recall for the heuristic methods. Subjective evaluation criteria include the user acceptance, the benefit of the approach, and the interestingness of the results. We present five case studies utilizing the presented techniques: The approach has been successfully implemented in medical and technical applications using real-world data sets. The method was very well accepted by the users that were able to discover novel, useful, and interesting knowledge.
Wireless communication is nothing new. The first data transmissions based on electromagnetic waves have been successfully performed at the end of the 19th century. However, it took almost another century until the technology was ripe for mass market. The first mobile communication systems based on the transmission of digital data were introduced in the late 1980s. Within just a couple of years they have caused a revolution in the way people communicate. The number of cellular phones started to outnumber the fixed telephone lines in many countries and is still rising. New technologies in 3G systems, such as UMTS, allow higher data rates and support various kinds of multimedia services. Nevertheless, the end of the road in wireless communication is far from being reached. In the near future, the Internet and cellular phone systems are expected to be integrated to a new form of wireless system. Bandwidth requirements for a rich set of wireless services, e.g.\ video telephony, video streaming, online gaming, will be easily met. The transmission of voice data will just be another IP based service. On the other hand, building such a system is by far not an easy task. The problems in the development of the UMTS system showed the high complexity of wireless systems with support for bandwidth-hungry, IP-based services. But the technological challenges are just one difficulty. Telecommunication systems are planned on a world-wide basis, such that standard bodies, governments, institutions, hardware vendors, and service providers have to find agreements and compromises on a number of different topics. In this work, we provide the reader with a discussion of many of the topics involved in the planning of a Wireless LAN system that is capable of being integrated into the 4th generation mobile networks (4G) that is being discussed nowadays. Therefore, it has to be able to cope with interactive voice and video traffic while still offering high data rates for best effort traffic. Let us assume a scenario where a huge office complex is completely covered with Wireless LAN access points. Different antenna systems are applied in order to reduce the number of access points that are needed on the one hand, while optimizing the coverage on the other. No additional infrastructure is implemented. Our goal is to evaluate whether the Wireless LAN technology is capable of dealing with the various demands of such a scenario. First, each single access point has to be capable of supporting best-effort and Quality of Service (QoS) demanding applications simultaneously. The IT infrastructure in our scenario consists solely of Wireless LAN, such that it has to allow users surfing the Web, while others are involved in voice calls or video conferences. Then, there is the problem of overlapping cells. Users attached to one access point produce interference for others. However, the QoS support has to be maintained, which is not an easy task. Finally, there are nomadic users, which roam from one Wireless LAN cell to another even during a voice call. There are mechanisms in the standard that allow for mobility, but their capabilities for QoS support are yet to be studied. This shows the large number of unresolved issues when it comes to Wireless LAN in the context of 4G networks. In this work we want to tackle some of the problems.
In the last years, visual methods have been introduced in industrial software production and teaching of software engineering. In particular, the international standardization of a graphical software engineering language, the Unified Modeling Language (UML) was a reason for this tendency. Unfortunately, various problems exist in concrete realizations of tools, e.g. due to a missing compliance to the standard. One problem is the automatic layout, which is required for a consistent automatic software design. The thesis derives reasons and criteria for an automatic layout method, which produces drawings of UML class diagrams according to the UML specification and issues of human computer interaction, e.g. readability. A unique set of aesthetic criteria is combined from four different disciplines involved in this topic. Based on these aethetic rules, a hierarchical layout algorithm is developed, analyzed, measured by specialized measuring techniques and compared to related work. Then, the realization of the algorithm as a Java framework is given as an architectural description. Finally, adaptions to anticipated future changes of the UML, improvements of the framework and example drawings of the implementation are given.
We use algebraic closures and structures which are derived from these in complexity theory. We classify problems with Boolean circuits and Boolean constraints according to their complexity. We transfer algebraic structures to structural complexity. We use the generation problem to classify important complexity classes.
Diagnostic Case Based Training Systems (D-CBT) provide learners with a means to learn and exercise knowledge in a realistic context. In medical education, D-CBT Systems present virtual patients to the learners who are asked to examine, diagnose and state therapies for these patients. Due a number of conflicting and changing requirements, e.g. time for learning, authoring effort, several systems were developed so far. These systems range from simple, easy-to-use presentation systems to highly complex knowledge based systems supporting explorative learning. This thesis presents an approach and tools to create D-CBT systems from existing sources (documents, e.g. dismissal records) using existing tools (word processors): Authors annotate and extend the documents to model the knowledge. A scalable knowledge representation is able to capture the content on multiple levels, from simple to highly structured knowledge. Thus, authoring of D-CBT systems requires less prerequisites and pre-knowledge and is faster than approaches using specialized authoring environments. Also, authors can iteratively add and structure more knowledge to adapt training cases to their learners needs. The theses also discusses the application of the same approach to other domains, especially to knowledge acquisition for the Semantic Web.
Die Realisierung einer koordinierten und effektiven Fortbewegung für einen mobilen Roboter in natürlichen, sich kontinuierlich verändernden Umgebungen unter sich ebenso bewegenden Hindernissen ist eine komplexe Aufgabe, die die Lösung einer Reihe von Unterproblemen voraussetzt. Die vorliegende Arbeit beschäftigt sich sowohl mit den Themen der Wahrnehmung und Fortbewegung in veränderlichen Umgebungen, als auch mit Methoden zur Analyse der Hindernisbewegungen in Zusammenhang mit der Roboterbewegung selbst. Die Wahrnehmung wird in erster Linie anhand von Laserscannern betrachtet, und ein entsprechendes Verfahren zur Hindernisdetektion und -verfolung wird vorgestellt. Dabei werden Verfahren der globalen Netzwerkoptimierung eingesetzt, um Korrespondenzen zwischen Objekten aus den Einzelbildern herzustellen, was sich positiv auf die Robustheit gegenüber Störungen durch sporadische kleine Objekte auswirkt. Die Navigation basiert auf einer Adaption des sog. "Velocity Obstacle" Ansatzes auf die vorhandene Fahrzeugkinematik, und eine kooperative Bewegungskoordination (Roboter begleitet Mensch) wird durch eine geeignete Auswahlregel für kollisionsfreie Geschwindigkeiten realisiert. Anschließend werden verschiedene Distanzmaße eingeführt, anhand derer sich etwa der Pfad des Roboters mit dem Pfad seiner Begleitperson vergleichen lässt. Weiter wird eine Klassifizierung von Situationen vorgenommen, in die der Roboter potentiell involviert sein kann, und nach einer Übersicht über existierende Ansätze zur automatischen Intentionserkennung wird ein praktikabler Ansatz zur Erkennung gezielter Behinderungen eines mobilen Roboters vorgestellt. Die Arbeit schließt mit einem neuen Ansatz der Bewegungsplanung in dynamischen Umgebungen, der auf rekursiven Modellen des Roboters von seinem Gegenüber basiert, d.h. der Roboter berechnet zunächst, wie er sich in der Situation des (intelligenten, beweglichen) Hindernisses fortbewegen würde, und bezieht dies in die Entscheidung über die eigene Fortbewegung mit ein. Je nach Rekursionstiefe entstehen hierdurch Verhaltensweisen unterschiedlichen Charakters für den Roboter.
This work is subdivided into two main areas: resilient admission control and resilient routing. The work gives an overview of the state of the art of quality of service mechanisms in communication networks and proposes a categorization of admission control (AC) methods. These approaches are investigated regarding performance, more precisely, regarding the potential resource utilization by dimensioning the capacity for a network with a given topology, traffic matrix, and a required flow blocking probability. In case of a failure, the affected traffic is rerouted over backup paths which increases the traffic rate on the respective links. To guarantee the effectiveness of admission control also in failure scenarios, the increased traffic rate must be taken into account for capacity dimensioning and leads to resilient AC. Capacity dimensioning is not feasible for existing networks with already given link capacities. For the application of resilient NAC in this case, the size of distributed AC budgets must be adapted according to the traffic matrix in such a way that the maximum blocking probability for all flows is minimized and that the capacity of all links is not exceeded by the admissible traffic rate in any failure scenario. Several algorithms for the solution of that problem are presented and compared regarding their efficiency and fairness. A prototype for resilient AC was implemented in the laboratories of Siemens AG in Munich within the scope of the project KING. Resilience requires additional capacity on the backup paths for failure scenarios. The amount of this backup capacity depends on the routing and can be minimized by routing optimization. New protection switching mechanisms are presented that deviate the traffic quickly around outage locations. They are simple and can be implemented, e.g, by MPLS technology. The Self-Protecting Multi-Path (SPM) is a multi-path consisting of disjoint partial paths. The traffic is distributed over all faultless partial paths according to an optimized load balancing function both in the working case and in failure scenarios. Performance studies show that the network topology and the traffic matrix also influence the amount of required backup capacity significantly. The example of the COST-239 network illustrates that conventional shortest path routing may need 50% more capacity than the optimized SPM if all single link and node failures are protected.