TY - JOUR A1 - Prasse, Paul A1 - Knaebel, Rene A1 - Machlica, Lukas A1 - Pevny, Tomas A1 - Scheffer, Tobias T1 - Joint detection of malicious domains and infected clients JF - Machine learning N2 - Detection of malware-infected computers and detection of malicious web domains based on their encrypted HTTPS traffic are challenging problems, because only addresses, timestamps, and data volumes are observable. The detection problems are coupled, because infected clients tend to interact with malicious domains. Traffic data can be collected at a large scale, and antivirus tools can be used to identify infected clients in retrospect. Domains, by contrast, have to be labeled individually after forensic analysis. We explore transfer learning based on sluice networks; this allows the detection models to bootstrap each other. In a large-scale experimental study, we find that the model outperforms known reference models and detects previously unknown malware, previously unknown malware families, and previously unknown malicious domains. KW - Machine learning KW - Neural networks KW - Computer security KW - Traffic data KW - Https traffic Y1 - 2019 U6 - https://doi.org/10.1007/s10994-019-05789-z SN - 0885-6125 SN - 1573-0565 VL - 108 IS - 8-9 SP - 1353 EP - 1368 PB - Springer CY - Dordrecht ER - TY - THES A1 - Ashouri, Mohammadreza T1 - TrainTrap BT - a hybrid technique for vulnerability analysis in JAVA Y1 - 2020 ER - TY - JOUR A1 - Laskov, Pavel A1 - Gehl, Christian A1 - Krüger, Stefan A1 - Müller, Klaus-Robert T1 - Incremental support vector learning: analysis, implementation and applications JF - Journal of machine learning research N2 - Incremental Support Vector Machines (SVM) are instrumental in practical applications of online learning. This work focuses on the design and analysis of efficient incremental SVM learning, with the aim of providing a fast, numerically stable and robust implementation. A detailed analysis of convergence and of algorithmic complexity of incremental SVM learning is carried out. Based on this analysis, a new design of storage and numerical operations is proposed, which speeds up the training of an incremental SVM by a factor of 5 to 20. The performance of the new algorithm is demonstrated in two scenarios: learning with limited resources and active learning. Various applications of the algorithm, such as in drug discovery, online monitoring of industrial devices and and surveillance of network traffic, can be foreseen. KW - incremental SVM KW - online learning KW - drug discovery KW - intrusion detection Y1 - 2006 SN - 1532-4435 VL - 7 SP - 1909 EP - 1936 PB - MIT Press CY - Cambridge, Mass. ER - TY - JOUR A1 - Steuer, Ralf A1 - Humburg, Peter A1 - Selbig, Joachim T1 - Validation and functional annotation of expression-based clusters based on gene ontology JF - BMC bioinformatics N2 - Background: The biological interpretation of large-scale gene expression data is one of the paramount challenges in current bioinformatics. In particular, placing the results in the context of other available functional genomics data, such as existing bio-ontologies, has already provided substantial improvement for detecting and categorizing genes of interest. One common approach is to look for functional annotations that are significantly enriched within a group or cluster of genes, as compared to a reference group. Results: In this work, we suggest the information-theoretic concept of mutual information to investigate the relationship between groups of genes, as given by data-driven clustering, and their respective functional categories. Drawing upon related approaches (Gibbons and Roth, Genome Research 12: 1574-1581, 2002), we seek to quantify to what extent individual attributes are sufficient to characterize a given group or cluster of genes. Conclusion: We show that the mutual information provides a systematic framework to assess the relationship between groups or clusters of genes and their functional annotations in a quantitative way. Within this framework, the mutual information allows us to address and incorporate several important issues, such as the interdependence of functional annotations and combinatorial combinations of attributes. It thus supplements and extends the conventional search for overrepresented attributes within a group or cluster of genes. In particular taking combinations of attributes into account, the mutual information opens the way to uncover specific functional descriptions of a group of genes or clustering result. All datasets and functional annotations used in this study are publicly available. All scripts used in the analysis are provided as additional files. Y1 - 2006 U6 - https://doi.org/10.1186/1471-2105-7-380 SN - 1471-2105 VL - 7 IS - 380 PB - BioMed Central CY - London ER - TY - JOUR A1 - Sarsakov, Vladimir A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - A compiler for nested logic programming Y1 - 2004 SN - 3-540- 20721-x ER - TY - JOUR A1 - Linke, Thomas A1 - Tompits, Hans A1 - Woltran, Stefan T1 - On Acyclic and head-cycle free nested logic programs Y1 - 2004 SN - 3-540-22671-01 ER - TY - JOUR A1 - Linke, Thomas A1 - Tompits, Hans A1 - Woltran, Stefan T1 - On acyclic and head-cycle free nested logic programs Y1 - 2004 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - On Computing belief change operations using quantifield boolean formulas N2 - In this paper, we show how an approach to belief revision and belief contraction can be axiomatized by means of quantified Boolean formulas. Specifically, we consider the approach of belief change scenarios, a general framework that has been introduced for expressing different forms of belief change. The essential idea is that for a belief change scenario (K, R, C), the set of formulas K, representing the knowledge base, is modified so that the sets of formulas R and C are respectively true in, and consistent with the result. By restricting the form of a belief change scenario, one obtains specific belief change operators including belief revision, contraction, update, and merging. For both the general approach and for specific operators, we give a quantified Boolean formula such that satisfying truth assignments to the free variables correspond to belief change extensions in the original approach. Hence, we reduce the problem of determining the results of a belief change operation to that of satisfiability. This approach has several benefits. First, it furnishes an axiomatic specification of belief change with respect to belief change scenarios. This then leads to further insight into the belief change framework. Second, this axiomatization allows us to identify strict complexity bounds for the considered reasoning tasks. Third, we have implemented these different forms of belief change by means of existing solvers for quantified Boolean formulas. As well, it appears that this approach may be straightforwardly applied to other specific approaches to belief change Y1 - 2004 SN - 0955-792X ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - On computing solutions to belief change scenarios Y1 - 2001 SN - 3-540- 42464-4 ER - TY - JOUR A1 - Pearce, David A1 - Sarsakov, Vladimir A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - A polynomial translation of logic programs with nested expressions into disjunctive logic programs Y1 - 2002 SN - 3-540-43930-7 ER - TY - JOUR A1 - Besnard, Philippe A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - Paraconsistent reasoning via quantified boolean formulas Y1 - 2002 SN - 3-540-44190-5 ER - TY - JOUR A1 - Brain, Martin A1 - Gebser, Martin A1 - Pührer, Jörg A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - "That is illogical, Captain!" : the debugging support tool spock for answer-set programs ; system description Y1 - 2007 ER - TY - JOUR A1 - Pearce, David A1 - Sarsakov, Vladimir A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - A polynomial translation of logic programs with nested expressions into disjunctive logic programs : preliminary report Y1 - 2002 ER - TY - JOUR A1 - Schaub, Torsten H. A1 - Woltran, Stefan T1 - Answer set programming unleashed! JF - Künstliche Intelligenz N2 - Answer Set Programming faces an increasing popularity for problem solving in various domains. While its modeling language allows us to express many complex problems in an easy way, its solving technology enables their effective resolution. In what follows, we detail some of the key factors of its success. Answer Set Programming [ASP; Brewka et al. Commun ACM 54(12):92–103, (2011)] is seeing a rapid proliferation in academia and industry due to its easy and flexible way to model and solve knowledge-intense combinatorial (optimization) problems. To this end, ASP offers a high-level modeling language paired with high-performance solving technology. As a result, ASP systems provide out-off-the-box, general-purpose search engines that allow for enumerating (optimal) solutions. They are represented as answer sets, each being a set of atoms representing a solution. The declarative approach of ASP allows a user to concentrate on a problem’s specification rather than the computational means to solve it. This makes ASP a prime candidate for rapid prototyping and an attractive tool for teaching key AI techniques since complex problems can be expressed in a succinct and elaboration tolerant way. This is eased by the tuning of ASP’s modeling language to knowledge representation and reasoning (KRR). The resulting impact is nicely reflected by a growing range of successful applications of ASP [Erdem et al. AI Mag 37(3):53–68, 2016; Falkner et al. Industrial applications of answer set programming. K++nstliche Intelligenz (2018)] Y1 - 2018 U6 - https://doi.org/10.1007/s13218-018-0550-z SN - 0933-1875 SN - 1610-1987 VL - 32 IS - 2-3 SP - 105 EP - 108 PB - Springer CY - Heidelberg ER - TY - GEN A1 - Schaub, Torsten H. A1 - Woltran, Stefan T1 - Special issue on answer set programming T2 - Künstliche Intelligenz Y1 - 2018 U6 - https://doi.org/10.1007/s13218-018-0554-8 SN - 0933-1875 SN - 1610-1987 VL - 32 IS - 2-3 SP - 101 EP - 103 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Besnard, Philippe A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - Paraconsistent reasoning via quantified boolean formulas : Part II: Circumscribing inconsistent theories Y1 - 2003 SN - 3-540- 409494-5 ER - TY - JOUR A1 - Delgrande, James A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - A model-theoretic approach to belief change in answer set programming JF - ACM transactions on computational logic N2 - We address the problem of belief change in (nonmonotonic) logic programming under answer set semantics. Our formal techniques are analogous to those of distance-based belief revision in propositional logic. In particular, we build upon the model theory of logic programs furnished by SE interpretations, where an SE interpretation is a model of a logic program in the same way that a classical interpretation is a model of a propositional formula. Hence we extend techniques from the area of belief revision based on distance between models to belief change in logic programs. We first consider belief revision: for logic programs P and Q, the goal is to determine a program R that corresponds to the revision of P by Q, denoted P * Q. We investigate several operators, including (logic program) expansion and two revision operators based on the distance between the SE models of logic programs. It proves to be the case that expansion is an interesting operator in its own right, unlike in classical belief revision where it is relatively uninteresting. Expansion and revision are shown to satisfy a suite of interesting properties; in particular, our revision operators satisfy all or nearly all of the AGM postulates for revision. We next consider approaches for merging a set of logic programs, P-1,...,P-n. Again, our formal techniques are based on notions of relative distance between the SE models of the logic programs. Two approaches are examined. The first informally selects for each program P-i those models of P-i that vary the least from models of the other programs. The second approach informally selects those models of a program P-0 that are closest to the models of programs P-1,...,P-n. In this case, P-0 can be thought of as a set of database integrity constraints. We examine these operators with regards to how they satisfy relevant postulate sets. Last, we present encodings for computing the revision as well as the merging of logic programs within the same logic programming framework. This gives rise to a direct implementation of our approach in terms of off-the-shelf answer set solvers. These encodings also reflect the fact that our change operators do not increase the complexity of the base formalism. KW - Theory KW - Answer set programming KW - belief revision KW - belief merging KW - program encodings KW - strong equivalence Y1 - 2013 U6 - https://doi.org/10.1145/2480759.2480766 SN - 1529-3785 VL - 14 IS - 2 PB - Association for Computing Machinery CY - New York ER - TY - JOUR A1 - Brain, Martin A1 - Gebser, Martin A1 - Pührer, Jörg A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - Debugging ASP programs by means of ASP Y1 - 2007 SN - 978-3-540- 72199-4 ER - TY - JOUR A1 - Gebser, Martin A1 - Schaub, Torsten H. A1 - Tompits, Hans A1 - Woltran, Stefan T1 - Alternative characterizations for program equivalence under aswer-set semantics : a preliminary report Y1 - 2007 ER - TY - JOUR A1 - Bordihn, Henning A1 - Fernau, Henning A1 - Holzer, Markus A1 - Manca, Vincenzo A1 - Martin-Vide, Carlos T1 - Iterated sequential transducers as language generating devices JF - Theoretical computer science N2 - Iterated finite state sequential transducers are considered as language generating devices. The hierarchy induced by the size of the state alphabet is proved to collapse to the fourth level. The corresponding language families are related to the families of languages generated by Lindenmayer systems and Chomsky grammars. Finally, some results on deterministic and extended iterated finite state transducers are established. KW - finite state sequential transducers KW - state complexity KW - Lindenmayer systems Y1 - 2006 U6 - https://doi.org/10.1016/j.tcs.2006.07.059 SN - 0304-3975 VL - 369 IS - 1 SP - 67 EP - 81 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Stoffel, Dominik A1 - Kunz, Wolfgang A1 - Gerber, Stefan T1 - And/Or reasoning graphs for determining prime implicants in multi-level combinational networks Y1 - 1997 ER - TY - THES A1 - Gerber, Stefan T1 - Using software for fault detection in arithmetical circuits Y1 - 1995 ER - TY - JOUR A1 - Baier, Thomas A1 - Di Ciccio, Claudio A1 - Mendling, Jan A1 - Weske, Mathias T1 - Matching events and activities by integrating behavioral aspects and label analysis JF - Software and systems modeling N2 - Nowadays, business processes are increasingly supported by IT services that produce massive amounts of event data during the execution of a process. These event data can be used to analyze the process using process mining techniques to discover the real process, measure conformance to a given process model, or to enhance existing models with performance information. Mapping the produced events to activities of a given process model is essential for conformance checking, annotation and understanding of process mining results. In order to accomplish this mapping with low manual effort, we developed a semi-automatic approach that maps events to activities using insights from behavioral analysis and label analysis. The approach extracts Declare constraints from both the log and the model to build matching constraints to efficiently reduce the number of possible mappings. These mappings are further reduced using techniques from natural language processing, which allow for a matching based on labels and external knowledge sources. The evaluation with synthetic and real-life data demonstrates the effectiveness of the approach and its robustness toward non-conforming execution logs. KW - Process mining KW - Event mapping KW - Business process intelligence KW - Constraint satisfaction KW - Declare KW - Natural language processing Y1 - 2018 U6 - https://doi.org/10.1007/s10270-017-0603-z SN - 1619-1366 SN - 1619-1374 VL - 17 IS - 2 SP - 573 EP - 598 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Przybylla, Mareen A1 - Romeike, Ralf T1 - Empowering learners with tools in CS education BT - physical computing in secondary schools JF - it - Information Technology N2 - In computer science, computer systems are both, objects of investigation and tools that enable creative learning and design. Tools for learning have a long tradition in computer science education. Already in the late 1960s, Papert developed a concept which had an immense impact on the development of informal education in the following years: his theory of constructionism understands learning as a creative process of knowledge construction that is most effective when learners create something purposeful that they can try out, show around, discuss, analyse and receive praise for. By now, there are numerous learning and programming environments that are based on the constructionist ideas. Modern tools offer opportunities for students to learn in motivating ways and gain impressive results in programming games, animations, implementing 3D models or developing interactive objects. This article gives an overview of computer science education research related to tools and media to be used in educational settings. We analyse different types of tools with a special focus on the categorization and development of tools for student adequate physical computing activities in the classroom. Research around the development and evaluation of tools and learning resources in the domain of physical computing is illustrated with the example of "My Interactive Garden", a constructionist learning and programming environment. It is explained how the results from empirical studies are integrated in the continuous development of the learning material. KW - tools KW - media KW - resources KW - computer science education KW - physical computing Y1 - 2018 U6 - https://doi.org/10.1515/itit-2017-0032 SN - 1611-2776 SN - 2196-7032 VL - 60 IS - 2 SP - 91 EP - 101 PB - De Gruyter CY - Berlin ER - TY - GEN A1 - Frank, Mario A1 - Kreitz, Christoph T1 - A theorem prover for scientific and educational purposes T2 - Electronic proceedings in theoretical computer science N2 - We present a prototype of an integrated reasoning environment for educational purposes. The presented tool is a fragment of a proof assistant and automated theorem prover. We describe the existing and planned functionality of the theorem prover and especially the functionality of the educational fragment. This currently supports working with terms of the untyped lambda calculus and addresses both undergraduate students and researchers. We show how the tool can be used to support the students' understanding of functional programming and discuss general problems related to the process of building theorem proving software that aims at supporting both research and education. Y1 - 2018 U6 - https://doi.org/10.4204/EPTCS.267.4 SN - 2075-2180 IS - 267 SP - 59 EP - 69 PB - Open Publishing Association CY - Sydney ER - TY - GEN A1 - Schäpers, Björn A1 - Niemueller, Tim A1 - Lakemeyer, Gerhard A1 - Gebser, Martin A1 - Schaub, Torsten H. T1 - ASP-Based Time-Bounded Planning for Logistics Robots T2 - Twenty-Eighth International Conference on Automated Planning and Scheduling (ICAPS 2018) N2 - Manufacturing industries are undergoing a major paradigm shift towards more autonomy. Automated planning and scheduling then becomes a necessity. The Planning and Execution Competition for Logistics Robots in Simulation held at ICAPS is based on this scenario and provides an interesting testbed. However, the posed problem is challenging as also demonstrated by the somewhat weak results in 2017. The domain requires temporal reasoning and dealing with uncertainty. We propose a novel planning system based on Answer Set Programming and the Clingo solver to tackle these problems and incentivize robot cooperation. Our results show a significant performance improvement, both, in terms of lowering computational requirements and better game metrics. Y1 - 2018 SN - 2334-0835 SN - 2334-0843 SP - 509 EP - 517 PB - ASSOC Association for the Advancement of Artificial Intelligence CY - Palo Alto ER - TY - CHAP A1 - Knoth, Alexander Henning A1 - Kiy, Alexander T1 - (Self-)confident through the introductory study phase with the Reflect App BT - (Self-)confident through the introductory study phase with the Reflect App T2 - CEUR Workshop Proceedings T2 - Selbst-bewusst durch die Studieneingangsphase mit der Reflect-App Y1 - 2014 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84921875162&partnerID=MN8TOARS SN - 1613-0073 IS - 1227 SP - 172 EP - 179 PB - CEUR-WS CY - Freiburg ER - TY - JOUR A1 - Ly, Ibrahim A1 - Tarkhanov, Nikolai Nikolaevich T1 - A variational approach to the Cauchy problem for nonlinear elliptic differential equations N2 - We discuss the relaxation of a class of nonlinear elliptic Cauchy problems with data on a piece S of the boundary surface by means of a variational approach known in the optimal control literature as "equation error method". By the Cauchy problem is meant any boundary value problem for an unknown function y in a domain X with the property that the data on S, if combined with the differential equations in X, allow one to determine all derivatives of y on S by means of functional equations. In the case of real analytic data of the Cauchy problem, the existence of a local solution near S is guaranteed by the Cauchy-Kovalevskaya theorem. We also admit overdetermined elliptic systems, in which case the set of those Cauchy data on S for which the Cauchy problem is solvable is very "thin". For this reason we discuss a variational setting of the Cauchy problem which always possesses a generalised solution. Y1 - 2009 UR - http://dx.doi.org/10.1515/jiip U6 - https://doi.org/10.1515/Jiip.2009.037 SN - 0928-0219 ER - TY - JOUR A1 - Prasse, Paul A1 - Iversen, Pascal A1 - Lienhard, Matthias A1 - Thedinga, Kristina A1 - Herwig, Ralf A1 - Scheffer, Tobias T1 - Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction JF - MDPI N2 - Large-scale databases that report the inhibitory capacities of many combinations of candidate drug compounds and cultivated cancer cell lines have driven the development of preclinical drug-sensitivity models based on machine learning. However, cultivated cell lines have devolved from human cancer cells over years or even decades under selective pressure in culture conditions. Moreover, models that have been trained on in vitro data cannot account for interactions with other types of cells. Drug-response data that are based on patient-derived cell cultures, xenografts, and organoids, on the other hand, are not available in the quantities that are needed to train high-capacity machine-learning models. We found that pre-training deep neural network models of drug sensitivity on in vitro drug-sensitivity databases before fine-tuning the model parameters on patient-derived data improves the models’ accuracy and improves the biological plausibility of the features, compared to training only on patient-derived data. From our experiments, we can conclude that pre-trained models outperform models that have been trained on the target domains in the vast majority of cases. KW - deep neural networks KW - drug-sensitivity prediction KW - anti-cancer drugs Y1 - 2022 U6 - https://doi.org/10.3390/cancers14163950 SN - 2072-6694 VL - 14 SP - 1 EP - 14 PB - MDPI CY - Basel, Schweiz ET - 16 ER - TY - JOUR A1 - Everardo Pérez, Flavio Omar A1 - Osorio, Mauricio T1 - Towards an answer set programming methodology for constructing programs following a semi-automatic approach BT - extended and revised version JF - Electronic notes in theoretical computer science N2 - Answer Set Programming (ASP) is a successful rule-based formalism for modeling and solving knowledge-intense combinatorial (optimization) problems. Despite its success in both academic and industry, open challenges like automatic source code optimization, and software engineering remains. This is because a problem encoded into an ASP might not have the desired solving performance compared to an equivalent representation. Motivated by these two challenges, this paper has three main contributions. First, we propose a developing process towards a methodology to implement ASP programs, being faithful to existing methods. Second, we present ASP encodings that serve as the basis from the developing process. Third, we demonstrate the use of ASP to reverse the standard solving process. That is, knowing answer sets in advance, and desired strong equivalent properties, “we” exhaustively reconstruct ASP programs if they exist. This paper was originally motivated by the search of propositional formulas (if they exist) that represent the semantics of a new aggregate operator. Particularly, a parity aggregate. This aggregate comes as an improvement from the already existing parity (xor) constraints from xorro, where lacks expressiveness, even though these constraints fit perfectly for reasoning modes like sampling or model counting. To this end, this extended version covers the fundaments from parity constraints as well as the xorro system. Hence, we delve a little more in the examples and the proposed methodology over parity constraints. Finally, we discuss our results by showing the only representation available, that satisfies different properties from the classical logic xor operator, which is also consistent with the semantics of parity constraints from xorro. KW - answer set programming KW - combinatorial optimization problems KW - parity aggregate operator Y1 - 2020 U6 - https://doi.org/10.1016/j.entcs.2020.10.004 SN - 1571-0661 VL - 354 SP - 29 EP - 44 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - THES A1 - Al-Saffar, Loay Talib Ahmed T1 - Analysing prerequisites, expectations, apprehensions, and attitudes of University students studying computer science Y1 - 2016 ER - TY - BOOK ED - Lambrecht, Anna-Lena ED - Margaria, Tizian T1 - Process design for natural scientists BT - an agile model-driven approach T3 - Communications in computer and information science ; 500 N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 PB - Springer CY - Wiesbaden ER - TY - THES A1 - Wust, Johannes T1 - Mixed workload managment for in-memory databases BT - executing mixed workloads of enterprise applications with TAMEX Y1 - 2015 ER - TY - JOUR A1 - Teske, Daniel T1 - Geocoder accuracy ranking JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 161 EP - 174 PB - Springer CY - Berlin ER - TY - JOUR A1 - Sens, Henriette T1 - Web-Based map generalization tools put to the test: a jABC workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 175 EP - 185 PB - Springer CY - Berlin ER - TY - JOUR A1 - Noack, Franziska T1 - CREADED: Colored-Relief application for digital elevation data JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 186 EP - 199 PB - Springer CY - Berlin ER - TY - JOUR A1 - Respondek, Tobias T1 - A workflow for computing potential areas for wind turbines JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 IS - 500 SP - 200 EP - 215 PB - Springer CY - Berlin ER - TY - JOUR A1 - Scheele, Lasse T1 - Location analysis for placing artificial reefs JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 216 EP - 228 PB - Springer CY - Berlin ER - TY - JOUR A1 - Holler, Robin T1 - GraffDok - a graffiti documentation application JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 239 EP - 251 PB - Springer CY - Berlin ER - TY - JOUR A1 - Reso, Judith ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Protein Classification Workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 65 EP - 72 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Schulze, Gunnar T1 - Workflow for rapid metagenome analysis JF - Process design for natural scientists: an agile model-driven approach N2 - 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 Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 88 EP - 100 PB - Springer CY - Berlin ER - TY - JOUR A1 - Vierheller, Janine ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Exploratory Data Analysis JF - Process Design for Natural Scientists: an agile model-driven approach N2 - In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 110 EP - 126 PB - Axel Springer Verlag CY - Berlin ER - TY - JOUR A1 - Schütt, Christine T1 - Identification of differentially expressed genes JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 127 EP - 139 PB - Springer CY - Berlin ER - TY - JOUR A1 - Kuntzsch, Christian T1 - Visualization of data transfer paths JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 140 EP - 148 PB - Springer CY - Berlin ER - TY - JOUR A1 - Hibbe, Marcel ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Spotlocator - Guess Where the Photo Was Taken! JF - Process Design for Natural Scientists: an agile model-driven approach N2 - Spotlocator is a game wherein people have to guess the spots of where photos were taken. The photos of a defined area for each game are from panoramio.com. They are published at http://spotlocator. drupalgardens.com with an ID. Everyone can guess the photo spots by sending a special tweet via Twitter that contains the hashtag #spotlocator, the guessed coordinates and the ID of the photo. An evaluation is published for all tweets. The players are informed about the distance to the real photo spots and the positions are shown on a map. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 149 EP - 160 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Blaese, Leif T1 - Data mining for unidentified protein squences JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 73 EP - 87 PB - Springer CY - Berlin ER - TY - JOUR A1 - Lis, Monika ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Constructing a Phylogenetic Tree JF - Process Design for Natural Scientists: an agile model-driven approach N2 - In this project I constructed a workflow that takes a DNA sequence as input and provides a phylogenetic tree, consisting of the input sequence and other sequences which were found during a database search. In this phylogenetic tree the sequences are arranged depending on similarities. In bioinformatics, constructing phylogenetic trees is often used to explore the evolutionary relationships of genes or organisms and to understand the mechanisms of evolution itself. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 101 EP - 109 PB - Springer Verlag CY - Berlin ER - TY - THES A1 - Lincke, Jens T1 - Evolving Tools in a Collaborative Self-supporting Development Environment Y1 - 2014 ER - TY - THES A1 - Gharib, Mona T1 - Incremental answer set programming Y1 - 2008 CY - Potsdam ER - TY - BOOK ED - Rabe, Bernhard ED - Rasche, Andreas T1 - Proceedings of the 2nd International Workshop on e-learning and Virtual and Remote Laboratories T3 - Technische Berichte des Hasso-Plattner-Instituts für Softwaresystemtechnik an der Universität Potsda Y1 - 2008 SN - 978-3-940793-17-1 SN - 1613-5652 VL - 21 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - BOOK A1 - de Carvalho, Jackson Marques A1 - Jürgensen, Helmut T1 - Document authoring environments and authoring mathematics T3 - Preprint / Universität Potsdam, Institut für Informatik Y1 - 2008 SN - 0946-7580 VL - 2008, 1 PB - Univ. CY - Potsdam ER - TY - BOOK A1 - Goessel, Michael A1 - Ocheretny, Vitaly A1 - Sogomonyan, Egor S. A1 - Marienfeld, Daniel T1 - New methods of concurrent checking T3 - Frontiers in electronic testing Y1 - 2008 SN - 978-1-402-08419-5 U6 - https://doi.org/10.1007/978-1-4020-8420-1 VL - 42 PB - Springer CY - Dordrecht; Heidelberg ER - TY - BOOK A1 - Tepoyan, Liparit T1 - The Mixed problem for a degenerate operator equation T3 - Preprint / Universität Potsdam, Institut für Mathematik, Arbeitsgruppe Partiell Y1 - 2008 SN - 1437-739X PB - Univ. CY - Potsdam ER - TY - THES A1 - Li, Nanjun T1 - Modeling, Simulation and Evaluation of TCP/IP Networks Y1 - 2008 CY - Potsdam ER - TY - THES A1 - Li, Nanjun T1 - Modeling, simulation and evaluation of TCP/IP Networks Y1 - 2008 ER - TY - BOOK A1 - Brauer, Uwe A1 - Karp, Lavi T1 - Well-posedness of Einstein-Euler Systems in asymptotically flat spacetimes T3 - Preprint / Universität Potsdam, Institut für Mathematik, Arbeitsgruppe Partiell Y1 - 2008 SN - 1437-739X PB - Univ. CY - Potsdam ER - TY - GEN A1 - Marques de Carvalho, Jackson W. A1 - Jürgensen, Helmut T1 - Flexible Structured Mathematics Notation : IADIS, International Conference Interfaces and Human Computer Interaction, Lisabon, 2007 T2 - Preprint / Universität Potsdam, Institut für Informatik Y1 - 2007 SN - 0946-7580 VL - 2007, 1 PB - Univ. CY - Potsdam ER - TY - BOOK A1 - Margaria, Tiziana A1 - Kubczak, Christian A1 - Steffen, Bernhard T1 - Bio-jETI: a Service Integration, Design, and Provisioning Platform for Orchestrated Bioinformatics Processes - ("part of From Components to Processes") T3 - Preprint / Universität Potsdam, Institut für Informatik Y1 - 2007 SN - 0946-7580 VL - 2007, 4 PB - Univ. CY - Potsdam ER - TY - BOOK A1 - Weske, Mathias T1 - Business Process Management : Concepts, Languages, Architectures Y1 - 2007 SN - 978-3-540-73521-2 U6 - https://doi.org/10.1007/978-3-540-73522-9 PB - Springer-Verlag Berlin Heidelberg CY - Berlin, Heidelberg ER - TY - BOOK A1 - Margaria, Tiziana ED - Messnarz, Richard T1 - Proceedings / EuroSPI 2007, European Software Process Improvement, 26.-28.09.2007, University of Potsdam, Germany Y1 - 2007 SN - 978-3-9809145-6-7 PB - ASQF CY - Erlangen ER - TY - THES A1 - Puhlmann, Frank T1 - On the application of a theory for mobile systems to business process management Y1 - 2007 CY - Potsdam ER - TY - BOOK A1 - Abrahamsson, Pekka A1 - Baddoo, Nathan A1 - Margaria, Tiziana A1 - Messnarz, Richard T1 - Software Process Improvement : 14th europea conference, EuroSpi 2007, Potsdam, Germany, September 26-28, 2007 ; Proceedings T3 - Lecture Notes in Computer Science Y1 - 2007 VL - 4764 PB - Springer CY - Berlin ER - TY - BOOK A1 - Polyvyanyy, Artem A1 - Kuropka, Dominik T1 - A Quantitative Evalution of the Enhanced Topic-based Vector Space Model T3 - Technische Berichte des Hasso-Plattner-Instituts für Softwaresystemtechnik an der Universität Potsda Y1 - 2007 SN - 978-3-939469-95-7 SN - 1613-5652 VL - 19 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - THES A1 - Rzeha, Jan T1 - Generation and Storage of Diagnosis Data On-Chip Y1 - 2007 CY - Potsdam ER - TY - JOUR A1 - Grell, Susanne A1 - Schaub, Torsten H. A1 - Selbig, Joachim T1 - Modelling biological networks by action languages via set programming Y1 - 2006 UR - http://www.cs.uni-potsdam.de/wv/pdfformat/gebsch06c.pdf U6 - https://doi.org/10.1007/11799573 SN - 0302-9743 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Schaub, Torsten H. A1 - Tompits, Hans T1 - A Preference-Based Framework for Updating logic Programs : preliminary reports Y1 - 2006 UR - http://www.easychair.org/FLoC-06/PREFS-preproceedings.pdf ER - TY - JOUR A1 - Gressmann, Jean A1 - Janhunen, Tomi A1 - Mercer, Robert E. A1 - Schaub, Torsten H. A1 - Thiele, Sven A1 - Tichy, Richard T1 - On probing and multi-threading in platypus Y1 - 2006 UR - http://www2.in.tu-clausthal.de/~tmbehrens/NMR_Proc_TR4.pdf ER - TY - BOOK ED - Jürgensen, Helmut T1 - Accessible Media : Pre-Proceedings of a Workshop Potsdam 8-9 May, 2006 T3 - Preprint / Universität Potsdam, Institut für Informatik Y1 - 2006 SN - 0946-7580 VL - 2006, 7 PB - Univ. CY - Potsdam ER - TY - BOOK A1 - Krahmer, Sebastian T1 - Generating runtime call graphs T3 - Preprint / Universität Potsdam, Institut für Informatik Y1 - 2006 SN - 0946-7580 VL - 2006, 8 PB - Univ. CY - Potsdam ER - TY - THES A1 - Leininger, Andreas T1 - New diagnosis and test methods with high compaction rates Y1 - 2006 SN - 3-86664-066-8 PB - Mensch & Buch Verl. CY - Berlin ER - TY - JOUR A1 - Anger, Christian A1 - Gebser, Martin A1 - Schaub, Torsten H. T1 - Approaching the core of unfounded sets Y1 - 2006 UR - http://www.cs.uni-potsdam.de/wv/pdfformat/angesc06a.pdf ER - TY - JOUR A1 - Shenoy, Pradeep A1 - Krauledat, Matthias A1 - Blankertz, Benjamin A1 - Rao, Rajesh P. N. A1 - Müller, Klaus-Robert T1 - Towards adaptive classification for BCI N2 - Non-stationarities are ubiquitous in EEG signals. They are especially apparent in the use of EEG-based brain- computer interfaces (BCIs): (a) in the differences between the initial calibration measurement and the online operation of a BCI, or (b) caused by changes in the subject's brain processes during an experiment (e.g. due to fatigue, change of task involvement, etc). In this paper, we quantify for the first time such systematic evidence of statistical differences in data recorded during offline and online sessions. Furthermore, we propose novel techniques of investigating and visualizing data distributions, which are particularly useful for the analysis of (non-) stationarities. Our study shows that the brain signals used for control can change substantially from the offline calibration sessions to online control, and also within a single session. In addition to this general characterization of the signals, we propose several adaptive classification schemes and study their performance on data recorded during online experiments. An encouraging result of our study is that surprisingly simple adaptive methods in combination with an offline feature selection scheme can significantly increase BCI performance Y1 - 2006 UR - http://iopscience.iop.org/1741-2552/3/1/R02/ U6 - https://doi.org/10.1088/1741-2560/3/1/R02 ER - TY - JOUR A1 - Bobda, Christophe T1 - Special issue on ReCoSoC 2007 : editorial Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/01419331 U6 - https://doi.org/10.1016/j.micpro.2009.01.001 SN - 0141-9331 ER - TY - JOUR A1 - Blankertz, Benjamin A1 - Dornhege, Guido A1 - Krauledat, Matthias A1 - Müller, Klaus-Robert A1 - Kunzmann, Volker A1 - Losch, Florian A1 - Curio, Gabriel T1 - The Berlin brain-computer interface : EEG-based communication without subject training N2 - The Berlin Brain-Computer Interface (BBCI) project develops a noninvasive BCI system whose key features are 1) the use of well-established motor competences as control paradigms, 2) high-dimensional features from 128-channel electroencephalogram (EEG), and 3) advanced machine learning techniques. As reported earlier, our experiments demonstrate that very high information transfer rates can be achieved using the readiness potential (RP) when predicting the laterality of upcoming left-versus right-hand movements in healthy subjects. A more recent study showed that the RP similarily accompanies phantom movements in arm amputees, but the signal strength decreases with longer loss of the limb. In a complementary approach, oscillatory features are used to discriminate imagined movements (left hand versus right hand versus foot). In a recent feedback study with six healthy subjects with no or very little experience with BCI control, three subjects achieved an information transfer rate above 35 bits per minute (bpm), and further two subjects above 24 and 15 bpm, while one subject could not achieve any BCI control. These results are encouraging for an EEG-based BCI system in untrained subjects that is independent of peripheral nervous system activity and does not rely on evoked potentials even when compared to results with very well-trained subjects operating other BCI systems Y1 - 2006 UR - http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=7333 U6 - https://doi.org/10.1109/Tnsre.2006.875557 SN - 1534-4320 ER - TY - THES A1 - Müller, Stephan Heinz T1 - Aggregates Caching for Enterprise Applications N2 - The introduction of columnar in-memory databases, along with hardware evolution, has made the execution of transactional and analytical enterprise application workloads on a single system both feasible and viable. Yet, we argue that executing analytical aggregate queries directly on the transactional data can decrease the overall system performance. Despite the aggregation capabilities of columnar in-memory databases, the direct access to records of a materialized aggregate is always more efficient than aggregating on the fly. The traditional approach to materialized aggregates, however, introduces significant overhead in terms of materialized view selection, maintenance, and exploitation. When this overhead is handled by the application, it increases the application complexity, and can slow down the transactional throughput of inserts, updates, and deletes. In this thesis, we motivate, propose, and evaluate the aggregate cache, a materialized aggregate engine in the main-delta architecture of a columnar in-memory database that provides efficient means to handle costly aggregate queries of enterprise applications. For our design, we leverage the specifics of the main-delta architecture that separates a table into a main and delta partition. The central concept is to only cache the partial aggregate query result as defined on the main partition of a table, because the main partition is relatively stable as records are only inserted into the delta partition. We contribute by proposing incremental aggregate maintenance and query compensation techniques for mixed workloads of enterprise applications. In addition, we introduce aggregate profit metrics that increase the likelihood of persisting the most profitable aggregates in the aggregate cache. Query compensation and maintenance of materialized aggregates based on joins of multiple tables is expensive due to the partitioned tables in the main-delta architecture. Our analysis of enterprise applications has revealed several data schema and workload patterns. This includes the observation that transactional data is persisted in header and item tables, whereas in many cases, the insertion of related header and item records is executed in a single database transaction. We contribute by proposing an approach to transport these application object semantics to the database system and optimize the query processing using the aggregate cache by applying partition pruning and predicate pushdown techniques. For the experimental evaluation, we propose the FICO benchmark that is based on data from a productive ERP system with extracted mixed workloads. Our evaluation reveals that the aggregate cache can accelerate the execution of aggregate queries up to a factor of 60 whereas the speedup highly depends on the number of aggregated records in the main and delta partitions. In mixed workloads, the proposed aggregate maintenance and query compensation techniques perform up to an order of magnitude better than traditional materialized aggregate maintenance approaches. The introduced aggregate profit metrics outperform existing costbased metrics by up to 20%. Lastly, the join pruning and predicate pushdown techniques can accelerate query execution in the aggregate cache in the presence of multiple partitioned tables by up to an order of magnitude. Y1 - 2016 ER - TY - JOUR A1 - Willig, Andreas A1 - Mitschke, Robert T1 - Results of bit error measurements with sensor nodes and casuistic consequences for design of energy-efficient error control schemes N2 - For the proper design of energy-efficient error control schemes some insight into channel error patterns is needed. This paper presents bit error and packet loss measurements taken with sensor nodes running the popular RFM Y1 - 2006 SN - 978-3-540-32158-3 ER - TY - JOUR A1 - Rozinat, A A1 - Van der Aalst, Wil M. P. T1 - Conformance testing: Measuring the fit and appropriateness of event logs and process models N2 - Most information systems log events (e.g., transaction logs, audit traits) to audit and monitor the processes they support. At the same time, many of these processes have been explicitly modeled. For example, SAP R/3 logs events in transaction logs and there are EPCs (Event-driven Process Chains) describing the so-called reference models. These reference models describe how the system should be used. The coexistence of event logs and process models raises an interesting question: "Does the event log conform to the process model and vice versa?". This paper demonstrates that there is not a simple answer to this question. To tackle the problem, we distinguish two dimensions of conformance: fitness (the event log may be the result of the process modeled) and appropriateness (the model is a likely candidate from a structural and behavioral point of view). Different metrics have been defined and a Conformance Checker has been implemented within the ProM Framework Y1 - 2006 ER - TY - JOUR A1 - Gerbser, Martin A1 - Schaub, Torsten H. T1 - Tableau calculi for answer set programming Y1 - 2006 UR - http://www.cs.uni-potsdam.de/wv/pdfformat/gebsch06c.pdf U6 - https://doi.org/10.1007/11799573 SN - 0302-9743 ER - TY - JOUR A1 - Konczak, Kathrin T1 - Voting Theory in Answer Set Programming Y1 - 2006 ER - TY - JOUR A1 - Anger, Christian A1 - Gebser, Martin A1 - Janhunen, Tomi A1 - Schaub, Torsten H. T1 - What's a head without a body? Y1 - 2006 ER - TY - JOUR A1 - Gerbser, Martin A1 - Lee, Joohyung A1 - Lierler, Yuliya T1 - Elementary sets for logic programs Y1 - 2006 SN - 978-1-57735-281-5 ER - TY - JOUR A1 - Gerbser, Martin A1 - Schaub, Torsten H. T1 - Characterizing (ASP) inferences by unit propagation Y1 - 2006 ER - TY - JOUR A1 - Konczak, Kathrin T1 - Weak order equivalence for Logic Programs with Prefernces Y1 - 2006 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Schaub, Torsten H. A1 - Tompits, Hans T1 - A preference-based framework for updating logic programs Y1 - 2007 SN - 978-3-540- 72199-4 ER - TY - JOUR A1 - Mileo, Alessandra A1 - Schaub, Torsten H. T1 - Qualitative constraint enforcement in advanced policy specification Y1 - 2007 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Lang, Jérôme A1 - Schaub, Torsten H. T1 - Belief change based on global minimisation Y1 - 2007 ER - TY - JOUR A1 - Konczak, Kathrin A1 - Linke, Thomas A1 - Schaub, Torsten H. T1 - Graphs and colorings for answer set programming N2 - We investigate the usage of rule dependency graphs and their colorings for characterizing and computing answer sets of logic programs. This approach provides us with insights into the interplay between rules when inducing answer sets. We start with different characterizations of answer sets in terms of totally colored dependency graphs that differ ill graph-theoretical aspects. We then develop a series of operational characterizations of answer sets in terms of operators on partial colorings. In analogy to the notion of a derivation in proof theory, our operational characterizations are expressed as (non-deterministically formed) sequences of colorings, turning an uncolored graph into a totally colored one. In this way, we obtain an operational framework in which different combinations of operators result in different formal properties. Among others, we identify the basic strategy employed by the noMoRe system and justify its algorithmic approach. Furthermore, we distinguish operations corresponding to Fitting's operator as well as to well-founded semantics Y1 - 2006 UR - http://www.cs.kuleuven.ac.be/~dtai/projects/ALP//TPLP/ U6 - https://doi.org/10.1017/S1471068405002528 SN - 1471-0684 ER - TY - BOOK A1 - Hüttenrauch, Stefan A1 - Kylau, Uwe A1 - Grund, Martin A1 - Queck, Tobias A1 - Ploskonos, Anna A1 - Schreiter, Torben A1 - Breest, Martin A1 - Haubrock, Sören A1 - Bouche, Paul T1 - Fundamentals of Service-Oriented Engineering BT - Proceedings of the Fall 2006 Workshop of the HPI Research School on Service-Oriented Systems Engineering T3 - Technische Berichte des Hasso-Plattner-Instituts für Softwaresystemtechnik an der Universität Potsdam Y1 - 2006 SN - 3-939469-35-1 SN - 1613-5652 VL - 18 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Gebser, Martin A1 - Schaub, Torsten H. A1 - Thiele, Sven T1 - GrinGo : a new grounder for answer set programming Y1 - 2007 SN - 978-3-540- 72199-4 ER - TY - BOOK A1 - Kuropka, Dominik A1 - Meyer, Harald T1 - Survey on service composition T3 - Technische Berichte des Hasso-Plattner-Instituts für Softwaresystemtechnik an der Universität Potsda Y1 - 2005 SN - 3-937786-78-3 SN - 1613-5652 VL - 10 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Konczak, Kathrin A1 - Vogel, Ralf T1 - Abduction and Preferences in Linguistics Y1 - 2005 UR - http://www.cs.uni-potsdam.de/~konczak/Papers/konvog05a.pdf ER - TY - JOUR A1 - Calude, C. S. A1 - Jurgensen, Helmut T1 - Is complexity a source of incompleteness? N2 - In this paper we prove Chaitin's "heuristic principle," the theorems of a finitely-specified theory cannot be significantly more complex than the theory itself, for an appropriate measure of complexity. We show that the measure is invariant under the change of the Godel numbering. For this measure, the theorems of a finitely-specified, sound, consistent theory strong enough to formalize arithmetic which is arithmetically sound (like Zermelo-Fraenkel set theory with choice or Peano Arithmetic) have bounded complexity, hence every sentence of the theory which is significantly more complex than the theory is unprovable. Previous results showing that incompleteness is not accidental, but ubiquitous are here reinforced in probabilistic terms: the probability that a true sentence of length n is provable in the theory tends to zero when n tends to infinity, while the probability that a sentence of length n is true is strictly positive. (c) 2004 Elsevier Inc. All rights reserved Y1 - 2005 SN - 0196-8858 ER - TY - JOUR A1 - Bordihn, Henning T1 - On the number of components in cooperating distributed grammar systems N2 - It is proved that the number of components in context-free cooperating distributed (CD) grammar systems can be reduced to 3 when they are working in the so-called sf-mode of derivation, which is the cooperation protocol which has been considered first for CD grammar systems. In this derivation mode, a component continues the derivation until and unless there is a nonterminal in the sentential form which cannot be rewritten according to that component. Moreover, it is shown that CD grammar systems in sf-mode with only one component can generate only the context-free languages but they can generate non-context-free languages if two components are used. The sf-mode of derivation is compared with other well-known cooperation protocols with respect to the hierarchies induced by the number of components. (C) 2004 Elsevier B.V. All rights reserved Y1 - 2005 SN - 0304-3975 ER - TY - JOUR A1 - Beerenwinkel, Niko A1 - Sing, Tobias A1 - Lengauer, Thomas A1 - Rahnenfuhrer, Joerg A1 - Roomp, Kirsten A1 - Savenkov, Igor A1 - Fischer, Roman A1 - Hoffmann, Daniel A1 - Selbig, Joachim A1 - Korn, Klaus A1 - Walter, Hauke A1 - Berg, Thomas A1 - Braun, Patrick A1 - Faetkenheuer, Gerd A1 - Oette, Mark A1 - Rockstroh, Juergen A1 - Kupfer, Bernd A1 - Kaiser, Rolf A1 - Daeumer, Martin T1 - Computational methods for the design of effective therapies against drug resistant HIV strains N2 - The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure exerted by the human immune system and by combination drug therapy. We have developed several computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genomic data Y1 - 2005 ER - TY - JOUR A1 - Brzozowski, J. A. A1 - Jürgensen, Helmut T1 - Representation of semiautomata by canonical words and equivalences N2 - We study a novel representation of semiautomata, which is motivated by the method of trace-assertion specifications of software modules. Each state of the semiautomaton is represented by an arbitrary word leading to that state, the canonical word. The transitions of the semiautomaton give rise to a right congruence, the state-equivalence, on the set of input words of the semiautomaton: two words are state-equivalent if and only if they lead to the same state. We present a simple algorithm for finding a set of generators for state-equivalence. Directly from this set of generators, we construct a confluent prefix-rewriting system which permits us to transform any word to its canonical representative. In general, the rewriting system may allow infinite derivations. To address this issue, we impose the condition of prefix-continuity on the set of canonical words. A set is prefix-continuous if, whenever a word w and a prefix u of w axe in the set, then all the prefixes of w longer than u are also in the set. Prefix-continuous sets include prefix-free and prefix-closed sets as special cases. We prove that the rewriting system is Noetherian if and only if the set of canonical words is prefix-continuous. Furthermore, if the set of canonical words is prefix- continuous, then the set of rewriting rules is irredundant. We show that each prefix-continuous canonical set corresponds to a spanning forest of the semiautomaton Y1 - 2005 SN - 0129-0541 ER - TY - JOUR A1 - Bordihn, Henning A1 - Holzer, Markus A1 - Kutrib, Martin T1 - Unsolvability levels of operation problems for subclasses of context-free languages N2 - We investigate the operation problem for linear and deterministic context-free languages: Fix an operation on formal languages. Given linear (deterministic, respectively) context-free languages, is the application of this operation to the given languages still a linear (deterministic, respectively) context-free language? Besides the classical operations, for which the linear and deterministic context-free languages are not closed, we also consider the recently introduced root and power operation. We show non-semidecidability, to be more precise, we show completeness for the second level of the arithmetic hierarchy for all of the aforementioned operations, except for the power operation, if the underlying alphabet contains at least two letters. The result for the power opera, tion solves an open problem stated in Theoret. Comput. Sci. 314 (2004) 445-449 Y1 - 2005 SN - 0129-0541 ER - TY - JOUR A1 - Bruggemeier, M. A1 - Dovifat, A. A1 - Kubisch, D. T1 - Micropolitical innovation arenas as a tool for analyzing innovation processes in the context of electronic government N2 - E-Government requires technical and organizational innovation. Research has already shown that the respective innovation process is complex and contingent upon specific organizational structures. Managing such innovation processes successfully is difficult. Drawing on assumptions of micropolitical behavior, a framework of innovation arenas is proposed. It supports the analysis of ongoing E-Government projects as well as the ex post investigation of successful or failed projects. Testing this framework in case studies already demonstrates its usefulness for individual actors making strategic choices about change management. Furthermore, the results indicate that many commonly held assumptions about successful change management have to be reconsidered Y1 - 2005 SN - 0937-6429 ER - TY - JOUR A1 - Meinecke, Frank C. A1 - Ziehe, Andreas A1 - Kurths, Jürgen A1 - Müller, Klaus-Robert T1 - Measuring phase synchronization of superimposed signals N2 - Phase synchronization is an important phenomenon that occurs in a wide variety of complex oscillatory processes. Measuring phase synchronization can therefore help to gain fundamental insight into nature. In this Letter we point out that synchronization analysis techniques can detect spurious synchronization, if they are fed with a superposition of signals such as in electroencephalography or magnetoencephalography data. We show how techniques from blind source separation can help to nevertheless measure the true synchronization and avoid such pitfalls Y1 - 2005 SN - 0031-9007 ER - TY - JOUR A1 - Scholz, Matthias A1 - Kaplan, F. A1 - Guy, C. L. A1 - Kopka, Joachim A1 - Selbig, Joachim T1 - Non-linear PCA : a missing data approach N2 - Motivation: Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values. Results: Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while optimizing the model, but can be estimated afterwards. Results are shown for both artificial and experimental datasets. In contrast to linear methods, non-linear methods were able to give better missing value estimations for non-linear structured data. Application: We applied this technique to a time course of metabolite data from a cold stress experiment on the model plant Arabidopsis thaliana, and could approximate the mapping function from any time point to the metabolite responses. Thus, the inverse NLPCA provides greatly improved information for better understanding the complex response to cold stress Y1 - 2005 SN - 1367-4803 ER - TY - JOUR A1 - Konczak, Kathrin A1 - Linke, Thomas A1 - Schaub, Torsten H. T1 - Graphs and cologings for answer set programming : adridged report Y1 - 2004 SN - 3-540- 20721-x ER -