@article{LinkeSchaub1995, author = {Linke, Thomas and Schaub, Torsten}, title = {Lemma handling in default logic theorem provers}, isbn = {3540601120}, year = {1995}, language = {en} } @article{GebserKaufmannNeumannetal.2007, author = {Gebser, Martin and Kaufmann, Benjamin and Neumann, Andr{\´e} and Schaub, Torsten}, title = {Conflict-driven answer set solving}, isbn = {978-1-57735-323-2}, year = {2007}, language = {en} } @article{BesnardSchaub1993, author = {Besnard, Philippe and Schaub, Torsten}, title = {A context-based framework for default logics}, isbn = {0-262-51071-5}, year = {1993}, language = {en} } @article{GebserGharibSchaub2007, author = {Gebser, Martin and Gharib, Mona and Schaub, Torsten}, title = {Incremental answer sets and their computation}, year = {2007}, language = {en} } @article{GebserSchaub2007, author = {Gebser, Martin and Schaub, Torsten}, title = {Generic tableaux for answer set programming}, year = {2007}, language = {en} } @article{DelgrandeSchaub2007, author = {Delgrande, James Patrick and Schaub, Torsten}, title = {A consistency-based framework for merging knowledge bases}, issn = {1570-8683}, year = {2007}, language = {en} } @article{KonczakLinkeSchaub2006, author = {Konczak, Kathrin and Linke, Thomas and Schaub, Torsten}, title = {Graphs and colorings for answer set programming}, issn = {1471-0684}, doi = {10.1017/S1471068405002528}, year = {2006}, abstract = {We investigate the usage of rule dependency graphs and their colorings for characterizing and computing answer sets of logic programs. This approach provides us with insights into the interplay between rules when inducing answer sets. We start with different characterizations of answer sets in terms of totally colored dependency graphs that differ ill graph-theoretical aspects. We then develop a series of operational characterizations of answer sets in terms of operators on partial colorings. In analogy to the notion of a derivation in proof theory, our operational characterizations are expressed as (non-deterministically formed) sequences of colorings, turning an uncolored graph into a totally colored one. In this way, we obtain an operational framework in which different combinations of operators result in different formal properties. Among others, we identify the basic strategy employed by the noMoRe system and justify its algorithmic approach. Furthermore, we distinguish operations corresponding to Fitting's operator as well as to well-founded semantics}, language = {en} } @article{GressmannJanhunenMerceretal.2006, author = {Gressmann, Jean and Janhunen, Tomi and Mercer, Robert E. and Schaub, Torsten and Thiele, Sven and Tichy, Richard}, title = {On probing and multi-threading in platypus}, year = {2006}, language = {en} } @article{AngerGebserLinkeetal.2005, author = {Anger, Christian and Gebser, Martin and Linke, Thomas and Neumann, Andre and Schaub, Torsten}, title = {The nomore++ approach to answer set solving}, year = {2005}, language = {en} } @article{GressmannJanhunenMerceretal.2005, author = {Gressmann, Jean and Janhunen, Tomi and Mercer, Robert E. and Schaub, Torsten and Thiele, Sven and Tichy, Richard}, title = {Platypus : a platform for distributed answer set solving}, year = {2005}, language = {en} } @article{SarsakovSchaubTompitsetal.2004, author = {Sarsakov, Vladimir and Schaub, Torsten and Tompits, Hans and Woltran, Stefan}, title = {A compiler for nested logic programming}, isbn = {3-540- 20721-x}, year = {2004}, language = {en} } @article{GebserLiuNamasivayametal.2007, author = {Gebser, Martin and Liu, Lengning and Namasivayam, Gayathri and Neumann, Andr{\´e} and Schaub, Torsten and Truszczynski, Miroslaw}, title = {The first answer set programming system competition}, isbn = {978-3-540- 72199-4}, year = {2007}, language = {en} } @article{AngerGebserLinkeetal.2005, author = {Anger, Christian and Gebser, Martin and Linke, Thomas and Neumann, Andre and Schaub, Torsten}, title = {The nomore++ approach to answer set solving}, year = {2005}, language = {en} } @article{AngerKonczakLinkeetal.2005, author = {Anger, Christian and Konczak, Kathrin and Linke, Thomas and Schaub, Torsten}, title = {A Glimpse of Answer Set Programming}, issn = {0170-4516}, year = {2005}, language = {en} } @article{GrellKonczakSchaub2005, author = {Grell, Susanne and Konczak, Kathrin and Schaub, Torsten}, title = {nomore) : a system for computing preferred Answer Sets}, issn = {0302-9743}, year = {2005}, language = {en} } @article{KonczakSchaubLinke2003, author = {Konczak, Kathrin and Schaub, Torsten and Linke, Thomas}, title = {Graphs and colorings for answer set programming with preferences}, issn = {0169-2968}, year = {2003}, abstract = {The integration of preferences into answer set programming constitutes an important practical device for distinguishing certain preferred answer sets from non-preferred ones. To this end, we elaborate upon rule dependency graphs and their colorings for characterizing different preference handling strategies found in the literature. We start from a characterization of (three types of) preferred answer sets in terms of totally colored dependency graphs. In particular, we demonstrate that this approach allows us to capture all three approaches to preferences in a uniform setting by means of the concept of a height function. In turn, we exemplarily develop an operational characterization of preferred answer sets in terms of operators on partial colorings for one particular strategy. In analogy to the notion of a derivation in proof theory, our operational characterization is expressed as a (non-deterministically formed) sequence of colorings, gradually turning an uncolored graph into a totally colored one}, language = {en} } @article{BesnardSchaubTompitsetal.2003, author = {Besnard, Philippe and Schaub, Torsten and Tompits, Hans and Woltran, Stefan}, title = {Paraconsistent reasoning via quantified boolean formulas : Part II: Circumscribing inconsistent theories}, isbn = {3-540- 409494-5}, year = {2003}, language = {en} } @article{DelgrandeHunterSchaub2002, author = {Delgrande, James Patrick and Hunter, Anthony and Schaub, Torsten}, title = {COBA: a consistency-based belief revision system}, isbn = {3-540-44190-5}, year = {2002}, language = {en} } @article{FloeterNicolasSchaubetal.2003, author = {Fl{\"o}ter, Andr{\´e} and Nicolas, Jacques and Schaub, Torsten and Selbig, Joachim}, title = {Threshold extraction in metabolite concentration data}, year = {2003}, language = {en} } @article{SchaubWang2002, author = {Schaub, Torsten and Wang, T.}, title = {Preferred well-founded semantics for logic programming by alternating fixpoints : preliminary report}, year = {2002}, language = {en} } @article{DelgrandeSchaub2003, author = {Delgrande, James Patrick and Schaub, Torsten}, title = {A concictency-based paradigm for belief change}, issn = {0004-3702}, year = {2003}, language = {en} } @article{BesnardFanselowSchaub2002, author = {Besnard, Philippe and Fanselow, Gisbert and Schaub, Torsten}, title = {Optimality theory as a family of cumulative logics}, year = {2002}, language = {en} } @article{DelgrandeSchaub2002, author = {Delgrande, James Patrick and Schaub, Torsten}, title = {Reasoning credulously and skeptically within a single extension}, year = {2002}, language = {en} } @article{Schaub2003, author = {Schaub, Torsten}, title = {Antwortmengenprogrammierung}, year = {2003}, language = {de} } @article{DelgrandeSchaubTompits2000, author = {Delgrande, James Patrick and Schaub, Torsten and Tompits, Hans}, title = {A compilation of Brewka and Eiter's approach to prioritizationtion}, isbn = {3-540-41131-3}, year = {2000}, language = {en} } @article{DelgrandeSchaubTompits2000, author = {Delgrande, James Patrick and Schaub, Torsten and Tompits, Hans}, title = {Logic programs with compiled preferences}, isbn = {1-58603-013-2}, year = {2000}, language = {en} } @article{DelgrandeSchaub2000, author = {Delgrande, James Patrick and Schaub, Torsten}, title = {A consistency-based model for belief change: preliminary report}, isbn = {0-262-51112-6}, year = {2000}, language = {en} } @article{BesnardSchaub2000, author = {Besnard, Philippe and Schaub, Torsten}, title = {Significant inferences}, isbn = {1-55860-690-4}, year = {2000}, language = {en} } @article{DelgrandeSchaubTompits2000, author = {Delgrande, James Patrick and Schaub, Torsten and Tompits, Hans}, title = {Logic programs with compiled preferences}, year = {2000}, language = {en} } @article{DelgrandeSchaubTompits2000, author = {Delgrande, James Patrick and Schaub, Torsten and Tompits, Hans}, title = {A compiler for ordered logic programs}, year = {2000}, language = {en} } @article{BesnardSchaub2000, author = {Besnard, Philippe and Schaub, Torsten}, title = {What is a (non-constructive) non-monotone logical system?}, issn = {0304-3975}, year = {2000}, language = {en} } @article{BrueningSchaub2000, author = {Br{\"u}ning, Stefan and Schaub, Torsten}, title = {A connection calculus for handling incomplete information}, year = {2000}, language = {en} } @article{DelgrandeSchaub2000, author = {Delgrande, James Patrick and Schaub, Torsten}, title = {Expressing preferences in default logic}, issn = {0004-3702}, year = {2000}, language = {en} } @article{SchaubNicolas1997, author = {Schaub, Torsten and Nicolas, Pascal}, title = {An implementation platform for query-answering in default logics : the XRay system, its implementation and evaluation}, isbn = {3-540-63255-7}, year = {1997}, language = {en} } @article{SchaubNicolas1997, author = {Schaub, Torsten and Nicolas, Pascal}, title = {An implementation platform for query-answering in default logics : theoretical underpinnings}, isbn = {3-540-63614-5}, year = {1997}, language = {en} } @article{DelgrandeSchaub1997, author = {Delgrande, James Patrick and Schaub, Torsten}, title = {Compiling reasoning with and about preferences into default logic}, isbn = {1-558-60480-4}, issn = {1045-0823}, year = {1997}, language = {en} } @article{SchaubThielscher1996, author = {Schaub, Torsten and Thielscher, Michael}, title = {Skeptical query-answering in constrained default logic}, isbn = {3-540-61313-7}, year = {1996}, language = {en} } @article{BrueningSchaub1996, author = {Br{\"u}ning, Stefan and Schaub, Torsten}, title = {A model-based approach to consistency-checking}, isbn = {3-540-61286-6}, year = {1996}, language = {en} } @article{BesnardSchaub1997, author = {Besnard, Philippe and Schaub, Torsten}, title = {Circumscribing inconsistency}, isbn = {1-558-60480-4}, issn = {1045-0823}, year = {1997}, language = {en} } @article{SchaubBruening1996, author = {Schaub, Torsten and Br{\"u}ning, Stefan}, title = {Prolog technology for default reasoning}, isbn = {0-471-96809-9}, year = {1996}, language = {en} } @article{DelgrandeSchaub1997, author = {Delgrande, James Patrick and Schaub, Torsten}, title = {Compiling specificity into approaches to nonmonotonic reasoning}, issn = {0004-3702}, year = {1997}, language = {en} } @article{LinkeSchaub1997, author = {Linke, Thomas and Schaub, Torsten}, title = {Towards a classification of default logic}, year = {1997}, 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 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} } @article{HoosKaminskiLindaueretal.2015, author = {Hoos, Holger and Kaminski, Roland and Lindauer, Marius and Schaub, Torsten}, title = {aspeed: Solver scheduling via answer set programming}, series = {Theory and practice of logic programming}, volume = {15}, journal = {Theory and practice of logic programming}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068414000015}, pages = {117 -- 142}, year = {2015}, abstract = {Although Boolean Constraint Technology has made tremendous progress over the last decade, the efficacy of state-of-the-art solvers is known to vary considerably across different types of problem instances, and is known to depend strongly on algorithm parameters. This problem was addressed by means of a simple, yet effective approach using handmade, uniform, and unordered schedules of multiple solvers in ppfolio, which showed very impressive performance in the 2011 Satisfiability Testing (SAT) Competition. Inspired by this, we take advantage of the modeling and solving capacities of Answer Set Programming (ASP) to automatically determine more refined, that is, nonuniform and ordered solver schedules from the existing benchmarking data. We begin by formulating the determination of such schedules as multi-criteria optimization problems and provide corresponding ASP encodings. The resulting encodings are easily customizable for different settings, and the computation of optimum schedules can mostly be done in the blink of an eye, even when dealing with large runtime data sets stemming from many solvers on hundreds to thousands of instances. Also, the fact that our approach can be customized easily enabled us to swiftly adapt it to generate parallel schedules for multi-processor machines.}, language = {en} } @article{GebserKaufmannKaminskietal.2011, author = {Gebser, Martin and Kaufmann, Benjamin and Kaminski, Roland and Ostrowski, Max and Schaub, Torsten and Schneider, Marius}, title = {Potassco the Potsdam answer set solving collection}, series = {AI communications : AICOM ; the European journal on artificial intelligence}, volume = {24}, journal = {AI communications : AICOM ; the European journal on artificial intelligence}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {0921-7126}, doi = {10.3233/AIC-2011-0491}, pages = {107 -- 124}, year = {2011}, abstract = {This paper gives an overview of the open source project Potassco, the Potsdam Answer Set Solving Collection, bundling tools for Answer Set Programming developed at the University of Potsdam.}, language = {en} } @article{CabalarFandinoSchaubetal.2019, author = {Cabalar, Pedro and Fandi{\~n}o, Jorge and Schaub, Torsten and Schellhorn, Sebastian}, title = {Gelfond-Zhang aggregates as propositional formulas}, series = {Artificial intelligence}, volume = {274}, journal = {Artificial intelligence}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0004-3702}, doi = {10.1016/j.artint.2018.10.007}, pages = {26 -- 43}, year = {2019}, abstract = {Answer Set Programming (ASP) has become a popular and widespread paradigm for practical Knowledge Representation thanks to its expressiveness and the available enhancements of its input language. One of such enhancements is the use of aggregates, for which different semantic proposals have been made. In this paper, we show that any ASP aggregate interpreted under Gelfond and Zhang's (GZ) semantics can be replaced (under strong equivalence) by a propositional formula. Restricted to the original GZ syntax, the resulting formula is reducible to a disjunction of conjunctions of literals but the formulation is still applicable even when the syntax is extended to allow for arbitrary formulas (including nested aggregates) in the condition. Once GZ-aggregates are represented as formulas, we establish a formal comparison (in terms of the logic of Here-and-There) to Ferraris' (F) aggregates, which are defined by a different formula translation involving nested implications. In particular, we prove that if we replace an F-aggregate by a GZ-aggregate in a rule head, we do not lose answer sets (although more can be gained). This extends the previously known result that the opposite happens in rule bodies, i.e., replacing a GZ-aggregate by an F-aggregate in the body may yield more answer sets. Finally, we characterize a class of aggregates for which GZ- and F-semantics coincide.}, language = {en} } @phdthesis{Videla2014, author = {Videla, Santiago}, title = {Reasoning on the response of logical signaling networks with answer set programming}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71890}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Deciphering the functioning of biological networks is one of the central tasks in systems biology. In particular, signal transduction networks are crucial for the understanding of the cellular response to external and internal perturbations. Importantly, in order to cope with the complexity of these networks, mathematical and computational modeling is required. We propose a computational modeling framework in order to achieve more robust discoveries in the context of logical signaling networks. More precisely, we focus on modeling the response of logical signaling networks by means of automated reasoning using Answer Set Programming (ASP). ASP provides a declarative language for modeling various knowledge representation and reasoning problems. Moreover, available ASP solvers provide several reasoning modes for assessing the multitude of answer sets. Therefore, leveraging its rich modeling language and its highly efficient solving capacities, we use ASP to address three challenging problems in the context of logical signaling networks: learning of (Boolean) logical networks, experimental design, and identification of intervention strategies. Overall, the contribution of this thesis is three-fold. Firstly, we introduce a mathematical framework for characterizing and reasoning on the response of logical signaling networks. Secondly, we contribute to a growing list of successful applications of ASP in systems biology. Thirdly, we present a software providing a complete pipeline for automated reasoning on the response of logical signaling networks.}, language = {en} } @article{DimopoulosGebserLuehneetal.2019, author = {Dimopoulos, Yannis and Gebser, Martin and L{\"u}hne, Patrick and Romero Davila, Javier and Schaub, Torsten}, title = {plasp 3}, series = {Theory and practice of logic programming}, volume = {19}, journal = {Theory and practice of logic programming}, number = {3}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068418000583}, pages = {477 -- 504}, year = {2019}, abstract = {We describe the new version of the Planning Domain Definition Language (PDDL)-to-Answer Set Programming (ASP) translator plasp. First, it widens the range of accepted PDDL features. Second, it contains novel planning encodings, some inspired by Satisfiability Testing (SAT) planning and others exploiting ASP features such as well-foundedness. All of them are designed for handling multivalued fluents in order to capture both PDDL as well as SAS planning formats. Third, enabled by multishot ASP solving, it offers advanced planning algorithms also borrowed from SAT planning. As a result, plasp provides us with an ASP-based framework for studying a variety of planning techniques in a uniform setting. Finally, we demonstrate in an empirical analysis that these techniques have a significant impact on the performance of ASP planning.}, language = {en} } @article{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 = {Theory and practice of logic programming}, volume = {13}, journal = {Theory and practice of logic programming}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068413000422}, 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} } @article{SchaubBrueningNicolas1996, author = {Schaub, Torsten and Br{\"u}ning, Stefan and Nicolas, Pascal}, title = {XRay : a prolog technology theorem prover for default reasoning: a system description}, isbn = {3-540-61511-3}, year = {1996}, language = {en} }