Motivation: Disease progression in cancer can vary substantially between patients. Yet, patients often receive the same treatment. Recently, there has been much work on predicting disease progression and patient outcome variables from gene expression in order to personalize treatment options. A widely used approach is high-throughput experiments that aim to explore predictive signature genes which would provide identification of clinical outcome of diseases. Microarray data analysis helps to reveal underlying biological mechanisms of tumor progression, metastasis, and drug-resistance in cancer studies. Despite first diagnostic kits in the market, there are open problems such as the choice of random gene signatures or noisy expression data. The experimental or computational noise in data and limited tissue samples collected from patients might furthermore reduce the predictive power and biological interpretability of such signature genes. Nevertheless, signature genes predicted by different studies generally represent poor similarity; even for the same type of cancer. Integration of network information with gene expression data could provide more efficient signatures for outcome prediction in cancer studies. One approach to deal with these problems employs gene-gene relationships and ranks genes using the random surfer model of Google's PageRank algorithm. Unfortunately, the majority of published network-based approaches solely tested their methods on a small amount of datasets, questioning the general applicability of network-based methods for outcome prediction. Methods: In this thesis, I provide a comprehensive and systematically evaluation of a network-based outcome prediction approach -- NetRank - a PageRank derivative -- applied on several types of gene expression cancer data and four different types of networks. The algorithm identifies a signature gene set for a specific cancer type by incorporating gene network information with given expression data. To assess the performance of NetRank, I created a benchmark dataset collection comprising 25 cancer outcome prediction datasets from literature and one in-house dataset. Results: NetRank performs significantly better than classical methods such as foldchange or t-test as it improves the prediction performance in average for 7%. Besides, we are approaching the accuracy level of the authors' signatures by applying a relatively unbiased but fully automated process for biomarker discovery. Despite an order of magnitude difference in network size, a regulatory, a protein-protein interaction and two predicted networks perform equally well. Signatures as published by the authors and the signatures generated with classical methods do not overlap -- not even for the same cancer type -- whereas the network-based signatures strongly overlap. I analyze and discuss these overlapping genes in terms of the Hallmarks of cancer and in particular single out six transcription factors and seven proteins and discuss their specific role in cancer progression. Furthermore several tests are conducted for the identification of a Universal Cancer Signature. No Universal Cancer Signature could be identified so far, but a cancer-specific combination of general master regulators with specific cancer genes could be discovered that achieves the best results for all cancer types. As NetRank offers a great value for cancer outcome prediction, first steps for a secure usage of NetRank in a public cloud are described. Conclusion: Experimental evaluation of network-based methods on a gene expression benchmark dataset suggests that these methods are especially suited for outcome prediction as they overcome the problems of random gene signatures and noisy expression data. Through the combination of network information with gene expression data, network-based methods identify highly similar signatures over all cancer types, in contrast to classical methods that fail to identify highly common gene sets across the same cancer types. In general allows the integration of additional information in gene expression analysis the identification of more reliable, accurate and reproducible biomarkers and provides a deeper understanding of processes occurring in cancer development and progression.:1 Definition of Open Problems 2 Introduction 2.1 Problems in cancer outcome prediction 2.2 Network-based cancer outcome prediction 2.3 Universal Cancer Signature 3 Methods 3.1 NetRank algorithm 3.2 Preprocessing and filtering of the microarray data 3.3 Accuracy 3.4 Signature similarity 3.5 Classical approaches 3.6 Random signatures 3.7 Networks 3.8 Direct neighbor method 3.9 Dataset extraction 4 Performance of NetRank 4.1 Benchmark dataset for evaluation 4.2 The influence of NetRank parameters 4.3 Evaluation of NetRank 4.4 General findings 4.5 Computational complexity of NetRank 4.6 Discussion 5 Universal Cancer Signature 5.1 Signature overlap – a sign for Universal Cancer Signature 5.2 NetRank genes are highly connected and confirmed in literature 5.3 Hallmarks of Cancer 5.4 Testing possible Universal Cancer Signatures 5.5 Conclusion 6 Cloud-based Biomarker Discovery 6.1 Introduction to secure Cloud computing 6.2 Cancer outcome prediction 6.3 Security analysis 6.4 Conclusion 7 Contributions and Conclusions

Modern information technology increases the use of computers in training systems as well as in command-and-control systems in military services and public-safety organizations. This computerization combined with new threats present a challenging complexity. Situational awareness in evolving distributed operations and follow-up in training systems depends on humans in the field reporting observations of events. The use of this observer-reported information can be largely improved by implementation of models supporting both reporting and computer representation of objects and phenomena in operations. This thesis characterises and describes observer model-based data collection in distributed tactical operations, where multiple, dispersed units work to achieve common goals. Reconstruction and exploration of multimedia representations of operations is becoming an established means for supporting taskforce training. We explore how modelling of operational processes and entities can support observer data collection and increase information content in mission histories. We use realistic exercises for testing developed models, methods and tools for observer data collection and transfer results to live operations. The main contribution of this thesis is the systematic description of the model-based approach to using observers for data collection. Methodological aspects in using humans to collect data to be used in information systems, and also modelling aspects for phenomena occurring in emergency response and communication areas contribute to the body of research. We describe a general methodology for using human observers to collect adequate data for use in information systems. In addition, we describe methods and tools to collect data on the chain of medical attendance in emergency response exercises, and on command-and-control processes in several domains.

Les services de communication, du courrier postal à la téléphonie, en passant par la voix et la vidéo sur IP (Internet Protocol), la messagerie électronique, les salons de discussion sur Internet, les visioconférences ou les télécommunications immersives ont évolué au fil du temps. Un système de communication voix-vidéo sur IP est réalisé grâce à deux couches architecturales fondamentales : la couche de signalisation et la couche média. Le protocole de signalisation est utilisé pour créer, modifier et terminer des sessions multimédias entre des participants. La couche de signalisation est divisée en deux sous-couches - la couche de service et celle de contrôle - selon la spécification de l’IP Multimedia Subsystem (IMS). Deux systèmes de communication largement utilisés sont l’IMS et SIP Pair-à- Pair (P2P SIP). Les fournisseurs de services, qui se comportent en tant qu’intermédiaires entre appelants et appelés, implémentent les systèmes de communication, contrôlant strictement la couche signalisation. Or ces fournisseurs de services ne prennent pas en compte la diversité des utilisateurs. Cette thèse identifie trois barrières technologiques dans les systèmes de communication actuels et plus précisément concernant la couche de signalisation. I. Un manque d’ouverture et de flexibilité dans la couche de signalisation pour les utilisateurs. II. Un développement difficile des services basés sur le réseau et les sessions. III. Une complexification du la couche de signalisation lors d’un très grand nombre d’appels. Ces barrières technologiques gênent l’innovation des utilisateurs avec ces services de communication. Basé sur les barrières technologiques listées cidessus, le but initial de cette thèse est de définir un concept et une architecture de système de communication dans lequel chaque individu devient un fournisseur de service. Le concept, "My Own Communication Service Provider" (MOCSP) et le système MOCSP sont proposés, accompagné d’un diagramme de séquence. Ensuite, la thèse fournit une analyse qui compare le système MOCSP avec les systèmes de communication existants en termes d’ouverture et de flexibilité. La seconde partie de la thèse présente des solutions pour les services basés sur le réseau ou les sessions, mettant en avant le système MOCSP proposé. Deux services innovants, user mobility et partial session transfer/retrieval (PSTR) sont pris comme exemples de services basés sur le réseau ou les sessions. Les services basés sur un réseau ou des sessions interagissent avec une session ou sont exécutés dans une session. Dans les deux cas, une seule entité fonctionnelle entre l’appelant et l’appelé déclenche le flux multimédia pendant l’initialisation de l’appel et/ou en cours de communication. De plus, la coopération entre le contrôle d’appel réseau et les différents pairs est facilement réalisé. La dernière partie de la thèse est dédiée à l’extension de MOCSP en cas de forte densité d’appels, elle inclut une analyse comparative. Cette analyse dépend de quatre facteurs - limite de passage à l’échelle, niveau de complexité, ressources de calcul requises et délais d’établissement de session - qui sont considérés pour évaluer le passage à l’échelle de la couche de signalisation. L’analyse comparative montre clairement que la solution basée sur MOCSP est simple et améliore l’usage effectif des ressources de calcul par rapport aux systèmes de communication traditionnels / Different communication services from delivery of written letters to telephones, voice/video over Internet Protocol(IP), email, Internet chat rooms, and video/audio conferences, immersive communications have evolved over time. A communication system of voice/video over IP is the realization of a two fundamental layered architecture, signaling layer and media layer. The signaling protocol is used to create, modify, and terminate media sessions between participants. The signaling layer is further divided into two layers, service layer and service control layer, in the IP Multimedia Subsystem (IMS) specification. Two widely used communication systems are IMS, and Peer-to-Peer Session Initiation Protocol (P2P SIP). Service providers, who behave as brokers between callers and callees, implement communication systems, heavily controlling the signaling layer. These providers do not take the diversity aspect of end users into account. This dissertation identifies three technical barriers in the current communication systems especially in the signaling layer. Those are: I. lack of openness and flexibility in the signaling layer for end users. II. difficulty of development of network-based, session-based services. III. the signaling layer becomes complex during the high call rate. These technical barriers hinder the end-user innovation with communication services. Based on the above listed technical barriers, the first part of this thesis defines a concept and architecture for a communication system in which an individual user becomes the service provider. The concept, My Own Communication Service Provider (MOCSP) and MOCSP system is proposed and followed by a call flow. Later, this thesis provides an analysis that compares the MOCSP system with existing communication systems in terms of openness and flexibility. The second part of this thesis presents solutions for network-based, session based services, leveraging the proposed MOCSP system. Two innovative services, user mobility and partial session transfer/retrieval are considered as examples for network-based, session-based services. The network-based, sessionbased services interwork with a session or are executed within a session. In both cases, a single functional entity between caller and callee consistently enables the media flow during the call initiation and/or mid-call. In addition, the cooperation of network call control and end-points is easily achieved. The last part of the thesis is devoted to extending the MOCSP for a high call rate and includes a preliminary comparative analysis. This analysis depends on four factors - scalability limit, complexity level, needed computing resources and session setup latency - that are considered to specify the scalability of the signaling layer. The preliminary analysis clearly shows that the MOCSP based solution is simple and has potential for improving the effective usage of computing resources over the traditional communication systems

With the rise of information technology and the dependence on these systems, it becomes increasingly more important to keep the systems secure. The possibility to detect an intrusion with intrusion detection systems (IDS) is one of multiple fundamental technologies that may increase the security of a system. One of the bigger challenges of an IDS, is to detect types of intrusions that have previously not been encountered, so called unknown intrusions. These types of intrusions are generally detected by using methods collectively called anomaly detection methods. In this thesis I evaluate the performance of the algorithm Tree Augmented Naive Bayes Classifier (TAN) as an intrusion detection classifier. More specifically, I created a TAN program from scratch in Python and tested the program on two data sets containing data traffic. The thesis aims to create a better understanding of how TAN works and evaluate if it is a reasonable algorithm for intrusion detection. The results show that TAN is able to perform at an acceptable level with a reasonably high accuracy. The results also highlights the importance of using the smoothing operator included in the standard version of TAN. / Med informationsteknikens utveckling och det ökade beroendet av dessa system, blir det alltmer viktigt att hålla systemen säkra. Intrångsdetektionssystem (IDS) är en av många fundamentala teknologier som kan öka säkerheten i ett system. En av de större utmaningarna inom IDS, är att upptäcka typer av intrång som tidigare inte stötts på, så kallade okända intrång. Dessa intrång upptäcks oftast med hjälp av metoder som kollektivt kallas för avvikelsedetektionsmetoder. I denna uppsats utvärderar jag algoritmen Tree Augmented Naive Bayes Classifiers (TAN) prestation som en intrångsdetektionsklassificerare. Jag programmerade ett TAN-program, i Python, och testade detta program på två dataset som innehöll datatrafik. Denna uppsats ämnar att skapa en bättre förståelse för hur TAN fungerar, samt utvärdera om det är en lämplig algoritm för detektion av intrång. Resultaten visar att TAN kan prestera på en acceptabel nivå, med rimligt hög noggrannhet. Resultaten markerar även betydelsen av "smoothing operator", som inkluderas i standardversionen av TAN.

Different communication services from delivery of written letters to telephones, voice/video over Internet Protocol(IP), email, Internet chat rooms, and video/audio conferences, immersive communications have evolved over time. A communication system of voice/video over IP is the realization of a two fundamental layered architecture, signaling layer and media layer. The signaling protocol is used to create, modify, and terminate media sessions between participants. The signaling layer is further divided into two layers, service layer and service control layer, in the IP Multimedia Subsystem (IMS) specification. Two widely used communication systems are IMS, and Peer-to-Peer Session Initiation Protocol (P2P SIP). Service providers, who behave as brokers between callers and callees, implement communication systems, heavily controlling the signaling layer. These providers do not take the diversity aspect of end users into account. This dissertation identifies three technical barriers in the current communication systems especially in the signaling layer. Those are: I. lack of openness and flexibility in the signaling layer for end users. II. difficulty of development of network-based, session-based services. III. the signaling layer becomes complex during the high call rate. These technical barriers hinder the end-user innovation with communication services. Based on the above listed technical barriers, the first part of this thesis defines a concept and architecture for a communication system in which an individual user becomes the service provider. The concept, My Own Communication Service Provider (MOCSP) and MOCSP system is proposed and followed by a call flow. Later, this thesis provides an analysis that compares the MOCSP system with existing communication systems in terms of openness and flexibility. The second part of this thesis presents solutions for network-based, session based services, leveraging the proposed MOCSP system. Two innovative services, user mobility and partial session transfer/retrieval are considered as examples for network-based, session-based services. The network-based, sessionbased services interwork with a session or are executed within a session. In both cases, a single functional entity between caller and callee consistently enables the media flow during the call initiation and/or mid-call. In addition, the cooperation of network call control and end-points is easily achieved. The last part of the thesis is devoted to extending the MOCSP for a high call rate and includes a preliminary comparative analysis. This analysis depends on four factors - scalability limit, complexity level, needed computing resources and session setup latency - that are considered to specify the scalability of the signaling layer. The preliminary analysis clearly shows that the MOCSP based solution is simple and has potential for improving the effective usage of computing resources over the traditional communication systems

Nesta dissertação são analisados métodos de localização baseados na rede, com destaque para os métodos de correlação de assinaturas de rádio-frequência (DCM - Database Correlation Methods). Métodos baseados na rede não requerem modificações nos terminais móveis (MS - Mobile Stations), sendo portanto capazes de estimar a localização de MS legados, i.e., sem suporte específico a posicionamento. Esta característica, associada a alta disponibilidade e precisão dos métodos DCM, torna-os candidatos viáveis para diversas aplicações baseadas em posição, e em particular para a localização de chamadas para números de emergência - polícia, defesa civil, corpo de bombeiros, etc. - originadas de telefones móveis celulares. Duas técnicas para diminuição do tempo médio para produção de uma estimativa de posição são formuladas: a filtragem determinística e a busca otimizada utilizando algoritmos genéticos. Uma modificação é realizada nas funções de avaliação utilizadas em métodos DCM, inserindo um fator representando a inacurácia intrínseca às medidas de nível de sinal realizadas pelos MS. As modificações propostas são avaliadas experimentalmente em redes de telefonia móvel celular de segunda e terceira gerações em ambientes urbanos e suburbanos, assim como em redes locais sem fio em ambiente indoor. A viabilidade da utilização de bancos de dados de correlação (CDB - Correlation Database) construídos a partir de modelagem de propagação é analisada, bem como o efeito da calibração de modelos de propagação empíricos na precisão de métodos DCM. Um dos métodos DCM propostos, utilizando um CDB calibrado, teve um desempenho superior ao de vários outros métodos DCM publicados na literatura, atingindo em área urbana a precisão exigida dos métodos baseados na rede pela regulamentação FCC (Federal Communications Commission) para o serviço E911 (Enhanced 911 ). / This work analyzes network based positioning methods, in particular the fingerprinting or database correlation methods. Network based methods do not require mobile station upgrading or replacement, thereby being capable of locating legacy mobile stations, i.e., without any specific positioning related features. This characteristic, coupled with the high availability and precision of fingerprinting methods, make them viable candidates for several location based applications, especially for the positioning of cellular mobile phones originating emergency calls - for police, fire brigade, etc. Two techniques to reduce the average positioning fix time are proposed: deterministic filtering and genetic algorithms optimized search. A modification is proposed in database correlation methods evaluation functions, by inserting a factor representing the inherent inaccuracy in the signal strength measurement made by the mobile station. The proposed improvements are experimentally evaluated in second and third generation cellular networks in urban and suburban environments, as well as in indoor wireless local area networks. The viability of using correlation databases built from propagation modeling is evaluated, as well as the effect of empirical propagation models calibration in the fingerprinting location precision. One of the proposed fingerprinting techniques, using a calibrated correlation database, achieved a performance superior to several other published fingerprinting methods, reaching in an urban area the precision requirements set by the Federal Communications Commission for network based methods providing the Enhanced 911 emergency location service.

Nesta dissertação são analisados métodos de localização baseados na rede, com destaque para os métodos de correlação de assinaturas de rádio-frequência (DCM - Database Correlation Methods). Métodos baseados na rede não requerem modificações nos terminais móveis (MS - Mobile Stations), sendo portanto capazes de estimar a localização de MS legados, i.e., sem suporte específico a posicionamento. Esta característica, associada a alta disponibilidade e precisão dos métodos DCM, torna-os candidatos viáveis para diversas aplicações baseadas em posição, e em particular para a localização de chamadas para números de emergência - polícia, defesa civil, corpo de bombeiros, etc. - originadas de telefones móveis celulares. Duas técnicas para diminuição do tempo médio para produção de uma estimativa de posição são formuladas: a filtragem determinística e a busca otimizada utilizando algoritmos genéticos. Uma modificação é realizada nas funções de avaliação utilizadas em métodos DCM, inserindo um fator representando a inacurácia intrínseca às medidas de nível de sinal realizadas pelos MS. As modificações propostas são avaliadas experimentalmente em redes de telefonia móvel celular de segunda e terceira gerações em ambientes urbanos e suburbanos, assim como em redes locais sem fio em ambiente indoor. A viabilidade da utilização de bancos de dados de correlação (CDB - Correlation Database) construídos a partir de modelagem de propagação é analisada, bem como o efeito da calibração de modelos de propagação empíricos na precisão de métodos DCM. Um dos métodos DCM propostos, utilizando um CDB calibrado, teve um desempenho superior ao de vários outros métodos DCM publicados na literatura, atingindo em área urbana a precisão exigida dos métodos baseados na rede pela regulamentação FCC (Federal Communications Commission) para o serviço E911 (Enhanced 911 ). / This work analyzes network based positioning methods, in particular the fingerprinting or database correlation methods. Network based methods do not require mobile station upgrading or replacement, thereby being capable of locating legacy mobile stations, i.e., without any specific positioning related features. This characteristic, coupled with the high availability and precision of fingerprinting methods, make them viable candidates for several location based applications, especially for the positioning of cellular mobile phones originating emergency calls - for police, fire brigade, etc. Two techniques to reduce the average positioning fix time are proposed: deterministic filtering and genetic algorithms optimized search. A modification is proposed in database correlation methods evaluation functions, by inserting a factor representing the inherent inaccuracy in the signal strength measurement made by the mobile station. The proposed improvements are experimentally evaluated in second and third generation cellular networks in urban and suburban environments, as well as in indoor wireless local area networks. The viability of using correlation databases built from propagation modeling is evaluated, as well as the effect of empirical propagation models calibration in the fingerprinting location precision. One of the proposed fingerprinting techniques, using a calibrated correlation database, achieved a performance superior to several other published fingerprinting methods, reaching in an urban area the precision requirements set by the Federal Communications Commission for network based methods providing the Enhanced 911 emergency location service.

Cell functions are steered by complex interactions of gene products, like forming a temporary or stable complex, altering gene expression or catalyzing a reaction. Mapping these interactions is the key in understanding biological processes and therefore is the focus of numerous experiments and studies. Small-scale experiments deliver high quality data but lack coverage whereas high-throughput techniques cover thousands of interactions but can be error-prone. Unfortunately all of these approaches can only focus on one type of interaction at the time. This makes experimental mapping of the genome-wide network a cost and time intensive procedure. However, to overcome these problems, different computational approaches have been suggested that integrate multiple data sets and/or different evidence types. This widens the stringent definition of an interaction and introduces a more general term - functional association.  FunCoup is a database for genome-wide functional association networks of Homo sapiens and 16 model organisms. FunCoup distinguishes between five different functional associations: co-membership in a protein complex, physical interaction, participation in the same signaling cascade, participation in the same metabolic process and for prokaryotic species, co-occurrence in the same operon. For each class, FunCoup applies naive Bayesian integration of ten different evidence types of data, to predict novel interactions. It further uses orthologs to transfer interaction evidence between species. This considerably increases coverage, and allows inference of comprehensive networks even for not well studied organisms.  BinoX is a novel method for pathway analysis and determining the relation between gene sets, using functional association networks. Traditionally, pathway annotation has been done using gene overlap only, but these methods only get a small part of the whole picture. Placing the gene sets in context of a network provides additional evidence for pathway analysis, revealing a global picture based on the whole genome. PathwAX is a web server based on the BinoX algorithm. A user can input a gene set and get online network crosstalk based pathway annotation. PathwAX uses the FunCoup networks and 280 pre-defined pathways. Most runs take just a few seconds and the results are summarized in an interactive chart the user can manipulate to gain further insights of the gene set's pathway associations. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.</p>

Det har kommit att bli allt vanligare att installera nätverksbaserade övervakningskameror i hemmet som en säkerhetsåtgärd. Tidigare studier som undersöker nätverksbaserade övervakningskameror visar att dessa kameror utgör en möjlig säkerhetsrisk för de boende då det teoretiskt sätt är möjligt för personer som har kunskaper i att bryta sig in i datorsystem att spionera på de boende i hemmet genom övervakningskamerorna. Detta arbete har syftat till att undersöka om människor uppfattar den nätverksbaserade övervakningskameran, vars avsedda verkan är att övervaka hemmet och skydda det mot inbrott, som en säkerhetsrisk för intrång i deras integritet. Genom kvalitativa intervjuer undersöktes användares upplevelse av nätverksbaserade övervakningskameror i hemmet. Studien omfattade sex deltagare vilka rekryterades genom ett kriteriebaserat snöbollsurval. Genom en kvalitativ innehållsanalys kom studien fram till ett resultat som visar på samband i hur dessa övervakningskameror påverkar deltagarnas upplevda integritet i hemmet. Till exempel visade resultatet att deltagarna initialt kände sig iakttagna av dessa kameror. Dessa samband kan ligga till grund för fortsatt forskning kring hur nätverksbaserade övervakningskameror kan utvecklas för att förbättra användarupplevelsen av dem. / It has become increasingly common to install network-based surveillance cameras in homes as a security measure. Previous studies examining network-based surveillance cameras shows that these cameras pose a possible security risk to users as it is theoretically possible for people who have the knowledge to break into computer systems to spy on the residents of a home through the surveillance cameras. This study aimed to investigate whether users perceive the network-based surveillance camera, whose purpose is to monitor the home and protect it from intruders, as a security risk of intrusion into their privacy. Through qualitative interviews the users experience of network-based surveillance cameras in home has been examined. The study included six participants who were recruited though a criterion-based snowball selection. Through a qualitative content analysis, the study resulted in correlations between the participants experience of the network-based surveillance cameras and their impact on the participants perceived integrity. For example, the result showed that the participants initially felt observed by these cameras. The findings can be basis for further research on how network-based surveillance cameras can evolve to improve the user experience.

Progressive download video services, such as YouTube, are responsible for a major part of the transmitted data volume in the Internet and it is expected, that they also will strongly affect mobile networks. Streaming video quality mainly depends on the sustainable throughput achieved during transmission. In order to achieve an acceptable video quality in mobile networks (with limited capacity resources), traffic engineering mechanisms have to be applied. For that, the streaming video quality needs to be measured and monitored permanently. Therefore, the video timestamps which are encoded within the payload of the TCP segments have to be extracted. For that it is necessary to decode the video within the transported payload. Algorithms for decoding Flash Video, MP4 and WebM Video have already been implemented as a demonstration implementation in support of the network based measurement contribution to SG12 by Chemnitz University for TCP encoded progressive download Internet services. In the demonstration, the derived play out buffering from the monitored traffic is being output internally. A second application is then used to graphically display the estimation result. The measurement and estimation is solely done within a measurement point of an operator network without access to the client’s end device.