TY - GEN A1 - Hägele, Claudia A1 - Schlagenhauf, Florian A1 - Rapp, Michael A. A1 - Sterzer, Philipp A1 - Beck, Anne A1 - Bermpohl, Felix A1 - Stoy, Meline A1 - Ströhle, Andreas A1 - Wittchen, Hans-Ulrich A1 - Dolan, Raymond J. A1 - Heinz, Andreas T1 - Dimensional psychiatry BT - reward dysfunction and depressive mood across psychiatric disorders T2 - Postprints der Universität Potsdam : Humanwissenschaftliche Reihe N2 - A dimensional approach in psychiatry aims to identify core mechanisms of mental disorders across nosological boundaries. We compared anticipation of reward between major psychiatric disorders, and investigated whether reward anticipation is impaired in several mental disorders and whether there is a common psychopathological correlate (negative mood) of such an impairment. We used functional magnetic resonance imaging (fMRI) and a monetary incentive delay (MID) task to study the functional correlates of reward anticipation across major psychiatric disorders in 184 subjects, with the diagnoses of alcohol dependence (n = 26), schizophrenia (n = 44), major depressive disorder (MDD, n = 24), bipolar disorder (acute manic episode, n = 13), attention deficit/hyperactivity disorder (ADHD, n = 23), and healthy controls (n = 54). Subjects' individual Beck Depression Inventory-and State-Trait Anxiety Inventory-scores were correlated with clusters showing significant activation during reward anticipation. During reward anticipation, we observed significant group differences in ventral striatal (VS) activation: patients with schizophrenia, alcohol dependence, and major depression showed significantly less ventral striatal activation compared to healthy controls. Depressive symptoms correlated with dysfunction in reward anticipation regardless of diagnostic entity. There was no significant correlation between anxiety symptoms and VS functional activation. Our findings demonstrate a neurobiological dysfunction related to reward prediction that transcended disorder categories and was related to measures of depressed mood. The findings underline the potential of a dimensional approach in psychiatry and strengthen the hypothesis that neurobiological research in psychiatric disorders can be targeted at core mechanisms that are likely to be implicated in a range of clinical entities. T3 - Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe - 653 KW - dimensional KW - fMRI KW - reward system KW - ventral striatum KW - monetary incentive delay task KW - depressive symptoms Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431064 SN - 1866-8364 IS - 653 SP - 331 EP - 341 ER - TY - GEN A1 - Banbara, Mutsunori A1 - Soh, Takehide A1 - Tamura, Naoyuki A1 - Inoue, Katsumi A1 - Schaub, Torsten H. T1 - Answer set programming as a modeling language for course timetabling T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The course timetabling problem can be generally defined as the task of assigning a number of lectures to a limited set of timeslots and rooms, subject to a given set of hard and soft constraints. The modeling language for course timetabling is required to be expressive enough to specify a wide variety of soft constraints and objective functions. Furthermore, the resulting encoding is required to be extensible for capturing new constraints and for switching them between hard and soft, and to be flexible enough to deal with different formulations. In this paper, we propose to make effective use of ASP as a modeling language for course timetabling. We show that our ASP-based approach can naturally satisfy the above requirements, through an ASP encoding of the curriculum-based course timetabling problem proposed in the third track of the second international timetabling competition (ITC-2007). Our encoding is compact and human-readable, since each constraint is individually expressed by either one or two rules. Each hard constraint is expressed by using integrity constraints and aggregates of ASP. Each soft constraint S is expressed by rules in which the head is the form of penalty (S, V, C), and a violation V and its penalty cost C are detected and calculated respectively in the body. We carried out experiments on four different benchmark sets with five different formulations. We succeeded either in improving the bounds or producing the same bounds for many combinations of problem instances and formulations, compared with the previous best known bounds. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 594 KW - answer set programming KW - educational timetabling KW - course timetabling Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415469 SN - 1866-8372 IS - 594 SP - 783 EP - 798 ER - TY - GEN A1 - Kaminski, Roland A1 - Schaub, Torsten H. A1 - Siegel, Anne A1 - Videla, Santiago T1 - Minimal intervention strategies in logical signaling networks with ASP T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 596 KW - systems biology KW - transduction KW - circuits KW - models KW - sets Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415704 SN - 1866-8372 IS - 4-5 SP - 675 EP - 690 ER - TY - GEN A1 - Larhlimi, Abdelhalim A1 - David, Laszlo A1 - Selbig, Joachim A1 - Bockmayr, Alexander T1 - F2C2 BT - a fast tool for the computation of flux coupling in genome-scale metabolic networks T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions. Results: We present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. Conclusions: We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 921 KW - balance analysis KW - reconstruction KW - pathways KW - models KW - metabolic network KW - couple reaction KW - reversible reaction KW - linear programming problem KW - coupling relationship Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432431 SN - 1866-8372 IS - 921 ER - TY - GEN A1 - Ostrowski, Max A1 - Schaub, Torsten H. T1 - ASP modulo CSP BT - the clingcon system T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 579 KW - answer set KW - constraints KW - logic KW - SMT Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413908 SN - 1866-8372 IS - 579 ER - TY - GEN A1 - Gebser, Martin A1 - Kaufmann, Benjamin A1 - Schaub, Torsten H. T1 - Multi-threaded ASP solving with clasp T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 586 KW - propositional satisfiability KW - clause elimination KW - parallel execution KW - SAT KW - algorithm KW - platypus KW - systems KW - search KW - solver Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413977 SN - 1866-8372 IS - 586 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 - 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 - 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 -