@misc{KaminskiSchaubSiegeletal.2013,
  author    = {Kaminski, Roland and Schaub, Torsten H. 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{GebserSchaubThieleetal.2011,
  author    = {Gebser, Martin and Schaub, Torsten H. 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{DurzinskyMarwanOstrowskietal.2011,
  author    = {Durzinsky, Markus and Marwan, Wolfgang and Ostrowski, Max and Schaub, Torsten H. and Wagler, Annegret},
  title     = {Automatic network reconstruction using ASP},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {560},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41241},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412419},
  pages     = {18},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@misc{EhrigGolasHabeletal.2014,
  author    = {Ehrig, Hartmut and Golas, Ulrike and Habel, Annegret and Lambers, Leen and Orejas, Fernando},
  title     = {M-adhesive transformation systems with nested application conditions},
  series = {Postprints der Universit{\"a}t Potsdam : Digital Engineering Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Digital Engineering Reihe},
  number    = {001},
  doi       = {10.25932/publishup-41565},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415651},
  pages     = {50},
  year      = {2014},
  abstract  = {Nested application conditions generalise the well-known negative application conditions and are important for several application domains. In this paper, we present Local Church-Rosser, Parallelism, Concurrency and Amalgamation Theorems for rules with nested application conditions in the framework of M-adhesive categories, where M-adhesive categories are slightly more general than weak adhesive high-level replacement categories. Most of the proofs are based on the corresponding statements for rules without application conditions and two shift lemmas stating that nested application conditions can be shifted over morphisms and rules.},
  language  = {en}
}
@misc{GebserKaufmannSchaub2012,
  author    = {Gebser, Martin and Kaufmann, Benjamin and Schaub, Torsten H.},
  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{HoosKaminskiLindaueretal.2015,
  author    = {Hoos, Holger and Kaminski, Roland and Lindauer, Marius and Schaub, Torsten H.},
  title     = {aspeed},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {588},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41474},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414743},
  pages     = {26},
  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}
}
@misc{GebserHarrisonKaminskietal.2015,
  author    = {Gebser, Martin and Harrison, Amelia and Kaminski, Roland and Lifschitz, Vladimir and Schaub, Torsten H.},
  title     = {Abstract gringo},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {592},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41475},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414751},
  pages     = {15},
  year      = {2015},
  abstract  = {This paper defines the syntax and semantics of the input language of the ASP grounder gringo. The definition covers several constructs that were not discussed in earlier work on the semantics of that language, including intervals, pools, division of integers, aggregates with non-numeric values, and lparse-style aggregate expressions. The definition is abstract in the sense that it disregards some details related to representing programs by strings of ASCII characters. It serves as a specification for gringo from Version 4.5 on.},
  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{HempelKoseskaNikoloskietal.2017,
  author    = {Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and Kurths, J{\"u}rgen},
  title     = {Unraveling gene regulatory networks from time-resolved gene expression data},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400924},
  pages     = {26},
  year      = {2017},
  abstract  = {Background: Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results: Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions: Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices.},
  language  = {en}
}
@misc{BenlianWienerCrametal.2022,
  author    = {Benlian, Alexander and Wiener, Martin and Cram, W. Alec and Krasnova, Hanna and Maedche, Alexander and Mohlmann, Mareike and Recker, Jan and Remus, Ulrich},
  title     = {Algorithmic management},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Wirtschafts- und Sozialwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Wirtschafts- und Sozialwissenschaftliche Reihe},
  number    = {6},
  issn      = {2363-7005},
  doi       = {10.25932/publishup-60711},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-607112},
  pages     = {17},
  year      = {2022},
  language  = {en}
}