TY - JOUR A1 - Gebser, Martin A1 - Schaub, Torsten A1 - Thiele, Sven A1 - Veber, Philippe T1 - Detecting inconsistencies in large biological networks with answer set programming JF - Theory and practice of logic programming 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. KW - answer set programming KW - bioinformatics KW - consistency KW - diagnosis Y1 - 2011 U6 - https://doi.org/10.1017/S1471068410000554 SN - 1471-0684 VL - 11 IS - 5-6 SP - 323 EP - 360 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Gebser, Martin A1 - Kaminski, Roland A1 - Schaub, Torsten T1 - Complex optimization in answer set programming JF - Theory and practice of logic programming 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. KW - Answer Set Programming KW - Preference Handling KW - Complex optimization KW - Meta-Programming Y1 - 2011 U6 - https://doi.org/10.1017/S1471068411000329 SN - 1471-0684 VL - 11 IS - 3 SP - 821 EP - 839 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Gebser, Martin A1 - Gharib, Mona A1 - Mercer, Robert E. A1 - Schaub, Torsten T1 - Monotonic answer set programming N2 - Answer set programming (ASP) does not allow for incrementally constructing answer sets or locally validating constructions like proofs by only looking at a part of the given program. In this article, we elaborate upon an alternative approach to ASP that allows for incremental constructions. Our approach draws its basic intuitions from the area of default logics. We investigate the feasibility of the concept of semi-monotonicity known from default logics as a basis of incrementality. On the one hand, every logic program has at least one answer set in our alternative setting, which moreover can be constructed incrementally based on generating rules. On the other hand, the approach may produce answer sets lacking characteristic properties of standard answer sets, such as being a model of the given program. We show how integrity constraints can be used to re-establish such properties, even up to correspondence with standard answer sets. Furthermore, we develop an SLD-like proof procedure for our incremental approach to ASP, which allows for query-oriented computations. Also, we provide a characterization of our definition of answer sets via a modification of Clarks completion. Based on this notion of program completion, we present an algorithm for computing the answer sets of a logic program in our approach. Y1 - 2009 UR - http://logcom.oxfordjournals.org/ U6 - https://doi.org/10.1093/logcom/exn040 SN - 0955-792X ER - TY - JOUR A1 - Gebser, Martin A1 - Kaufmann, Benjamin A1 - Schaub, Torsten T1 - Multi-threaded ASP solving with clasp JF - Theory and practice of logic programming 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. Y1 - 2012 U6 - https://doi.org/10.1017/S1471068412000166 SN - 1471-0684 VL - 12 IS - 8 SP - 525 EP - 545 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Hermenegildo, Manuel A1 - Schaub, Torsten T1 - Introduction to the technical communications of the 26th International Conference on Logic Programming : special issue Y1 - 2010 UR - http://www.cs.kuleuven.ac.be/~dtai/projects/ALP//TPLP/ U6 - https://doi.org/10.1017/S1471068410000153 SN - 1471-0684 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Liu, Daphne H. A1 - Schaub, Torsten A1 - Thiele, Sven T1 - COBA 2.0 : a consistency-based belief change system Y1 - 2007 ER - TY - JOUR A1 - Gharib, Mona A1 - Schaub, Torsten A1 - Mercer, Robert E. T1 - Incremental answer set programming : a preliminary report Y1 - 2007 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Schaub, Torsten A1 - Tompits, Hans T1 - An Extended Query language for action languages (and its application to aggregates and preferences) Y1 - 2006 UR - http://www2.in.tu-clausthal.de/~tmbehrens/NMR_Proc_TR4.pdf ER - TY - JOUR A1 - Konczak, Kathrin A1 - Linke, Thomas A1 - Schaub, Torsten T1 - Graphs and colorings for answer set programming : abridged report Y1 - 2003 UR - http://www.cs.uni-potsdam.de/wv/pdfformat/kolisch03a.pdf SN - 1613-0073 ER - TY - JOUR A1 - Anger, Christian A1 - Gebser, Martin A1 - Schaub, Torsten T1 - Approaching the core of unfounded sets Y1 - 2006 UR - http://www.cs.uni-potsdam.de/wv/pdfformat/angesc06a.pdf ER - TY - JOUR A1 - Mileo, Alessandra A1 - Schaub, Torsten T1 - Extending ordered disjunctions for policy enforcement : preliminary report Y1 - 2006 UR - http://www.easychair.org/FLoC-06/PREFS-preproceedings.pdf ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Schaub, Torsten A1 - Tompits, Hans T1 - A preference-based framework for updating logic programs Y1 - 2007 SN - 978-3-540- 72199-4 ER - TY - JOUR A1 - Gressmann, Jean A1 - Janhunen, Tomi A1 - Mercer, Robert E. A1 - Schaub, Torsten A1 - Thiele, Sven A1 - Tichy, Richard T1 - On probing and multi-threading in platypus Y1 - 2006 ER - TY - JOUR A1 - Grell, Susanne A1 - Schaub, Torsten A1 - Selbig, Joachim T1 - Modelling biological networks by action languages via set programming Y1 - 2006 UR - http://www.cs.uni-potsdam.de/wv/pdfformat/gebsch06c.pdf U6 - https://doi.org/10.1007/11799573 SN - 0302-9743 ER - TY - JOUR A1 - Gerbser, Martin A1 - Schaub, Torsten T1 - Tableau calculi for answer set programming Y1 - 2006 UR - http://www.cs.uni-potsdam.de/wv/pdfformat/gebsch06c.pdf U6 - https://doi.org/10.1007/11799573 SN - 0302-9743 ER - TY - JOUR A1 - Gerbser, Martin A1 - Schaub, Torsten T1 - Characterizing (ASP) inferences by unit propagation Y1 - 2006 ER - TY - THES A1 - Kaufmann, Benjamin T1 - High performance answer set solving Y1 - 2015 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Schaub, Torsten A1 - Tompits, Hans A1 - Woltran, Stefan T1 - On Computing belief change operations using quantifield boolean formulas N2 - 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 Y1 - 2004 SN - 0955-792X ER - TY - JOUR A1 - Flöter, André A1 - Nicolas, Jacques A1 - Schaub, Torsten A1 - Selbig, Joachim T1 - Threshold extraction in metabolite concentration data N2 - Motivation: Continued development of analytical techniques based on gas chromatography and mass spectrometry now facilitates the generation of larger sets of metabolite concentration data. An important step towards the understanding of metabolite dynamics is the recognition of stable states where metabolite concentrations exhibit a simple behaviour. Such states can be characterized through the identification of significant thresholds in the concentrations. But general techniques for finding discretization thresholds in continuous data prove to be practically insufficient for detecting states due to the weak conditional dependences in concentration data. Results: We introduce a method of recognizing states in the framework of decision tree induction. It is based upon a global analysis of decision forests where stability and quality are evaluated. It leads to the detection of thresholds that are both comprehensible and robust. Applied to metabolite concentration data, this method has led to the discovery of hidden states in the corresponding variables. Some of these reflect known properties of the biological experiments, and others point to putative new states Y1 - 2004 ER - TY - JOUR A1 - Delgrande, James Patrick A1 - Gharib, Mona A1 - Mercer, Robert E. A1 - Risch, V. A1 - Schaub, Torsten T1 - Lukaszewicz-style answer set programming : a preliminary report Y1 - 2003 UR - http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-78/ SN - 1613-0073 ER -