@article{PrasseKnaebelMachlicaetal.2019,
  author    = {Prasse, Paul and Knaebel, Rene and Machlica, Lukas and Pevny, Tomas and Scheffer, Tobias},
  title     = {Joint detection of malicious domains and infected clients},
  series = {Machine learning},
  volume    = {108},
  journal   = {Machine learning},
  number    = {8-9},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0885-6125},
  doi       = {10.1007/s10994-019-05789-z},
  pages     = {1353 -- 1368},
  year      = {2019},
  abstract  = {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.},
  language  = {en}
}
@article{CabalarFandinnoSchaubetal.2019,
  author    = {Cabalar, Pedro and Fandinno, Jorge and Schaub, Torsten H. and Schellhorn, Sebastian},
  title     = {Gelfond-Zhang aggregates as propositional formulas},
  series = {Artificial intelligence},
  volume    = {274},
  journal   = {Artificial intelligence},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0004-3702},
  doi       = {10.1016/j.artint.2018.10.007},
  pages     = {26 -- 43},
  year      = {2019},
  abstract  = {Answer Set Programming (ASP) has become a popular and widespread paradigm for practical Knowledge Representation thanks to its expressiveness and the available enhancements of its input language. One of such enhancements is the use of aggregates, for which different semantic proposals have been made. In this paper, we show that any ASP aggregate interpreted under Gelfond and Zhang's (GZ) semantics can be replaced (under strong equivalence) by a propositional formula. Restricted to the original GZ syntax, the resulting formula is reducible to a disjunction of conjunctions of literals but the formulation is still applicable even when the syntax is extended to allow for arbitrary formulas (including nested aggregates) in the condition. Once GZ-aggregates are represented as formulas, we establish a formal comparison (in terms of the logic of Here-and-There) to Ferraris' (F) aggregates, which are defined by a different formula translation involving nested implications. In particular, we prove that if we replace an F-aggregate by a GZ-aggregate in a rule head, we do not lose answer sets (although more can be gained). This extends the previously known result that the opposite happens in rule bodies, i.e., replacing a GZ-aggregate by an F-aggregate in the body may yield more answer sets. Finally, we characterize a class of aggregates for which GZ- and F-semantics coincide.},
  language  = {en}
}
@phdthesis{Ashouri2020,
  author    = {Ashouri, Mohammadreza},
  title     = {TrainTrap},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XIX, 103},
  year      = {2020},
  language  = {en}
}
@article{AguadoCabalarFandinoetal.2019,
  author    = {Aguado, Felicidad and Cabalar, Pedro and Fandi{\~n}o, Jorge and Pearce, David and Perez, Gilberto and Vidal-Peracho, Concepcion},
  title     = {Revisiting Explicit Negation in Answer Set Programming},
  series = {Theory and practice of logic programming},
  volume    = {19},
  journal   = {Theory and practice of logic programming},
  number    = {5-6},
  publisher = {Cambridge Univ. Press},
  address   = {New York},
  issn      = {1471-0684},
  doi       = {10.1017/S1471068419000267},
  pages     = {908 -- 924},
  year      = {2019},
  language  = {en}
}
@article{LaskovGehlKruegeretal.2006,
  author    = {Laskov, Pavel and Gehl, Christian and Kr{\"u}ger, Stefan and M{\"u}ller, Klaus-Robert},
  title     = {Incremental support vector learning: analysis, implementation and applications},
  series = {Journal of machine learning research},
  volume    = {7},
  journal   = {Journal of machine learning research},
  publisher = {MIT Press},
  address   = {Cambridge, Mass.},
  issn      = {1532-4435},
  pages     = {1909 -- 1936},
  year      = {2006},
  abstract  = {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.},
  language  = {en}
}
@article{SteuerHumburgSelbig2006,
  author    = {Steuer, Ralf and Humburg, Peter and Selbig, Joachim},
  title     = {Validation and functional annotation of expression-based clusters based on gene ontology},
  series = {BMC bioinformatics},
  volume    = {7},
  journal   = {BMC bioinformatics},
  number    = {380},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2105},
  doi       = {10.1186/1471-2105-7-380},
  pages     = {12},
  year      = {2006},
  abstract  = {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.},
  language  = {en}
}
@article{SarsakovSchaubTompitsetal.2004,
  author    = {Sarsakov, Vladimir and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {A compiler for nested logic programming},
  isbn      = {3-540- 20721-x},
  year      = {2004},
  language  = {en}
}
@article{LinkeTompitsWoltran2004,
  author    = {Linke, Thomas and Tompits, Hans and Woltran, Stefan},
  title     = {On Acyclic and head-cycle free nested logic programs},
  isbn      = {3-540-22671-01},
  year      = {2004},
  language  = {en}
}
@article{LinkeTompitsWoltran2004,
  author    = {Linke, Thomas and Tompits, Hans and Woltran, Stefan},
  title     = {On acyclic and head-cycle free nested logic programs},
  year      = {2004},
  language  = {en}
}
@article{DelgrandeSchaubTompitsetal.2004,
  author    = {Delgrande, James Patrick and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {On Computing belief change operations using quantifield boolean formulas},
  issn      = {0955-792X},
  year      = {2004},
  abstract  = {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},
  language  = {en}
}
@article{DelgrandeSchaubTompitsetal.2001,
  author    = {Delgrande, James Patrick and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {On computing solutions to belief change scenarios},
  isbn      = {3-540- 42464-4},
  year      = {2001},
  language  = {en}
}
@article{PearceSarsakovSchaubetal.2002,
  author    = {Pearce, David and Sarsakov, Vladimir and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {A polynomial translation of logic programs with nested expressions into disjunctive logic programs},
  isbn      = {3-540-43930-7},
  year      = {2002},
  language  = {en}
}
@article{BesnardSchaubTompitsetal.2002,
  author    = {Besnard, Philippe and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {Paraconsistent reasoning via quantified boolean formulas},
  isbn      = {3-540-44190-5},
  year      = {2002},
  language  = {en}
}
@article{BrainGebserPuehreretal.2007,
  author    = {Brain, Martin and Gebser, Martin and P{\"u}hrer, J{\"o}rg and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {"That is illogical, Captain!" : the debugging support tool spock for answer-set programs ; system description},
  year      = {2007},
  language  = {en}
}
@article{PearceSarsakovSchaubetal.2002,
  author    = {Pearce, David and Sarsakov, Vladimir and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {A polynomial translation of logic programs with nested expressions into disjunctive logic programs : preliminary report},
  year      = {2002},
  language  = {en}
}
@article{SchaubWoltran2018,
  author    = {Schaub, Torsten H. and Woltran, Stefan},
  title     = {Answer set programming unleashed!},
  series = {K{\"u}nstliche Intelligenz},
  volume    = {32},
  journal   = {K{\"u}nstliche Intelligenz},
  number    = {2-3},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {0933-1875},
  doi       = {10.1007/s13218-018-0550-z},
  pages     = {105 -- 108},
  year      = {2018},
  abstract  = {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)]},
  language  = {en}
}
@misc{SchaubWoltran2018,
  author    = {Schaub, Torsten H. and Woltran, Stefan},
  title     = {Special issue on answer set programming},
  series = {K{\"u}nstliche Intelligenz},
  volume    = {32},
  journal   = {K{\"u}nstliche Intelligenz},
  number    = {2-3},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {0933-1875},
  doi       = {10.1007/s13218-018-0554-8},
  pages     = {101 -- 103},
  year      = {2018},
  language  = {en}
}
@article{BesnardSchaubTompitsetal.2003,
  author    = {Besnard, Philippe and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {Paraconsistent reasoning via quantified boolean formulas : Part II: Circumscribing inconsistent theories},
  isbn      = {3-540- 409494-5},
  year      = {2003},
  language  = {en}
}
@article{DelgrandeSchaubTompitsetal.2013,
  author    = {Delgrande, James and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {A model-theoretic approach to belief change in answer set programming},
  series = {ACM transactions on computational logic},
  volume    = {14},
  journal   = {ACM transactions on computational logic},
  number    = {2},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {1529-3785},
  doi       = {10.1145/2480759.2480766},
  pages     = {46},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}
@article{BrainGebserPuehreretal.2007,
  author    = {Brain, Martin and Gebser, Martin and P{\"u}hrer, J{\"o}rg and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {Debugging ASP programs by means of ASP},
  isbn      = {978-3-540- 72199-4},
  year      = {2007},
  language  = {en}
}
@article{GebserSchaubTompitsetal.2007,
  author    = {Gebser, Martin and Schaub, Torsten H. and Tompits, Hans and Woltran, Stefan},
  title     = {Alternative characterizations for program equivalence under aswer-set semantics : a preliminary report},
  year      = {2007},
  language  = {en}
}
@inproceedings{CurzonKalasSchubertetal.2015,
  author    = {Curzon, Paul and Kalas, Ivan and Schubert, Sigrid and Schaper, Niclas and Barnes, Jan and Kennewell, Steve and Br{\"o}ker, Kathrin and Kastens, Uwe and Magenheim, Johannes and Dagiene, Valentina and Stupuriene, Gabriele and Ellis, Jason Brent and Abreu-Ellis, Carla Reis and Grillenberger, Andreas and Romeike, Ralf and Haugsbakken, Halvdan and Jones, Anthony and Lewin, Cathy and McNicol, Sarah and Nelles, Wolfgang and Neugebauer, Jonas and Ohrndorf, Laura and Schaper, Niclas and Schubert, Sigrid and Opel, Simone and Kramer, Matthias and Trommen, Michael and Pottb{\"a}cker, Florian and Ilaghef, Youssef and Passig, David and Tzuriel, David and Kedmi, Ganit Eshel and Saito, Toshinori and Webb, Mary and Weigend, Michael and Bottino, Rosa and Chioccariello, Augusto and Christensen, Rhonda and Knezek, Gerald and Gioko, Anthony Maina and Angondi, Enos Kiforo and Waga, Rosemary and Ohrndorf, Laura and Or-Bach, Rachel and Preston, Christina and Younie, Sarah and Przybylla, Mareen and Romeike, Ralf and Reynolds, Nicholas and Swainston, Andrew and Bendrups, Faye and Sysło, Maciej M. and Kwiatkowska, Anna Beata and Zieris, Holger and Gerstberger, Herbert and M{\"u}ller, Wolfgang and B{\"u}chner, Steffen and Opel, Simone and Schiller, Thomas and Wegner, Christian and Zender, Raphael and Lucke, Ulrike and Diethelm, Ira and Syrbe, J{\"o}rn and Lai, Kwok-Wing and Davis, Niki and Eickelmann, Birgit and Erstad, Ola and Fisser, Petra and Gibson, David and Khaddage, Ferial and Knezek, Gerald and Micheuz, Peter and Kloos, Carlos Delgado},
  title     = {KEYCIT 2014},
  editor    = {Brinda, Torsten and Reynolds, Nicholas and Romeike, Ralf and Schwill, Andreas},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-292-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-70325},
  pages     = {438},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@article{BordihnFernauHolzeretal.2006,
  author    = {Bordihn, Henning and Fernau, Henning and Holzer, Markus and Manca, Vincenzo and Martin-Vide, Carlos},
  title     = {Iterated sequential transducers as language generating devices},
  series = {Theoretical computer science},
  volume    = {369},
  journal   = {Theoretical computer science},
  number    = {1},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3975},
  doi       = {10.1016/j.tcs.2006.07.059},
  pages     = {67 -- 81},
  year      = {2006},
  abstract  = {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.},
  language  = {en}
}
@article{StoffelKunzGerber1997,
  author    = {Stoffel, Dominik and Kunz, Wolfgang and Gerber, Stefan},
  title     = {And/Or reasoning graphs for determining prime implicants in multi-level combinational networks},
  year      = {1997},
  language  = {en}
}
@phdthesis{Gerber1995,
  author    = {Gerber, Stefan},
  title     = {Using software for fault detection in arithmetical circuits},
  pages     = {123 S.},
  year      = {1995},
  language  = {en}
}
@article{BaierDiCiccioMendlingetal.2018,
  author    = {Baier, Thomas and Di Ciccio, Claudio and Mendling, Jan and Weske, Mathias},
  title     = {Matching events and activities by integrating behavioral aspects and label analysis},
  series = {Software and systems modeling},
  volume    = {17},
  journal   = {Software and systems modeling},
  number    = {2},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1619-1366},
  doi       = {10.1007/s10270-017-0603-z},
  pages     = {573 -- 598},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@article{PrzybyllaRomeike2018,
  author    = {Przybylla, Mareen and Romeike, Ralf},
  title     = {Empowering learners with tools in CS education},
  series = {it - Information Technology},
  volume    = {60},
  journal   = {it - Information Technology},
  number    = {2},
  publisher = {De Gruyter},
  address   = {Berlin},
  issn      = {1611-2776},
  doi       = {10.1515/itit-2017-0032},
  pages     = {91 -- 101},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@misc{FrankKreitz2018,
  author    = {Frank, Mario and Kreitz, Christoph},
  title     = {A theorem prover for scientific and educational purposes},
  series = {Electronic proceedings in theoretical computer science},
  journal   = {Electronic proceedings in theoretical computer science},
  number    = {267},
  publisher = {Open Publishing Association},
  address   = {Sydney},
  issn      = {2075-2180},
  doi       = {10.4204/EPTCS.267.4},
  pages     = {59 -- 69},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@misc{SchaepersNiemuellerLakemeyeretal.2018,
  author    = {Sch{\"a}pers, Bj{\"o}rn and Niemueller, Tim and Lakemeyer, Gerhard and Gebser, Martin and Schaub, Torsten H.},
  title     = {ASP-Based Time-Bounded Planning for Logistics Robots},
  series = {Twenty-Eighth International Conference on Automated Planning and Scheduling (ICAPS 2018)},
  journal   = {Twenty-Eighth International Conference on Automated Planning and Scheduling (ICAPS 2018)},
  publisher = {ASSOC Association for the Advancement of Artificial Intelligence},
  address   = {Palo Alto},
  issn      = {2334-0835},
  pages     = {509 -- 517},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@inproceedings{KnothKiy2014,
  author    = {Knoth, Alexander Henning and Kiy, Alexander},
  title     = {(Self-)confident through the introductory study phase with the Reflect App},
  series = {CEUR Workshop Proceedings},
  booktitle = {CEUR Workshop Proceedings},
  number    = {1227},
  publisher = {CEUR-WS},
  address   = {Freiburg},
  issn      = {1613-0073},
  pages     = {172 -- 179},
  year      = {2014},
  language  = {en}
}
@article{LyTarkhanov2009,
  author    = {Ly, Ibrahim and Tarkhanov, Nikolai Nikolaevich},
  title     = {A variational approach to the Cauchy problem for nonlinear elliptic differential equations},
  issn      = {0928-0219},
  doi       = {10.1515/Jiip.2009.037},
  year      = {2009},
  abstract  = {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.},
  language  = {en}
}
@article{PrasseIversenLienhardetal.2022,
  author    = {Prasse, Paul and Iversen, Pascal and Lienhard, Matthias and Thedinga, Kristina and Herwig, Ralf and Scheffer, Tobias},
  title     = {Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction},
  series = {MDPI},
  volume    = {14},
  journal   = {MDPI},
  edition   = {16},
  publisher = {MDPI},
  address   = {Basel, Schweiz},
  issn      = {2072-6694},
  doi       = {10.3390/cancers14163950},
  pages     = {1 -- 14},
  year      = {2022},
  abstract  = {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.},
  language  = {en}
}
@article{EverardoPerezOsorio2020,
  author    = {Everardo P{\´e}rez, Flavio Omar and Osorio, Mauricio},
  title     = {Towards an answer set programming methodology for constructing programs following a semi-automatic approach},
  series = {Electronic notes in theoretical computer science},
  volume    = {354},
  journal   = {Electronic notes in theoretical computer science},
  publisher = {Elsevier},
  address   = {Amsterdam [u.a.]},
  issn      = {1571-0661},
  doi       = {10.1016/j.entcs.2020.10.004},
  pages     = {29 -- 44},
  year      = {2020},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Kluth2011,
  author    = {Kluth, Stephan},
  title     = {Quantitative modeling and analysis with FMC-QE},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52987},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {The modeling and evaluation calculus FMC-QE, the Fundamental Modeling Concepts for Quanti-tative Evaluation [1], extends the Fundamental Modeling Concepts (FMC) for performance modeling and prediction. In this new methodology, the hierarchical service requests are in the main focus, because they are the origin of every service provisioning process. Similar to physics, these service requests are a tuple of value and unit, which enables hierarchical service request transformations at the hierarchical borders and therefore the hierarchical modeling. Through reducing the model complexity of the models by decomposing the system in different hierarchical views, the distinction between operational and control states and the calculation of the performance values on the assumption of the steady state, FMC-QE has a scalable applica-bility on complex systems. According to FMC, the system is modeled in a 3-dimensional hierarchical representation space, where system performance parameters are described in three arbitrarily fine-grained hierarchi-cal bipartite diagrams. The hierarchical service request structures are modeled in Entity Relationship Diagrams. The static server structures, divided into logical and real servers, are de-scribed as Block Diagrams. The dynamic behavior and the control structures are specified as Petri Nets, more precisely Colored Time Augmented Petri Nets. From the structures and pa-rameters of the performance model, a hierarchical set of equations is derived. The calculation of the performance values is done on the assumption of stationary processes and is based on fundamental laws of the performance analysis: Little's Law and the Forced Traffic Flow Law. Little's Law is used within the different hierarchical levels (horizontal) and the Forced Traffic Flow Law is the key to the dependencies among the hierarchical levels (vertical). This calculation is suitable for complex models and allows a fast (re-)calculation of different performance scenarios in order to support development and configuration decisions. Within the Research Group Zorn at the Hasso Plattner Institute, the work is embedded in a broader research in the development of FMC-QE. While this work is concentrated on the theoretical background, description and definition of the methodology as well as the extension and validation of the applicability, other topics are in the development of an FMC-QE modeling and evaluation tool and the usage of FMC-QE in the design of an adaptive transport layer in order to fulfill Quality of Service and Service Level Agreements in volatile service based environments. This thesis contains a state-of-the-art, the description of FMC-QE as well as extensions of FMC-QE in representative general models and case studies. In the state-of-the-art part of the thesis in chapter 2, an overview on existing Queueing Theory and Time Augmented Petri Net models and other quantitative modeling and evaluation languages and methodologies is given. Also other hierarchical quantitative modeling frameworks will be considered. The description of FMC-QE in chapter 3 consists of a summary of the foundations of FMC-QE, basic definitions, the graphical notations, the FMC-QE Calculus and the modeling of open queueing networks as an introductory example. The extensions of FMC-QE in chapter 4 consist of the integration of the summation method in order to support the handling of closed networks and the modeling of multiclass and semaphore scenarios. Furthermore, FMC-QE is compared to other performance modeling and evaluation approaches. In the case study part in chapter 5, proof-of-concept examples, like the modeling of a service based search portal, a service based SAP NetWeaver application and the Axis2 Web service framework will be provided. Finally, conclusions are given by a summary of contributions and an outlook on future work in chapter 6. [1] Werner Zorn. FMC-QE - A New Approach in Quantitative Modeling. In Hamid R. Arabnia, editor, Procee-dings of the International Conference on Modeling, Simulation and Visualization Methods (MSV 2007) within WorldComp '07, pages 280 - 287, Las Vegas, NV, USA, June 2007. CSREA Press. ISBN 1-60132-029-9.},
  language  = {en}
}
@phdthesis{AlSaffar2016,
  author    = {Al-Saffar, Loay Talib Ahmed},
  title     = {Analysing prerequisites, expectations, apprehensions, and attitudes of University students studying computer science},
  school      = {Universit{\"a}t Potsdam},
  pages     = {128},
  year      = {2016},
  language  = {en}
}
@book{OPUS4-7534,
  title     = {Process design for natural scientists},
  series = {Communications in computer and information science ; 500},
  journal   = {Communications in computer and information science ; 500},
  editor    = {Lambrecht, Anna-Lena and Margaria, Tizian},
  publisher = {Springer},
  address   = {Wiesbaden},
  isbn      = {978-3-662-45005-5},
  pages     = {X, 251},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Wust2015,
  author    = {Wust, Johannes},
  title     = {Mixed workload managment for in-memory databases},
  pages     = {VIII, 167},
  year      = {2015},
  language  = {en}
}
@article{Teske2014,
  author    = {Teske, Daniel},
  title     = {Geocoder accuracy ranking},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {161 -- 174},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Sens2014,
  author    = {Sens, Henriette},
  title     = {Web-Based map generalization tools put to the test: a jABC workflow},
  series = {Process Design for Natural Scientists: an agile model-driven approach},
  journal   = {Process Design for Natural Scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {175 -- 185},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Noack2014,
  author    = {Noack, Franziska},
  title     = {CREADED: Colored-Relief application for digital elevation data},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {186 -- 199},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Respondek2014,
  author    = {Respondek, Tobias},
  title     = {A workflow for computing potential areas for wind turbines},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  pages     = {200 -- 215},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Scheele2014,
  author    = {Scheele, Lasse},
  title     = {Location analysis for placing artificial reefs},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {216 -- 228},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Holler2014,
  author    = {Holler, Robin},
  title     = {GraffDok - a graffiti documentation application},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {239 -- 251},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Reso2014,
  author    = {Reso, Judith},
  title     = {Protein Classification Workflow},
  series = {Process Design for Natural Scientists: an agile model-driven approach},
  journal   = {Process Design for Natural Scientists: an agile model-driven approach},
  number    = {500},
  editor    = {Lambrecht, Anna-Lena and Margaria, Tiziana},
  publisher = {Springer Verlag},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {65 -- 72},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Schulze2014,
  author    = {Schulze, Gunnar},
  title     = {Workflow for rapid metagenome analysis},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {88 -- 100},
  year      = {2014},
  abstract  = {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},
  language  = {en}
}
@article{Vierheller2014,
  author    = {Vierheller, Janine},
  title     = {Exploratory Data Analysis},
  series = {Process Design for Natural Scientists: an agile model-driven approach},
  journal   = {Process Design for Natural Scientists: an agile model-driven approach},
  number    = {500},
  editor    = {Lambrecht, Anna-Lena and Margaria, Tiziana},
  publisher = {Axel Springer Verlag},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {110 -- 126},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Schuett2014,
  author    = {Sch{\"u}tt, Christine},
  title     = {Identification of differentially expressed genes},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {127 -- 139},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Kuntzsch2014,
  author    = {Kuntzsch, Christian},
  title     = {Visualization of data transfer paths},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {140 -- 148},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Hibbe2014,
  author    = {Hibbe, Marcel},
  title     = {Spotlocator - Guess Where the Photo Was Taken!},
  series = {Process Design for Natural Scientists: an agile model-driven approach},
  journal   = {Process Design for Natural Scientists: an agile model-driven approach},
  number    = {500},
  editor    = {Lambrecht, Anna-Lena and Margaria, Tiziana},
  publisher = {Springer Verlag},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {149 -- 160},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Blaese2014,
  author    = {Blaese, Leif},
  title     = {Data mining for unidentified protein squences},
  series = {Process design for natural scientists: an agile model-driven approach},
  journal   = {Process design for natural scientists: an agile model-driven approach},
  number    = {500},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {73 -- 87},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}