@article{ChildsGrimbsSelbig2015, author = {Childs, Dorothee and Grimbs, Sergio and Selbig, Joachim}, title = {Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns}, series = {Bioinformatics}, volume = {31}, journal = {Bioinformatics}, number = {12}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btv243}, pages = {214 -- 220}, year = {2015}, abstract = {Motivation: Structural kinetic modelling (SKM) is a framework to analyse whether a metabolic steady state remains stable under perturbation, without requiring detailed knowledge about individual rate equations. It provides a representation of the system's Jacobian matrix that depends solely on the network structure, steady state measurements, and the elasticities at the steady state. For a measured steady state, stability criteria can be derived by generating a large number of SKMs with randomly sampled elasticities and evaluating the resulting Jacobian matrices. The elasticity space can be analysed statistically in order to detect network positions that contribute significantly to the perturbation response. Here, we extend this approach by examining the kinetic feasibility of the elasticity combinations created during Monte Carlo sampling. Results: Using a set of small example systems, we show that the majority of sampled SKMs would yield negative kinetic parameters if they were translated back into kinetic models. To overcome this problem, a simple criterion is formulated that mitigates such infeasible models. After evaluating the small example pathways, the methodology was used to study two steady states of the neuronal TCA cycle and the intrinsic mechanisms responsible for their stability or instability. The findings of the statistical elasticity analysis confirm that several elasticities are jointly coordinated to control stability and that the main source for potential instabilities are mutations in the enzyme alpha-ketoglutarate dehydrogenase.}, language = {en} } @article{LemckeHaedgeZenderetal.2015, author = {Lemcke, Stefanie and Haedge, Kora and Zender, Raphael and Lucke, Ulrike}, title = {RouteMe: a multilevel pervasive game on mobile ad hoc routing}, series = {Personal and ubiquitous computing}, volume = {19}, journal = {Personal and ubiquitous computing}, number = {3-4}, publisher = {Springer}, address = {London}, issn = {1617-4909}, doi = {10.1007/s00779-015-0843-2}, pages = {537 -- 549}, year = {2015}, abstract = {Pervasive educational games have the potential to transfer learning content to real-life experiences beyond lecture rooms, through realizing field trips in an augmented or virtual manner. This article introduces the pervasive educational game "RouteMe" that brings the rather abstract topic of routing in ad hoc networks to real-world environments. The game is designed for university-level courses and supports these courses in a motivating manner to deepen the learning experience. Students slip into the role of either routing nodes or applications with routing demands. On three consecutive levels of difficulty, they get introduced with the game concept, learn the basic routing mechanisms and become aware of the general limitations and functionality of routing nodes. This paper presents the pedagogical and technical game concept as well as findings from an evaluation in a university setting.}, language = {en} } @article{BaierMendlingWeske2014, author = {Baier, Thomas and Mendling, Jan and Weske, Mathias}, title = {Bridging abstraction layers in process mining}, series = {Information systems}, volume = {46}, journal = {Information systems}, publisher = {Elsevier}, address = {Oxford}, issn = {0306-4379}, doi = {10.1016/j.is.2014.04.004}, pages = {123 -- 139}, year = {2014}, abstract = {While the maturity of process mining algorithms increases and more process mining tools enter the market, process mining projects still face the problem of different levels of abstraction when comparing events with modeled business activities. Current approaches for event log abstraction try to abstract from the events in an automated way that does not capture the required domain knowledge to fit business activities. This can lead to misinterpretation of discovered process models. We developed an approach that aims to abstract an event log to the same abstraction level that is needed by the business. We use domain knowledge extracted from existing process documentation to semi-automatically match events and activities. Our abstraction approach is able to deal with n:m relations between events and activities and also supports concurrency. We evaluated our approach in two case studies with a German IT outsourcing company. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @article{GieseHildebrandtLambers2014, author = {Giese, Holger and Hildebrandt, Stephan and Lambers, Leen}, title = {Bridging the gap between formal semantics and implementation of triple graph grammars}, series = {Software and systems modeling}, volume = {13}, journal = {Software and systems modeling}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1619-1366}, doi = {10.1007/s10270-012-0247-y}, pages = {273 -- 299}, year = {2014}, abstract = {The correctness of model transformations is a crucial element for model-driven engineering of high-quality software. A prerequisite to verify model transformations at the level of the model transformation specification is that an unambiguous formal semantics exists and that the implementation of the model transformation language adheres to this semantics. However, for existing relational model transformation approaches, it is usually not really clear under which constraints particular implementations really conform to the formal semantics. In this paper, we will bridge this gap for the formal semantics of triple graph grammars (TGG) and an existing efficient implementation. While the formal semantics assumes backtracking and ignores non-determinism, practical implementations do not support backtracking, require rule sets that ensure determinism, and include further optimizations. Therefore, we capture how the considered TGG implementation realizes the transformation by means of operational rules, define required criteria, and show conformance to the formal semantics if these criteria are fulfilled. We further outline how static and runtime checks can be employed to guarantee these criteria.}, language = {en} } @article{WeiherHirschfeld2014, author = {Weiher, Marcel and Hirschfeld, Robert}, title = {Polymorphic identifiers: uniform resource access in objective-smalltalk}, series = {ACM SIGPLAN notices}, volume = {49}, journal = {ACM SIGPLAN notices}, number = {2}, publisher = {Association for Computing Machinery}, address = {New York}, issn = {0362-1340}, doi = {10.1145/2508168.2508169}, pages = {61 -- 71}, year = {2014}, abstract = {In object-oriented programming, polymorphic dispatch of operations decouples clients from specific providers of services and allows implementations to be modified or substituted without affecting clients. The Uniform Access Principle (UAP) tries to extend these qualities to resource access by demanding that access to state be indistinguishable from access to operations. Despite language features supporting the UAP, the overall goal of substitutability has not been achieved for either alternative resources such as keyed storage, files or web pages, or for alternate access mechanisms: specific kinds of resources are bound to specific access mechanisms and vice versa. Changing storage or access patterns either requires changes to both clients and service providers and trying to maintain the UAP imposes significant penalties in terms of code-duplication and/or performance overhead. We propose introducing first class identifiers as polymorphic names for storage locations to solve these problems. With these Polymorphic Identifiers, we show that we can provide uniform access to a wide variety of resource types as well as storage and access mechanisms, whether parametrized or direct, without affecting client code, without causing code duplication or significant performance penalties.}, language = {en} } @article{GebserKaufmannSchaub2012, author = {Gebser, Martin and Kaufmann, Benjamin and Schaub, Torsten H.}, title = {Conflict-driven answer set solving: From theory to practice}, series = {Artificial intelligence}, volume = {187}, journal = {Artificial intelligence}, number = {8}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0004-3702}, doi = {10.1016/j.artint.2012.04.001}, pages = {52 -- 89}, year = {2012}, abstract = {We introduce an approach to computing answer sets of logic programs, based on concepts successfully applied in Satisfiability (SAT) checking. The idea is to view inferences in Answer Set Programming (ASP) as unit propagation on nogoods. This provides us with a uniform constraint-based framework capturing diverse inferences encountered in ASP solving. Moreover, our approach allows us to apply advanced solving techniques from the area of SAT. As a result, we present the first full-fledged algorithmic framework for native conflict-driven ASP solving. Our approach is implemented in the ASP solver clasp that has demonstrated its competitiveness and versatility by winning first places at various solver contests.}, language = {en} } @article{OstrowskiSchaub2012, author = {Ostrowski, Max and Schaub, Torsten H.}, title = {ASP modulo CSP The clingcon system}, series = {Theory and practice of logic programming}, volume = {12}, journal = {Theory and practice of logic programming}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068412000142}, pages = {485 -- 503}, year = {2012}, abstract = {We present the hybrid ASP solver clingcon, combining the simple modeling language and the high performance Boolean solving capacities of Answer Set Programming (ASP) with techniques for using non-Boolean constraints from the area of Constraint Programming (CP). The new clingcon system features an extended syntax supporting global constraints and optimize statements for constraint variables. The major technical innovation improves the interaction between ASP and CP solver through elaborated learning techniques based on irreducible inconsistent sets. A broad empirical evaluation shows that these techniques yield a performance improvement of an order of magnitude.}, language = {en} } @article{GebserKaufmannSchaub2012, author = {Gebser, Martin and Kaufmann, Benjamin and Schaub, Torsten H.}, title = {Multi-threaded ASP solving with clasp}, series = {Theory and practice of logic programming}, volume = {12}, journal = {Theory and practice of logic programming}, number = {8}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068412000166}, pages = {525 -- 545}, year = {2012}, abstract = {We present the new multi-threaded version of the state-of-the-art answer set solver clasp. We detail its component and communication architecture and illustrate how they support the principal functionalities of clasp. Also, we provide some insights into the data representation used for different constraint types handled by clasp. All this is accompanied by an extensive experimental analysis of the major features related to multi-threading in clasp.}, language = {en} } @article{HoosLindauerSchaub2014, author = {Hoos, Holger and Lindauer, Marius and Schaub, Torsten H.}, title = {claspfolio 2}, series = {Theory and practice of logic programming}, volume = {14}, journal = {Theory and practice of logic programming}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068414000210}, pages = {569 -- 585}, year = {2014}, abstract = {Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.}, language = {en} } @article{VidelaGuziolowskiEduatietal.2015, author = {Videla, Santiago and Guziolowski, Carito and Eduati, Federica and Thiele, Sven and Gebser, Martin and Nicolas, Jacques and Saez-Rodriguez, Julio and Schaub, Torsten H. and Siegel, Anne}, title = {Learning Boolean logic models of signaling networks with ASP}, series = {Theoretical computer science}, volume = {599}, journal = {Theoretical computer science}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3975}, doi = {10.1016/j.tcs.2014.06.022}, pages = {79 -- 101}, year = {2015}, abstract = {Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge network and the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in silico numerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A-B. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} }