@misc{HaegeleSchlagenhaufRappetal.2014, author = {H{\"a}gele, Claudia and Schlagenhauf, Florian and Rapp, Michael A. and Sterzer, Philipp and Beck, Anne and Bermpohl, Felix and Stoy, Meline and Str{\"o}hle, Andreas and Wittchen, Hans-Ulrich and Dolan, Raymond J. and Heinz, Andreas}, title = {Dimensional psychiatry}, series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, number = {653}, issn = {1866-8364}, doi = {10.25932/publishup-43106}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431064}, pages = {331 -- 341}, year = {2014}, abstract = {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.}, language = {en} } @misc{BanbaraSohTamuraetal.2013, author = {Banbara, Mutsunori and Soh, Takehide and Tamura, Naoyuki and Inoue, Katsumi and Schaub, Torsten}, title = {Answer set programming as a modeling language for course timetabling}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {594}, issn = {1866-8372}, doi = {10.25932/publishup-41546}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415469}, pages = {783 -- 798}, year = {2013}, abstract = {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.}, language = {en} } @misc{KaminskiSchaubSiegeletal.2013, author = {Kaminski, Roland and Schaub, Torsten and Siegel, Anne and Videla, Santiago}, title = {Minimal intervention strategies in logical signaling networks with ASP}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {4-5}, issn = {1866-8372}, doi = {10.25932/publishup-41570}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415704}, pages = {675 -- 690}, year = {2013}, abstract = {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.}, language = {en} } @misc{LarhlimiDavidSelbigetal.2012, author = {Larhlimi, Abdelhalim and David, Laszlo and Selbig, Joachim and Bockmayr, Alexander}, title = {F2C2}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {921}, issn = {1866-8372}, doi = {10.25932/publishup-43243}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432431}, pages = {11}, year = {2012}, abstract = {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/.}, language = {en} } @misc{OstrowskiSchaub2012, author = {Ostrowski, Max and Schaub, Torsten}, title = {ASP modulo CSP}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {579}, issn = {1866-8372}, doi = {10.25932/publishup-41390}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413908}, pages = {19}, 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} } @misc{GebserKaufmannSchaub2012, author = {Gebser, Martin and Kaufmann, Benjamin and Schaub, Torsten}, title = {Multi-threaded ASP solving with clasp}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {586}, issn = {1866-8372}, doi = {10.25932/publishup-41397}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413977}, pages = {21}, 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} } @misc{BoumaHendriks2011, author = {Bouma, Gerlof J. and Hendriks, Petra}, title = {Partial word order freezing in Dutch}, series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, number = {625}, issn = {1866-8364}, doi = {10.25932/publishup-43049}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430496}, pages = {23}, year = {2011}, abstract = {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.}, language = {en} } @misc{GebserLeeLierler2011, author = {Gebser, Martin and Lee, Joohyung and Lierler, Yuliya}, title = {On elementary loops of logic programs}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {566}, issn = {1866-8372}, doi = {10.25932/publishup-41309}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413091}, pages = {36}, year = {2011}, abstract = {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.}, language = {en} } @misc{GebserSchaubThieleetal.2011, author = {Gebser, Martin and Schaub, Torsten and Thiele, Sven and Veber, Philippe}, title = {Detecting inconsistencies in large biological networks with answer set programming}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {561}, issn = {1866-8372}, doi = {10.25932/publishup-41246}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412467}, pages = {38}, year = {2011}, abstract = {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.}, language = {en} } @misc{GebserKaminskiSchaub2011, author = {Gebser, Martin and Kaminski, Roland and Schaub, Torsten}, title = {Complex optimization in answer set programming}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {554}, issn = {1866-8372}, doi = {10.25932/publishup-41243}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412436}, pages = {19}, year = {2011}, abstract = {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.}, language = {en} }