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The paper presents two approaches to the development of
a Computer Science Competence Model for the needs of curriculum
development and evaluation in Higher Education. A normativetheoretical
approach is based on the AKT and ACM/IEEE curriculum
and will be used within the recommendations of the German
Informatics Society (GI) for the design of CS curricula. An empirically
oriented approach refines the categories of the first one with regard to
specific subject areas by conducting content analysis on CS curricula of
important universities from several countries. The refined model will be
used for the needs of students’ e-assessment and subsequent affirmative
action of the CS departments.
Regardless of what is intended by government curriculum
specifications and advised by educational experts, the competencies
taught and learned in and out of classrooms can vary considerably.
In this paper, we discuss in particular how we can investigate the
perceptions that individual teachers have of competencies in ICT,
and how these and other factors may influence students’ learning. We
report case study research which identifies contradictions within the
teaching of ICT competencies as an activity system, highlighting issues
concerning the object of the curriculum, the roles of the participants and
the school cultures. In a particular case, contradictions in the learning
objectives between higher order skills and the use of application tools
have been resolved by a change in the teacher’s perceptions which
have not led to changes in other aspects of the activity system. We look
forward to further investigation of the effects of these contradictions in
other case studies and on forthcoming curriculum change.
As a result of the Bologna reform of educational systems in
Europe the outcome orientation of learning processes, competence-oriented
descriptions of the curricula and competence-oriented assessment
procedures became standard also in Computer Science Education
(CSE). The following keynote addresses important issues of shaping
a CSE competence model especially in the area of informatics system
comprehension and object-oriented modelling. Objectives and research
methodology of the project MoKoM (Modelling and Measurement
of Competences in CSE) are explained. Firstly, the CSE competence
model was derived based on theoretical concepts and then secondly the
model was empirically examined and refined using expert interviews.
Furthermore, the paper depicts the development and examination of
a competence measurement instrument, which was derived from the
competence model. Therefore, the instrument was applied to a large
sample of students at the gymnasium’s upper class level. Subsequently,
efforts to develop a competence level model, based on the retrieved empirical
results and on expert ratings are presented. Finally, further demands
on research on competence modelling in CSE will be outlined.
Computational thinking is a fundamental skill set that is learned
by studying Informatics and ICT. We argue that its core ideas can
be introduced in an inspiring and integrated way to both teachers and
students using fun and contextually rich cs4fn ‘Computer Science for
Fun’ stories combined with ‘unplugged’ activities including games and
magic tricks. We also argue that understanding people is an important
part of computational thinking. Computational thinking can be fun for
everyone when taught in kinaesthetic ways away from technology.
KEYCIT 2014
(2015)
In our rapidly changing world it is increasingly important not only to be an expert in a chosen field of study but also to be able to respond to developments, master new approaches to solving problems, and fulfil changing requirements in the modern world and in the job market. In response to these needs key competencies in understanding, developing and using new digital technologies are being brought into focus in school and university programmes. The IFIP TC3 conference "KEYCIT – Key Competences in Informatics and ICT (KEYCIT 2014)" was held at the University of Potsdam in Germany from July 1st to 4th, 2014 and addressed the combination of key competencies, Informatics and ICT in detail. The conference was organized into strands focusing on secondary education, university education and teacher education (organized by IFIP WGs 3.1 and 3.3) and provided a forum to present and to discuss research, case studies, positions, and national perspectives in this field.
Through the use of next generation sequencing (NGS) technology, a lot of newly sequenced organisms are now available. Annotating those genes is one of the most challenging tasks in sequence biology. Here, we present an automated workflow to find homologue proteins, annotate sequences according to function and create a three-dimensional model.
With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment.
A workflow for visualizing server connections using the Google Maps API was built in the jABC. It makes use of three basic services: An XML-based IP address geolocation web service, a command line tool and the Static Maps API. The result of the workflow is an URL leading to an image file of a map, showing server connections between a client and a target host.
Geocoder accuracy ranking
(2014)
Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address.
Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database
This book presents an agile and model-driven approach to manage scientific workflows. The approach is based on the Extreme Model Driven Design (XMDD) paradigm and aims at simplifying and automating the complex data analysis processes carried out by scientists in their day-to-day work. Besides documenting the impact the workflow modeling might have on the work of natural scientists, this book serves three major purposes: 1. It acts as a primer for practitioners who are interested to learn how to think in terms of services and workflows when facing domain-specific scientific processes. 2. It provides interesting material for readers already familiar with this kind of tools, because it introduces systematically both the technologies used in each case study and the basic concepts behind them. 3. As the addressed thematic field becomes increasingly relevant for lectures in both computer science and experimental sciences, it also provides helpful material for teachers that plan similar courses.
Geometric generalization is a fundamental concept in the digital mapping process. An increasing amount of spatial data is provided on the web as well as a range of tools to process it. This jABC workflow is used for the automatic testing of web-based generalization services like mapshaper.org by executing its functionality, overlaying both datasets before and after the transformation and displaying them visually in a .tif file. Mostly Web Services and command line tools are used to build an environment where ESRI shapefiles can be uploaded, processed through a chosen generalization service and finally visualized in Irfanview.
In the geoinformatics field, remote sensing data is often used for analyzing the characteristics of the current investigation area. This includes DEMs, which are simple raster grids containing grey scales representing the respective elevation values. The project CREADED that is presented in this paper aims at making these monochrome raster images more significant and more intuitively interpretable. For this purpose, an executable interactive model for creating a colored and relief-shaded Digital Elevation Model (DEM) has been designed using the jABC framework. The process is based on standard jABC-SIBs and SIBs that provide specific GIS functions, which are available as Web services, command line tools and scripts.
This paper describes the implementation of a workflow model for service-oriented computing of potential areas for wind turbines in jABC. By implementing a re-executable model the manual effort of a multi-criteria site analysis can be reduced. The aim is to determine the shift of typical geoprocessing tools of geographic information systems (GIS) from the desktop to the web. The analysis is based on a vector data set and mainly uses web services of the “Center for Spatial Information Science and Systems” (CSISS). This paper discusses effort, benefits and problems associated with the use of the web services.
Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs.
GraffDok is an application helping to maintain an overview over sprayed images somewhere in a city. At the time of writing it aims at vandalism rather than at beautiful photographic graffiti in an underpass. Looking at hundreds of tags and scribbles on monuments, house walls, etc. it would be interesting to not only record them in writing but even make them accessible electronically, including images.
GraffDok’s workflow is simple and only requires an EXIF-GPS-tagged photograph of a graffito. It automatically determines its location by using reverse geocoding with the given GPS-coordinates and the Gisgraphy WebService. While asking the user for some more meta data, GraffDok analyses the image in parallel with this and tries to detect fore- and background – before extracting the drawing lines and make them stand alone. The command line based tool ImageMagick is used here as well as for accessing EXIF data.
Any meta data is written to csv-files, which will stay easily accessible and can be integrated in TeX-files as well. The latter ones are converted to PDF at the end of the workflow, containing a table about all graffiti and a summary for each – including the generated characteristic graffiti pattern image.
The in-memory revolution
(2015)
This book describes the next generation of business applications enabled by SAP's in-memory database, SAP HANA. In particular, the authors show the substantial changes introduced in S4/HANA by switching to SAP HANA. Using numerous examples and use cases from the authors' wealth of real-world experience, it illustrates the quantum leap in performance made possible by the new technology. The book is written by two of the most prominent actors in the area of business application systems: Hasso Plattner, co-founder of SAP and inaugurator of the Hasso Plattner Institute at the University of Potsdam, and Bernd Leukert, member of the Executive Board and the Global Managing Board of SAP. This clearly structured, highly illustrated book takes an exciting new technology and presents the practicality and success of first mover applications.
Boolean constraint solving technology has made tremendous progress over the last decade, leading to industrial-strength solvers, for example, in the areas of answer set programming (ASP), the constraint satisfaction problem (CSP), propositional satisfiability (SAT) and satisfiability of quantified Boolean formulas (QBF). However, in all these areas, there exist multiple solving strategies that work well on different applications; no strategy dominates all other strategies. Therefore, no individual solver shows robust state-of-the-art performance in all kinds of applications. Additionally, the question arises how to choose a well-performing solving strategy for a given application; this is a challenging question even for solver and domain experts. One way to address this issue is the use of portfolio solvers, that is, a set of different solvers or solver configurations. We present three new automatic portfolio methods: (i) automatic construction of parallel portfolio solvers (ACPP) via algorithm configuration,(ii) solving the $NP$-hard problem of finding effective algorithm schedules with Answer Set Programming (aspeed), and (iii) a flexible algorithm selection framework (claspfolio2) allowing for fair comparison of different selection approaches. All three methods show improved performance and robustness in comparison to individual solvers on heterogeneous instance sets from many different applications. Since parallel solvers are important to effectively solve hard problems on parallel computation systems (e.g., multi-core processors), we extend all three approaches to be effectively applicable in parallel settings. We conducted extensive experimental studies different instance sets from ASP, CSP, MAXSAT, Operation Research (OR), SAT and QBF that indicate an improvement in the state-of-the-art solving heterogeneous instance sets. Last but not least, from our experimental studies, we deduce practical advice regarding the question when to apply which of our methods.
This document presents a formula selection system for classical first order theorem proving based on the relevance of formulae for the proof of a conjecture. It is based on unifiability of predicates and is also able to use a linguistic approach for the selection. The scope of the technique is the reduction of the set of formulae and the increase of the amount of provable conjectures in a given time. Since the technique generates a subset of the formula set, it can be used as a preprocessor for automated theorem proving. The document contains the conception, implementation and evaluation of both selection concepts. While the one concept generates a search graph over the negation normal forms or Skolem normal forms of the given formulae, the linguistic concept analyses the formulae and determines frequencies of lexemes and uses a tf-idf weighting algorithm to determine the relevance of the formulae. Though the concept is built for first order logic, it is not limited to it. The concept can be used for higher order and modal logik, too, with minimal adoptions. The system was also evaluated at the world championship of automated theorem provers (CADE ATP Systems Competition, CASC-24) in combination with the leanCoP theorem prover and the evaluation of the results of the CASC and the benchmarks with the problems of the CASC of the year 2012 (CASC-J6) show that the concept of the system has positive impact to the performance of automated theorem provers. Also, the benchmarks with two different theorem provers which use different calculi have shown that the selection is independent from the calculus. Moreover, the concept of TEMPLAR has shown to be competitive to some extent with the concept of SinE and even helped one of the theorem provers to solve problems that were not (or slower) solved with SinE selection in the CASC. Finally, the evaluation implies that the combination of the unification based and linguistic selection yields more improved results though no optimisation was done for the problems.
This document presents an axiom selection technique for classic first order theorem proving based on the relevance of axioms for the proof of a conjecture. It is based on unifiability of predicates and does not need statistical information like symbol frequency. The scope of the technique is the reduction of the set of axioms and the increase of the amount of provable conjectures in a given time. Since the technique generates a subset of the axiom set, it can be used as a preprocessor for automated theorem proving. This technical report describes the conception, implementation and evaluation of ARDE. The selection method, which is based on a breadth-first graph search by unifiability of predicates, is a weakened form of the connection calculus and uses specialised variants or unifiability to speed up the selection. The implementation of the concept is evaluated with comparison to the results of the world championship of theorem provers of the year 2012 (CASC J6). It is shown that both the theorem prover leanCoP which uses the connection calculus and E which uses equality reasoning, can benefit from the selection approach. Also, the evaluation shows that the concept is applyable for theorem proving problems with thousands of formulae and that the selection is independent from the calculus used by the theorem prover.
Deciphering the functioning of biological networks is one of the central tasks in systems biology. In particular, signal transduction networks are crucial for the understanding of the cellular response to external and internal perturbations. Importantly, in order to cope with the complexity of these networks, mathematical and computational modeling is required. We propose a computational modeling framework in order to achieve more robust discoveries in the context of logical signaling networks. More precisely, we focus on modeling the response of logical signaling networks by means of automated reasoning using Answer Set Programming (ASP). ASP provides a declarative language for modeling various knowledge representation and reasoning problems. Moreover, available ASP solvers provide several reasoning modes for assessing the multitude of answer sets. Therefore, leveraging its rich modeling language and its highly efficient solving capacities, we use ASP to address three challenging problems in the context of logical signaling networks: learning of (Boolean) logical networks, experimental design, and identification of intervention strategies. Overall, the contribution of this thesis is three-fold. Firstly, we introduce a mathematical framework for characterizing and reasoning on the response of logical signaling networks. Secondly, we contribute to a growing list of successful applications of ASP in systems biology. Thirdly, we present a software providing a complete pipeline for automated reasoning on the response of logical signaling networks.
The objective and motivation behind this research is to provide applications with easy-to-use interfaces to communities of deaf and functionally illiterate users, which enables them to work without any human assistance. Although recent years have witnessed technological advancements, the availability of technology does not ensure accessibility to information and communication technologies (ICT). Extensive use of text from menus to document contents means that deaf or functionally illiterate can not access services implemented on most computer software. Consequently, most existing computer applications pose an accessibility barrier to those who are unable to read fluently. Online technologies intended for such groups should be developed in continuous partnership with primary users and include a thorough investigation into their limitations, requirements and usability barriers. In this research, I investigated existing tools in voice, web and other multimedia technologies to identify learning gaps and explored ways to enhance the information literacy for deaf and functionally illiterate users. I worked on the development of user-centered interfaces to increase the capabilities of deaf and low literacy users by enhancing lexical resources and by evaluating several multimedia interfaces for them. The interface of the platform-independent Italian Sign Language (LIS) Dictionary has been developed to enhance the lexical resources for deaf users. The Sign Language Dictionary accepts Italian lemmas as input and provides their representation in the Italian Sign Language as output. The Sign Language dictionary has 3082 signs as set of Avatar animations in which each sign is linked to a corresponding Italian lemma. I integrated the LIS lexical resources with MultiWordNet (MWN) database to form the first LIS MultiWordNet(LMWN). LMWN contains information about lexical relations between words, semantic relations between lexical concepts (synsets), correspondences between Italian and sign language lexical concepts and semantic fields (domains). The approach enhances the deaf users’ understanding of written Italian language and shows that a relatively small set of lexicon can cover a significant portion of MWN. Integration of LIS signs with MWN made it useful tool for computational linguistics and natural language processing. The rule-based translation process from written Italian text to LIS has been transformed into service-oriented system. The translation process is composed of various modules including parser, semantic interpreter, generator, and spatial allocation planner. This translation procedure has been implemented in the Java Application Building Center (jABC), which is a framework for extreme model driven design (XMDD). The XMDD approach focuses on bringing software development closer to conceptual design, so that the functionality of a software solution could be understood by someone who is unfamiliar with programming concepts. The transformation addresses the heterogeneity challenge and enhances the re-usability of the system. For enhancing the e-participation of functionally illiterate users, two detailed studies were conducted in the Republic of Rwanda. In the first study, the traditional (textual) interface was compared with the virtual character-based interactive interface. The study helped to identify usability barriers and users evaluated these interfaces according to three fundamental areas of usability, i.e. effectiveness, efficiency and satisfaction. In another study, we developed four different interfaces to analyze the usability and effects of online assistance (consistent help) for functionally illiterate users and compared different help modes including textual, vocal and virtual character on the performance of semi-literate users. In our newly designed interfaces the instructions were automatically translated in Swahili language. All the interfaces were evaluated on the basis of task accomplishment, time consumption, System Usability Scale (SUS) rating and number of times the help was acquired. The results show that the performance of semi-literate users improved significantly when using the online assistance. The dissertation thus introduces a new development approach in which virtual characters are used as additional support for barely literate or naturally challenged users. Such components enhanced the application utility by offering a variety of services like translating contents in local language, providing additional vocal information, and performing automatic translation from text to sign language. Obviously, there is no such thing as one design solution that fits for all in the underlying domain. Context sensitivity, literacy and mental abilities are key factors on which I concentrated and the results emphasize that computer interfaces must be based on a thoughtful definition of target groups, purposes and objectives.
Learning a model for the relationship between the attributes and the annotated labels of data examples serves two purposes. Firstly, it enables the prediction of the label for examples without annotation. Secondly, the parameters of the model can provide useful insights into the structure of the data. If the data has an inherent partitioned structure, it is natural to mirror this structure in the model. Such mixture models predict by combining the individual predictions generated by the mixture components which correspond to the partitions in the data. Often the partitioned structure is latent, and has to be inferred when learning the mixture model. Directly evaluating the accuracy of the inferred partition structure is, in many cases, impossible because the ground truth cannot be obtained for comparison. However it can be assessed indirectly by measuring the prediction accuracy of the mixture model that arises from it. This thesis addresses the interplay between the improvement of predictive accuracy by uncovering latent cluster structure in data, and further addresses the validation of the estimated structure by measuring the accuracy of the resulting predictive model. In the application of filtering unsolicited emails, the emails in the training set are latently clustered into advertisement campaigns. Uncovering this latent structure allows filtering of future emails with very low false positive rates. In order to model the cluster structure, a Bayesian clustering model for dependent binary features is developed in this thesis. Knowing the clustering of emails into campaigns can also aid in uncovering which emails have been sent on behalf of the same network of captured hosts, so-called botnets. This association of emails to networks is another layer of latent clustering. Uncovering this latent structure allows service providers to further increase the accuracy of email filtering and to effectively defend against distributed denial-of-service attacks. To this end, a discriminative clustering model is derived in this thesis that is based on the graph of observed emails. The partitionings inferred using this model are evaluated through their capacity to predict the campaigns of new emails. Furthermore, when classifying the content of emails, statistical information about the sending server can be valuable. Learning a model that is able to make use of it requires training data that includes server statistics. In order to also use training data where the server statistics are missing, a model that is a mixture over potentially all substitutions thereof is developed. Another application is to predict the navigation behavior of the users of a website. Here, there is no a priori partitioning of the users into clusters, but to understand different usage scenarios and design different layouts for them, imposing a partitioning is necessary. The presented approach simultaneously optimizes the discriminative as well as the predictive power of the clusters. Each model is evaluated on real-world data and compared to baseline methods. The results show that explicitly modeling the assumptions about the latent cluster structure leads to improved predictions compared to the baselines. It is beneficial to incorporate a small number of hyperparameters that can be tuned to yield the best predictions in cases where the prediction accuracy can not be optimized directly.
This thesis presents novel ideas and research findings for the Web of Data – a global data space spanning many so-called Linked Open Data sources. Linked Open Data adheres to a set of simple principles to allow easy access and reuse for data published on the Web. Linked Open Data is by now an established concept and many (mostly academic) publishers adopted the principles building a powerful web of structured knowledge available to everybody. However, so far, Linked Open Data does not yet play a significant role among common web technologies that currently facilitate a high-standard Web experience. In this work, we thoroughly discuss the state-of-the-art for Linked Open Data and highlight several shortcomings – some of them we tackle in the main part of this work. First, we propose a novel type of data source meta-information, namely the topics of a dataset. This information could be published with dataset descriptions and support a variety of use cases, such as data source exploration and selection. For the topic retrieval, we present an approach coined Annotated Pattern Percolation (APP), which we evaluate with respect to topics extracted from Wikipedia portals. Second, we contribute to entity linking research by presenting an optimization model for joint entity linking, showing its hardness, and proposing three heuristics implemented in the LINked Data Alignment (LINDA) system. Our first solution can exploit multi-core machines, whereas the second and third approach are designed to run in a distributed shared-nothing environment. We discuss and evaluate the properties of our approaches leading to recommendations which algorithm to use in a specific scenario. The distributed algorithms are among the first of their kind, i.e., approaches for joint entity linking in a distributed fashion. Also, we illustrate that we can tackle the entity linking problem on the very large scale with data comprising more than 100 millions of entity representations from very many sources. Finally, we approach a sub-problem of entity linking, namely the alignment of concepts. We again target a method that looks at the data in its entirety and does not neglect existing relations. Also, this concept alignment method shall execute very fast to serve as a preprocessing for further computations. Our approach, called Holistic Concept Matching (HCM), achieves the required speed through grouping the input by comparing so-called knowledge representations. Within the groups, we perform complex similarity computations, relation conclusions, and detect semantic contradictions. The quality of our result is again evaluated on a large and heterogeneous dataset from the real Web. In summary, this work contributes a set of techniques for enhancing the current state of the Web of Data. All approaches have been tested on large and heterogeneous real-world input.
Cloud computing is a model for enabling on-demand access to a shared pool of computing resources. With virtually limitless on-demand resources, a cloud environment enables the hosted Internet application to quickly cope when there is an increase in the workload. However, the overhead of provisioning resources exposes the Internet application to periods of under-provisioning and performance degradation. Moreover, the performance interference, due to the consolidation in the cloud environment, complicates the performance management of the Internet applications. In this dissertation, we propose two approaches to mitigate the impact of the resources provisioning overhead. The first approach employs control theory to scale resources vertically and cope fast with workload. This approach assumes that the provider has knowledge and control over the platform running in the virtual machines (VMs), which limits it to Platform as a Service (PaaS) and Software as a Service (SaaS) providers. The second approach is a customer-side one that deals with the horizontal scalability in an Infrastructure as a Service (IaaS) model. It addresses the trade-off problem between cost and performance with a multi-goal optimization solution. This approach finds the scale thresholds that achieve the highest performance with the lowest increase in the cost. Moreover, the second approach employs a proposed time series forecasting algorithm to scale the application proactively and avoid under-utilization periods. Furthermore, to mitigate the interference impact on the Internet application performance, we developed a system which finds and eliminates the VMs suffering from performance interference. The developed system is a light-weight solution which does not imply provider involvement. To evaluate our approaches and the designed algorithms at large-scale level, we developed a simulator called (ScaleSim). In the simulator, we implemented scalability components acting as the scalability components of Amazon EC2. The current scalability implementation in Amazon EC2 is used as a reference point for evaluating the improvement in the scalable application performance. ScaleSim is fed with realistic models of the RUBiS benchmark extracted from the real environment. The workload is generated from the access logs of the 1998 world cup website. The results show that optimizing the scalability thresholds and adopting proactive scalability can mitigate 88% of the resources provisioning overhead impact with only a 9% increase in the cost.
This thesis proposes a privacy protection framework for the controlled distribution and use of personal private data. The framework is based on the idea that privacy policies can be set directly by the data owner and can be automatically enforced against the data user. Data privacy continues to be a very important topic, as our dependency on electronic communication maintains its current growth, and private data is shared between multiple devices, users and locations. The growing amount and the ubiquitous availability of personal private data increases the likelihood of data misuse. Early privacy protection techniques, such as anonymous email and payment systems have focused on data avoidance and anonymous use of services. They did not take into account that data sharing cannot be avoided when people participate in electronic communication scenarios that involve social interactions. This leads to a situation where data is shared widely and uncontrollably and in most cases the data owner has no control over further distribution and use of personal private data. Previous efforts to integrate privacy awareness into data processing workflows have focused on the extension of existing access control frameworks with privacy aware functions or have analysed specific individual problems such as the expressiveness of policy languages. So far, very few implementations of integrated privacy protection mechanisms exist and can be studied to prove their effectiveness for privacy protection. Second level issues that stem from practical application of the implemented mechanisms, such as usability, life-time data management and changes in trustworthiness have received very little attention so far, mainly because they require actual implementations to be studied. Most existing privacy protection schemes silently assume that it is the privilege of the data user to define the contract under which personal private data is released. Such an approach simplifies policy management and policy enforcement for the data user, but leaves the data owner with a binary decision to submit or withhold his or her personal data based on the provided policy. We wanted to empower the data owner to express his or her privacy preferences through privacy policies that follow the so-called Owner-Retained Access Control (ORAC) model. ORAC has been proposed by McCollum, et al. as an alternate access control mechanism that leaves the authority over access decisions by the originator of the data. The data owner is given control over the release policy for his or her personal data, and he or she can set permissions or restrictions according to individually perceived trust values. Such a policy needs to be expressed in a coherent way and must allow the deterministic policy evaluation by different entities. The privacy policy also needs to be communicated from the data owner to the data user, so that it can be enforced. Data and policy are stored together as a Protected Data Object that follows the Sticky Policy paradigm as defined by Mont, et al. and others. We developed a unique policy combination approach that takes usability aspects for the creation and maintenance of policies into consideration. Our privacy policy consists of three parts: A Default Policy provides basic privacy protection if no specific rules have been entered by the data owner. An Owner Policy part allows the customisation of the default policy by the data owner. And a so-called Safety Policy guarantees that the data owner cannot specify disadvantageous policies, which, for example, exclude him or her from further access to the private data. The combined evaluation of these three policy-parts yields the necessary access decision. The automatic enforcement of privacy policies in our protection framework is supported by a reference monitor implementation. We started our work with the development of a client-side protection mechanism that allows the enforcement of data-use restrictions after private data has been released to the data user. The client-side enforcement component for data-use policies is based on a modified Java Security Framework. Privacy policies are translated into corresponding Java permissions that can be automatically enforced by the Java Security Manager. When we later extended our work to implement server-side protection mechanisms, we found several drawbacks for the privacy enforcement through the Java Security Framework. We solved this problem by extending our reference monitor design to use Aspect-Oriented Programming (AOP) and the Java Reflection API to intercept data accesses in existing applications and provide a way to enforce data owner-defined privacy policies for business applications.
3D from 2D touch
(2013)
While interaction with computers used to be dominated by mice and keyboards, new types of sensors now allow users to interact through touch, speech, or using their whole body in 3D space. These new interaction modalities are often referred to as "natural user interfaces" or "NUIs." While 2D NUIs have experienced major success on billions of mobile touch devices sold, 3D NUI systems have so far been unable to deliver a mobile form factor, mainly due to their use of cameras. The fact that cameras require a certain distance from the capture volume has prevented 3D NUI systems from reaching the flat form factor mobile users expect. In this dissertation, we address this issue by sensing 3D input using flat 2D sensors. The systems we present observe the input from 3D objects as 2D imprints upon physical contact. By sampling these imprints at very high resolutions, we obtain the objects' textures. In some cases, a texture uniquely identifies a biometric feature, such as the user's fingerprint. In other cases, an imprint stems from the user's clothing, such as when walking on multitouch floors. By analyzing from which part of the 3D object the 2D imprint results, we reconstruct the object's pose in 3D space. While our main contribution is a general approach to sensing 3D input on 2D sensors upon physical contact, we also demonstrate three applications of our approach. (1) We present high-accuracy touch devices that allow users to reliably touch targets that are a third of the size of those on current touch devices. We show that different users and 3D finger poses systematically affect touch sensing, which current devices perceive as random input noise. We introduce a model for touch that compensates for this systematic effect by deriving the 3D finger pose and the user's identity from each touch imprint. We then investigate this systematic effect in detail and explore how users conceptually touch targets. Our findings indicate that users aim by aligning visual features of their fingers with the target. We present a visual model for touch input that eliminates virtually all systematic effects on touch accuracy. (2) From each touch, we identify users biometrically by analyzing their fingerprints. Our prototype Fiberio integrates fingerprint scanning and a display into the same flat surface, solving a long-standing problem in human-computer interaction: secure authentication on touchscreens. Sensing 3D input and authenticating users upon touch allows Fiberio to implement a variety of applications that traditionally require the bulky setups of current 3D NUI systems. (3) To demonstrate the versatility of 3D reconstruction on larger touch surfaces, we present a high-resolution pressure-sensitive floor that resolves the texture of objects upon touch. Using the same principles as before, our system GravitySpace analyzes all imprints and identifies users based on their shoe soles, detects furniture, and enables accurate touch input using feet. By classifying all imprints, GravitySpace detects the users' body parts that are in contact with the floor and then reconstructs their 3D body poses using inverse kinematics. GravitySpace thus enables a range of applications for future 3D NUI systems based on a flat sensor, such as smart rooms in future homes. We conclude this dissertation by projecting into the future of mobile devices. Focusing on the mobility aspect of our work, we explore how NUI devices may one day augment users directly in the form of implanted devices.
Interactive rendering techniques for focus+context visualization of 3D geovirtual environments
(2013)
This thesis introduces a collection of new real-time rendering techniques and applications for focus+context visualization of interactive 3D geovirtual environments such as virtual 3D city and landscape models. These environments are generally characterized by a large number of objects and are of high complexity with respect to geometry and textures. For these reasons, their interactive 3D rendering represents a major challenge. Their 3D depiction implies a number of weaknesses such as occlusions, cluttered image contents, and partial screen-space usage. To overcome these limitations and, thus, to facilitate the effective communication of geo-information, principles of focus+context visualization can be used for the design of real-time 3D rendering techniques for 3D geovirtual environments (see Figure). In general, detailed views of a 3D geovirtual environment are combined seamlessly with abstracted views of the context within a single image. To perform the real-time image synthesis required for interactive visualization, dedicated parallel processors (GPUs) for rasterization of computer graphics primitives are used. For this purpose, the design and implementation of appropriate data structures and rendering pipelines are necessary. The contribution of this work comprises the following five real-time rendering methods: • The rendering technique for 3D generalization lenses enables the combination of different 3D city geometries (e.g., generalized versions of a 3D city model) in a single image in real time. The method is based on a generalized and fragment-precise clipping approach, which uses a compressible, raster-based data structure. It enables the combination of detailed views in the focus area with the representation of abstracted variants in the context area. • The rendering technique for the interactive visualization of dynamic raster data in 3D geovirtual environments facilitates the rendering of 2D surface lenses. It enables a flexible combination of different raster layers (e.g., aerial images or videos) using projective texturing for decoupling image and geometry data. Thus, various overlapping and nested 2D surface lenses of different contents can be visualized interactively. • The interactive rendering technique for image-based deformation of 3D geovirtual environments enables the real-time image synthesis of non-planar projections, such as cylindrical and spherical projections, as well as multi-focal 3D fisheye-lenses and the combination of planar and non-planar projections. • The rendering technique for view-dependent multi-perspective views of 3D geovirtual environments, based on the application of global deformations to the 3D scene geometry, can be used for synthesizing interactive panorama maps to combine detailed views close to the camera (focus) with abstract views in the background (context). This approach reduces occlusions, increases the usage the available screen space, and reduces the overload of image contents. • The object-based and image-based rendering techniques for highlighting objects and focus areas inside and outside the view frustum facilitate preattentive perception. The concepts and implementations of interactive image synthesis for focus+context visualization and their selected applications enable a more effective communication of spatial information, and provide building blocks for design and development of new applications and systems in the field of 3D geovirtual environments.
The field of machine learning studies algorithms that infer predictive models from data. Predictive models are applicable for many practical tasks such as spam filtering, face and handwritten digit recognition, and personalized product recommendation. In general, they are used to predict a target label for a given data instance. In order to make an informed decision about the deployment of a predictive model, it is crucial to know the model’s approximate performance. To evaluate performance, a set of labeled test instances is required that is drawn from the distribution the model will be exposed to at application time. In many practical scenarios, unlabeled test instances are readily available, but the process of labeling them can be a time- and cost-intensive task and may involve a human expert. This thesis addresses the problem of evaluating a given predictive model accurately with minimal labeling effort. We study an active model evaluation process that selects certain instances of the data according to an instrumental sampling distribution and queries their labels. We derive sampling distributions that minimize estimation error with respect to different performance measures such as error rate, mean squared error, and F-measures. An analysis of the distribution that governs the estimator leads to confidence intervals, which indicate how precise the error estimation is. Labeling costs may vary across different instances depending on certain characteristics of the data. For instance, documents differ in their length, comprehensibility, and technical requirements; these attributes affect the time a human labeler needs to judge relevance or to assign topics. To address this, the sampling distribution is extended to incorporate instance-specific costs. We empirically study conditions under which the active evaluation processes are more accurate than a standard estimate that draws equally many instances from the test distribution. We also address the problem of comparing the risks of two predictive models. The standard approach would be to draw instances according to the test distribution, label the selected instances, and apply statistical tests to identify significant differences. Drawing instances according to an instrumental distribution affects the power of a statistical test. We derive a sampling procedure that maximizes test power when used to select instances, and thereby minimizes the likelihood of choosing the inferior model. Furthermore, we investigate the task of comparing several alternative models; the objective of an evaluation could be to rank the models according to the risk that they incur or to identify the model with lowest risk. An experimental study shows that the active procedure leads to higher test power than the standard test in many application domains. Finally, we study the problem of evaluating the performance of ranking functions, which are used for example for web search. In practice, ranking performance is estimated by applying a given ranking model to a representative set of test queries and manually assessing the relevance of all retrieved items for each query. We apply the concepts of active evaluation and active comparison to ranking functions and derive optimal sampling distributions for the commonly used performance measures Discounted Cumulative Gain and Expected Reciprocal Rank. Experiments on web search engine data illustrate significant reductions in labeling costs.
This talk will describe My Digital Life (TU100), a distance learning module that introduces computer science through immediate engagement with ubiquitous computing (ubicomp). This talk will describe some of the principles and concepts we have adopted for this modern computing introduction: the idea of the ‘informed digital citizen’; engagement through narrative; playful pedagogy; making the power of ubicomp available to novices; setting technical skills in real contexts. It will also trace how the pedagogy is informed by experiences and research in Computer Science education.
A survey has been carried out in the Computer Science (CS) department at the University of Baghdad to investigate the attitudes of CS students in a female dominant environment, showing the differences between male and female students in different academic years. We also compare the attitudes of the freshman students of two different cultures (University of Baghdad, Iraq, and the University of Potsdam).
Scientific writing is an important skill for computer science and computer engineering professionals. In this paper we present a writing concept across the curriculum program directed towards scientific writing. The program is built around a hierarchy of learning outcomes. The hierarchy is constructed through analyzing the learning outcomes in relation to competencies that are needed to fulfill them.
Nowadays, model-driven engineering (MDE) promises to ease software development by decreasing the inherent complexity of classical software development. In order to deliver on this promise, MDE increases the level of abstraction and automation, through a consideration of domain-specific models (DSMs) and model operations (e.g. model transformations or code generations). DSMs conform to domain-specific modeling languages (DSMLs), which increase the level of abstraction, and model operations are first-class entities of software development because they increase the level of automation. Nevertheless, MDE has to deal with at least two new dimensions of complexity, which are basically caused by the increased linguistic and technological heterogeneity. The first dimension of complexity is setting up an MDE environment, an activity comprised of the implementation or selection of DSMLs and model operations. Setting up an MDE environment is both time-consuming and error-prone because of the implementation or adaptation of model operations. The second dimension of complexity is concerned with applying MDE for actual software development. Applying MDE is challenging because a collection of DSMs, which conform to potentially heterogeneous DSMLs, are required to completely specify a complex software system. A single DSML can only be used to describe a specific aspect of a software system at a certain level of abstraction and from a certain perspective. Additionally, DSMs are usually not independent but instead have inherent interdependencies, reflecting (partial) similar aspects of a software system at different levels of abstraction or from different perspectives. A subset of these dependencies are applications of various model operations, which are necessary to keep the degree of automation high. This becomes even worse when addressing the first dimension of complexity. Due to continuous changes, all kinds of dependencies, including the applications of model operations, must also be managed continuously. This comprises maintaining the existence of these dependencies and the appropriate (re-)application of model operations. The contribution of this thesis is an approach that combines traceability and model management to address the aforementioned challenges of configuring and applying MDE for software development. The approach is considered as a traceability approach because it supports capturing and automatically maintaining dependencies between DSMs. The approach is considered as a model management approach because it supports managing the automated (re-)application of heterogeneous model operations. In addition, the approach is considered as a comprehensive model management. Since the decomposition of model operations is encouraged to alleviate the first dimension of complexity, the subsequent composition of model operations is required to counteract their fragmentation. A significant portion of this thesis concerns itself with providing a method for the specification of decoupled yet still highly cohesive complex compositions of heterogeneous model operations. The approach supports two different kinds of compositions - data-flow compositions and context compositions. Data-flow composition is used to define a network of heterogeneous model operations coupled by sharing input and output DSMs alone. Context composition is related to a concept used in declarative model transformation approaches to compose individual model transformation rules (units) at any level of detail. In this thesis, context composition provides the ability to use a collection of dependencies as context for the composition of other dependencies, including model operations. In addition, the actual implementation of model operations, which are going to be composed, do not need to implement any composition concerns. The approach is realized by means of a formalism called an executable and dynamic hierarchical megamodel, based on the original idea of megamodels. This formalism supports specifying compositions of dependencies (traceability and model operations). On top of this formalism, traceability is realized by means of a localization concept, and model management by means of an execution concept.
Virtual 3D city and landscape models are the main subject investigated in this thesis. They digitally represent urban space and have many applications in different domains, e.g., simulation, cadastral management, and city planning. Visualization is an elementary component of these applications. Photo-realistic visualization with an increasingly high degree of detail leads to fundamental problems for comprehensible visualization. A large number of highly detailed and textured objects within a virtual 3D city model may create visual noise and overload the users with information. Objects are subject to perspective foreshortening and may be occluded or not displayed in a meaningful way, as they are too small. In this thesis we present abstraction techniques that automatically process virtual 3D city and landscape models to derive abstracted representations. These have a reduced degree of detail, while essential characteristics are preserved. After introducing definitions for model, scale, and multi-scale representations, we discuss the fundamentals of map generalization as well as techniques for 3D generalization. The first presented technique is a cell-based generalization of virtual 3D city models. It creates abstract representations that have a highly reduced level of detail while maintaining essential structures, e.g., the infrastructure network, landmark buildings, and free spaces. The technique automatically partitions the input virtual 3D city model into cells based on the infrastructure network. The single building models contained in each cell are aggregated to abstracted cell blocks. Using weighted infrastructure elements, cell blocks can be computed on different hierarchical levels, storing the hierarchy relation between the cell blocks. Furthermore, we identify initial landmark buildings within a cell by comparing the properties of individual buildings with the aggregated properties of the cell. For each block, the identified landmark building models are subtracted using Boolean operations and integrated in a photo-realistic way. Finally, for the interactive 3D visualization we discuss the creation of the virtual 3D geometry and their appearance styling through colors, labeling, and transparency. We demonstrate the technique with example data sets. Additionally, we discuss applications of generalization lenses and transitions between abstract representations. The second technique is a real-time-rendering technique for geometric enhancement of landmark objects within a virtual 3D city model. Depending on the virtual camera distance, landmark objects are scaled to ensure their visibility within a specific distance interval while deforming their environment. First, in a preprocessing step a landmark hierarchy is computed, this is then used to derive distance intervals for the interactive rendering. At runtime, using the virtual camera distance, a scaling factor is computed and applied to each landmark. The scaling factor is interpolated smoothly at the interval boundaries using cubic Bézier splines. Non-landmark geometry that is near landmark objects is deformed with respect to a limited number of landmarks. We demonstrate the technique by applying it to a highly detailed virtual 3D city model and a generalized 3D city model. In addition we discuss an adaptation of the technique for non-linear projections and mobile devices. The third technique is a real-time rendering technique to create abstract 3D isocontour visualization of virtual 3D terrain models. The virtual 3D terrain model is visualized as a layered or stepped relief. The technique works without preprocessing and, as it is implemented using programmable graphics hardware, can be integrated with minimal changes into common terrain rendering techniques. Consequently, the computation is done in the rendering pipeline for each vertex, primitive, i.e., triangle, and fragment. For each vertex, the height is quantized to the nearest isovalue. For each triangle, the vertex configuration with respect to their isovalues is determined first. Using the configuration, the triangle is then subdivided. The subdivision forms a partial step geometry aligned with the triangle. For each fragment, the surface appearance is determined, e.g., depending on the surface texture, shading, and height-color-mapping. Flexible usage of the technique is demonstrated with applications from focus+context visualization, out-of-core terrain rendering, and information visualization. This thesis presents components for the creation of abstract representations of virtual 3D city and landscape models. Re-using visual language from cartography, the techniques enable users to build on their experience with maps when interpreting these representations. Simultaneously, characteristics of 3D geovirtual environments are taken into account by addressing and discussing, e.g., continuous scale, interaction, and perspective.
In the early days of computer graphics, research was mainly driven by the goal to create realistic synthetic imagery. By contrast, non-photorealistic computer graphics, established as its own branch of computer graphics in the early 1990s, is mainly motivated by concepts and principles found in traditional art forms, such as painting, illustration, and graphic design, and it investigates concepts and techniques that abstract from reality using expressive, stylized, or illustrative rendering techniques. This thesis focuses on the artistic stylization of two-dimensional content and presents several novel automatic techniques for the creation of simplified stylistic illustrations from color images, video, and 3D renderings. Primary innovation of these novel techniques is that they utilize the smooth structure tensor as a simple and efficient way to obtain information about the local structure of an image. More specifically, this thesis contributes to knowledge in this field in the following ways. First, a comprehensive review of the structure tensor is provided. In particular, different methods for integrating the minor eigenvector field of the smoothed structure tensor are developed, and the superiority of the smoothed structure tensor over the popular edge tangent flow is demonstrated. Second, separable implementations of the popular bilateral and difference of Gaussians filters that adapt to the local structure are presented. These filters avoid artifacts while being computationally highly efficient. Taken together, both provide an effective way to create a cartoon-style effect. Third, a generalization of the Kuwahara filter is presented that avoids artifacts by adapting the shape, scale, and orientation of the filter to the local structure. This causes directional image features to be better preserved and emphasized, resulting in overall sharper edges and a more feature-abiding painterly effect. In addition to the single-scale variant, a multi-scale variant is presented, which is capable of performing a highly aggressive abstraction. Fourth, a technique that builds upon the idea of combining flow-guided smoothing with shock filtering is presented, allowing for an aggressive exaggeration and an emphasis of directional image features. All presented techniques are suitable for temporally coherent per-frame filtering of video or dynamic 3D renderings, without requiring expensive extra processing, such as optical flow. Moreover, they can be efficiently implemented to process content in real-time on a GPU.
In many applications one is faced with the problem of inferring some functional relation between input and output variables from given data. Consider, for instance, the task of email spam filtering where one seeks to find a model which automatically assigns new, previously unseen emails to class spam or non-spam. Building such a predictive model based on observed training inputs (e.g., emails) with corresponding outputs (e.g., spam labels) is a major goal of machine learning. Many learning methods assume that these training data are governed by the same distribution as the test data which the predictive model will be exposed to at application time. That assumption is violated when the test data are generated in response to the presence of a predictive model. This becomes apparent, for instance, in the above example of email spam filtering. Here, email service providers employ spam filters and spam senders engineer campaign templates such as to achieve a high rate of successful deliveries despite any filters. Most of the existing work casts such situations as learning robust models which are unsusceptible against small changes of the data generation process. The models are constructed under the worst-case assumption that these changes are performed such to produce the highest possible adverse effect on the performance of the predictive model. However, this approach is not capable to realistically model the true dependency between the model-building process and the process of generating future data. We therefore establish the concept of prediction games: We model the interaction between a learner, who builds the predictive model, and a data generator, who controls the process of data generation, as an one-shot game. The game-theoretic framework enables us to explicitly model the players' interests, their possible actions, their level of knowledge about each other, and the order at which they decide for an action. We model the players' interests as minimizing their own cost function which both depend on both players' actions. The learner's action is to choose the model parameters and the data generator's action is to perturbate the training data which reflects the modification of the data generation process with respect to the past data. We extensively study three instances of prediction games which differ regarding the order in which the players decide for their action. We first assume that both player choose their actions simultaneously, that is, without the knowledge of their opponent's decision. We identify conditions under which this Nash prediction game has a meaningful solution, that is, a unique Nash equilibrium, and derive algorithms that find the equilibrial prediction model. As a second case, we consider a data generator who is potentially fully informed about the move of the learner. This setting establishes a Stackelberg competition. We derive a relaxed optimization criterion to determine the solution of this game and show that this Stackelberg prediction game generalizes existing prediction models. Finally, we study the setting where the learner observes the data generator's action, that is, the (unlabeled) test data, before building the predictive model. As the test data and the training data may be governed by differing probability distributions, this scenario reduces to learning under covariate shift. We derive a new integrated as well as a two-stage method to account for this data set shift. In case studies on email spam filtering we empirically explore properties of all derived models as well as several existing baseline methods. We show that spam filters resulting from the Nash prediction game as well as the Stackelberg prediction game in the majority of cases outperform other existing baseline methods.
Business process models are used within a range of organizational initiatives, where every stakeholder has a unique perspective on a process and demands the respective model. As a consequence, multiple process models capturing the very same business process coexist. Keeping such models in sync is a challenge within an ever changing business environment: once a process is changed, all its models have to be updated. Due to a large number of models and their complex relations, model maintenance becomes error-prone and expensive. Against this background, business process model abstraction emerged as an operation reducing the number of stored process models and facilitating model management. Business process model abstraction is an operation preserving essential process properties and leaving out insignificant details in order to retain information relevant for a particular purpose. Process model abstraction has been addressed by several researchers. The focus of their studies has been on particular use cases and model transformations supporting these use cases. This thesis systematically approaches the problem of business process model abstraction shaping the outcome into a framework. We investigate the current industry demand in abstraction summarizing it in a catalog of business process model abstraction use cases. The thesis focuses on one prominent use case where the user demands a model with coarse-grained activities and overall process ordering constraints. We develop model transformations that support this use case starting with the transformations based on process model structure analysis. Further, abstraction methods considering the semantics of process model elements are investigated. First, we suggest how semantically related activities can be discovered in process models-a barely researched challenge. The thesis validates the designed abstraction methods against sets of industrial process models and discusses the method implementation aspects. Second, we develop a novel model transformation, which combined with the related activity discovery allows flexible non-hierarchical abstraction. In this way this thesis advocates novel model transformations that facilitate business process model management and provides the foundations for innovative tool support.
The constantly growing capacity of reconfigurable devices allows simultaneous execution of complex applications on those devices. The mere diversity of applications deems it impossible to design an interconnection network matching the requirements of every possible application perfectly, leading to suboptimal performance in many cases. However, the architecture of the interconnection network is not the only aspect affecting performance of communication. The resource manager places applications on the device and therefore influences latency between communicating partners and overall network load. Communication protocols affect performance by introducing data and processing overhead putting higher load on the network and increasing resource demand. Approaching communication holistically not only considers the architecture of the interconnect, but communication-aware resource management, communication protocols and resource usage just as well. Incorporation of different parts of a reconfigurable system during design- and runtime and optimizing them with respect to communication demand results in more resource efficient communication. Extensive evaluation shows enhanced performance and flexibility, if communication on reconfigurable devices is regarded in a holistic fashion.
Parsability approaches of several grammar formalisms generating also non-context-free languages are explored. Chomsky grammars, Lindenmayer systems, grammars with controlled derivations, and grammar systems are treated. Formal properties of these mechanisms are investigated, when they are used as language acceptors. Furthermore, cooperating distributed grammar systems are restricted so that efficient deterministic parsing without backtracking becomes possible. For this class of grammar systems, the parsing algorithm is presented and the feature of leftmost derivations is investigated in detail.
Biology has made great progress in identifying and measuring the building blocks of life. The availability of high-throughput methods in molecular biology has dramatically accelerated the growth of biological knowledge for various organisms. The advancements in genomic, proteomic and metabolomic technologies allow for constructing complex models of biological systems. An increasing number of biological repositories is available on the web, incorporating thousands of biochemical reactions and genetic regulations. Systems Biology is a recent research trend in life science, which fosters a systemic view on biology. In Systems Biology one is interested in integrating the knowledge from all these different sources into models that capture the interaction of these entities. By studying these models one wants to understand the emerging properties of the whole system, such as robustness. However, both measurements as well as biological networks are prone to considerable incompleteness, heterogeneity and mutual inconsistency, which makes it highly non-trivial to draw biologically meaningful conclusions in an automated way. Therefore, we want to promote Answer Set Programming (ASP) as a tool for discrete modeling in Systems Biology. ASP is a declarative problem solving paradigm, in which a problem is encoded as a logic program such that its answer sets represent solutions to the problem. ASP has intrinsic features to cope with incompleteness, offers a rich modeling language and highly efficient solving technology. We present ASP solutions, for the analysis of genetic regulatory networks, determining consistency with observed measurements and identifying minimal causes for inconsistency. We extend this approach for computing minimal repairs on model and data that restore consistency. This method allows for predicting unobserved data even in case of inconsistency. Further, we present an ASP approach to metabolic network expansion. This approach exploits the easy characterization of reachability in ASP and its various reasoning methods, to explore the biosynthetic capabilities of metabolic reaction networks and generate hypotheses for extending the network. Finally, we present the BioASP library, a Python library which encapsulates our ASP solutions into the imperative programming paradigm. The library allows for an easy integration of ASP solution into system rich environments, as they exist in Systems Biology.
Most of the microelectronic circuits fabricated today are synchronous, i.e. they are driven by one or several clock signals. Synchronous circuit design faces several fundamental challenges such as high-speed clock distribution, integration of multiple cores operating at different clock rates, reduction of power consumption and dealing with voltage, temperature, manufacturing and runtime variations. Asynchronous or clockless design plays a key role in alleviating these challenges, however the design and test of asynchronous circuits is much more difficult in comparison to their synchronous counterparts. A driving force for a widespread use of asynchronous technology is the availability of mature EDA (Electronic Design Automation) tools which provide an entire automated design flow starting from an HDL (Hardware Description Language) specification yielding the final circuit layout. Even though there was much progress in developing such EDA tools for asynchronous circuit design during the last two decades, the maturity level as well as the acceptance of them is still not comparable with tools for synchronous circuit design. In particular, logic synthesis (which implies the application of Boolean minimisation techniques) for the entire system's control path can significantly improve the efficiency of the resulting asynchronous implementation, e.g. in terms of chip area and performance. However, logic synthesis, in particular for asynchronous circuits, suffers from complexity problems. Signal Transitions Graphs (STGs) are labelled Petri nets which are a widely used to specify the interface behaviour of speed independent (SI) circuits - a robust subclass of asynchronous circuits. STG decomposition is a promising approach to tackle complexity problems like state space explosion in logic synthesis of SI circuits. The (structural) decomposition of STGs is guided by a partition of the output signals and generates a usually much smaller component STG for each partition member, i.e. a component STG with a much smaller state space than the initial specification. However, decomposition can result in component STGs that in isolation have so-called irreducible CSC conflicts (i.e. these components are not SI synthesisable anymore) even if the specification has none of them. A new approach is presented to avoid such conflicts by introducing internal communication between the components. So far, STG decompositions are guided by the finest output partitions, i.e. one output per component. However, this might not yield optimal circuit implementations. Efficient heuristics are presented to determine coarser partitions leading to improved circuits in terms of chip area. For the new algorithms correctness proofs are given and their implementations are incorporated into the decomposition tool DESIJ. The presented techniques are successfully applied to some benchmarks - including 'real-life' specifications arising in the context of control resynthesis - which delivered promising results.
Service-oriented Architectures (SOA) facilitate the provision and orchestration of business services to enable a faster adoption to changing business demands. Web Services provide a technical foundation to implement this paradigm on the basis of XML-messaging. However, the enhanced flexibility of message-based systems comes along with new threats and risks. To face these issues, a variety of security mechanisms and approaches is supported by the Web Service specifications. The usage of these security mechanisms and protocols is configured by stating security requirements in security policies. However, security policy languages for SOA are complex and difficult to create due to the expressiveness of these languages. To facilitate and simplify the creation of security policies, this thesis presents a model-driven approach that enables the generation of complex security policies on the basis of simple security intentions. SOA architects can specify these intentions in system design models and are not required to deal with complex technical security concepts. The approach introduced in this thesis enables the enhancement of any system design modelling languages – for example FMC or BPMN – with security modelling elements. The syntax, semantics, and notion of these elements is defined by our security modelling language SecureSOA. The metamodel of this language provides extension points to enable the integration into system design modelling languages. In particular, this thesis demonstrates the enhancement of FMC block diagrams with SecureSOA. To enable the model-driven generation of security policies, a domain-independent policy model is introduced in this thesis. This model provides an abstraction layer for security policies. Mappings are used to perform the transformation from our model to security policy languages. However, expert knowledge is required to generate instances of this model on the basis of simple security intentions. Appropriate security mechanisms, protocols and options must be chosen and combined to fulfil these security intentions. In this thesis, a formalised system of security patterns is used to represent this knowledge and to enable an automated transformation process. Moreover, a domain-specific language is introduced to state security patterns in an accessible way. On the basis of this language, a system of security configuration patterns is provided to transform security intentions related to data protection and identity management. The formal semantics of the security pattern language enable the verification of the transformation process introduced in this thesis and prove the correctness of the pattern application. Finally, our SOA Security LAB is presented that demonstrates the application of our model-driven approach to facilitate a dynamic creation, configuration, and execution of secure Web Service-based composed applications.
Structuring process models
(2012)
One can fairly adopt the ideas of Donald E. Knuth to conclude that process modeling is both a science and an art. Process modeling does have an aesthetic sense. Similar to composing an opera or writing a novel, process modeling is carried out by humans who undergo creative practices when engineering a process model. Therefore, the very same process can be modeled in a myriad number of ways. Once modeled, processes can be analyzed by employing scientific methods. Usually, process models are formalized as directed graphs, with nodes representing tasks and decisions, and directed arcs describing temporal constraints between the nodes. Common process definition languages, such as Business Process Model and Notation (BPMN) and Event-driven Process Chain (EPC) allow process analysts to define models with arbitrary complex topologies. The absence of structural constraints supports creativity and productivity, as there is no need to force ideas into a limited amount of available structural patterns. Nevertheless, it is often preferable that models follow certain structural rules. A well-known structural property of process models is (well-)structuredness. A process model is (well-)structured if and only if every node with multiple outgoing arcs (a split) has a corresponding node with multiple incoming arcs (a join), and vice versa, such that the set of nodes between the split and the join induces a single-entry-single-exit (SESE) region; otherwise the process model is unstructured. The motivations for well-structured process models are manifold: (i) Well-structured process models are easier to layout for visual representation as their formalizations are planar graphs. (ii) Well-structured process models are easier to comprehend by humans. (iii) Well-structured process models tend to have fewer errors than unstructured ones and it is less probable to introduce new errors when modifying a well-structured process model. (iv) Well-structured process models are better suited for analysis with many existing formal techniques applicable only for well-structured process models. (v) Well-structured process models are better suited for efficient execution and optimization, e.g., when discovering independent regions of a process model that can be executed concurrently. Consequently, there are process modeling languages that encourage well-structured modeling, e.g., Business Process Execution Language (BPEL) and ADEPT. However, the well-structured process modeling implies some limitations: (i) There exist processes that cannot be formalized as well-structured process models. (ii) There exist processes that when formalized as well-structured process models require a considerable duplication of modeling constructs. Rather than expecting well-structured modeling from start, we advocate for the absence of structural constraints when modeling. Afterwards, automated methods can suggest, upon request and whenever possible, alternative formalizations that are "better" structured, preferably well-structured. In this thesis, we study the problem of automatically transforming process models into equivalent well-structured models. The developed transformations are performed under a strong notion of behavioral equivalence which preserves concurrency. The findings are implemented in a tool, which is publicly available.