TY - GEN A1 - Durzinsky, Markus A1 - Marwan, Wolfgang A1 - Ostrowski, Max A1 - Schaub, Torsten H. A1 - Wagler, Annegret T1 - Automatic network reconstruction using ASP T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 560 KW - regulatory networks KW - biological networks KW - answer Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412419 SN - 1866-8372 IS - 560 ER - TY - GEN A1 - Gebser, Martin A1 - Kaminski, Roland A1 - Schaub, Torsten H. T1 - Complex optimization in answer set programming T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Preference handling and optimization are indispensable means for addressing nontrivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-prpogramming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 554 KW - answer set programming KW - preference handling KW - complex optimization KW - meta-programming Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412436 SN - 1866-8372 IS - 554 ER - TY - GEN A1 - Gebser, Martin A1 - Schaub, Torsten H. A1 - Thiele, Sven A1 - Veber, Philippe T1 - Detecting inconsistencies in large biological networks with answer set programming T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 561 KW - answer set programming KW - bioinformatics KW - consistency KW - diagnosis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412467 SN - 1866-8372 IS - 561 ER - TY - GEN A1 - Gebser, Martin A1 - Lee, Joohyung A1 - Lierler, Yuliya T1 - On elementary loops of logic programs T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Using the notion of an elementary loop, Gebser and Schaub (2005. Proceedings of the Eighth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR’05 ), 53–65) refined the theorem on loop formulas attributable to Lin and Zhao (2004) by considering loop formulas of elementary loops only. In this paper, we reformulate the definition of an elementary loop, extend it to disjunctive programs, and study several properties of elementary loops, including how maximal elementary loops are related to minimal unfounded sets. The results provide useful insights into the stable model semantics in terms of elementary loops. For a nondisjunctive program, using a graph-theoretic characterization of an elementary loop, we show that the problem of recognizing an elementary loop is tractable. On the other hand, we also show that the corresponding problem is coNP-complete for a disjunctive program. Based on the notion of an elementary loop, we present the class of Head-Elementary-loop-Free (HEF) programs, which strictly generalizes the class of Head-Cycle-Free (HCF) programs attributable to Ben-Eliyahu and Dechter (1994. Annals of Mathematics and Artificial Intelligence 12, 53–87). Like an HCF program, an HEF program can be turned into an equivalent nondisjunctive program in polynomial time by shifting head atoms into the body. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 566 KW - stable model semantics KW - loop formulas KW - unfounded sets Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413091 SN - 1866-8372 IS - 566 ER - TY - GEN A1 - Bouma, Gerlof J. A1 - Hendriks, Petra T1 - Partial word order freezing in Dutch T2 - Postprints der Universität Potsdam : Humanwissenschaftliche Reihe N2 - Dutch allows for variation as to whether the first position in the sentence is occupied by the subject or by some other constituent, such as the direct object. In particular situations, however, this commonly observed variation in word order is ‘frozen’ and only the subject appears in first position. We hypothesize that this partial freezing of word order in Dutch can be explained from the dependence of the speaker’s choice of word order on the hearer’s interpretation of this word order. A formal model of this interaction between the speaker’s perspective and the hearer’s perspective is presented in terms of bidirectional Optimality Theory. Empirical predictions of this model regarding the interaction between word order and definiteness are confirmed by a quantitative corpus study. T3 - Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe - 625 KW - bidirectional optimality theory KW - corpus study KW - definiteness KW - variation KW - word order freezing Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-430496 SN - 1866-8364 IS - 625 ER -