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Robinson-Foulds Supertrees
Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca
Algorithms for Molecular Biology , 2010, DOI: 10.1186/1748-7188-5-18
Abstract: We introduce efficient, local search based, hill-climbing heuristics for the intrinsically hard RF supertree problem on rooted trees. These heuristics use novel non-trivial algorithms for the SPR and TBR local search problems which improve on the time complexity of the best known (na?ve) solutions by a factor of Θ(n) and Θ(n2) respectively (where n is the number of taxa, or leaves, in the supertree). We use an implementation of our new algorithms to examine the performance of the RF supertree method and compare it to matrix representation with parsimony (MRP) and the triplet supertree method using four supertree data sets. Not only did our RF heuristic provide fast estimates of RF supertrees in all data sets, but the RF supertrees also retained more of the information from the input trees (based on the RF distance) than the other supertree methods.Our heuristics for the RF supertree problem, based on our new local search algorithms, make it possible for the first time to estimate large supertrees by directly optimizing the RF distance from rooted input trees to the supertrees. This provides a new and fast method to build accurate supertrees. RF supertrees may also be useful for estimating majority-rule(-) supertrees, which are a generalization of majority-rule consensus trees.Supertree methods provide a formal approach for combining small phylogenetic trees with incomplete species overlap in order to build comprehensive species phylogenies, or supertrees, that contain all species found in the input trees. Supertree analyses have produced the first family-level phylogeny of flowering plants [1] and the first phylogeny of nearly all extant mammal species [2]. They have also enabled phylogenetic analyses using large-scale genomic data sets in bacteria, across eukaryotes, and within plants [3,4] and have helped elucidate the origin of eukaryotic genomes [5]. Furthermore, supertrees have been used to examine rates and patterns of species diversification [1,2], to test hy
Temporal Phylogenetic Networks and Logic Programming  [PDF]
Esra Erdem,Vladimir Lifschitz,Don Ringe
Computer Science , 2005,
Abstract: The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages. To appear in Theory and Practice of Logic Programming (TPLP).
Answer Set Programming Techniques and Methods
Omar El-khatib
International Journal of ACM Jordan , 2010,
Abstract: Answer set programming is a new program paradigm that is builton the foundation of logic programming with negation. To solve aproblem in answer set, the problem is represented as a set of rulessuch that their answer sets represents the solution to the problem. Inthis work we examine techniques and methods on writing answer setprograms
A primer on Answer Set Programming  [PDF]
Alessandro Provetti
Computer Science , 2005,
Abstract: A introduction to the syntax and Semantics of Answer Set Programming intended as an handout to [under]graduate students taking Artificial Intlligence or Logic Programming classes.
Functional Answer Set Programming  [PDF]
Pedro Cabalar
Computer Science , 2010,
Abstract: In this paper we propose an extension of Answer Set Programming (ASP), and in particular, of its most general logical counterpart, Quantified Equilibrium Logic (QEL), to deal with partial functions. Although the treatment of equality in QEL can be established in different ways, we first analyse the choice of decidable equality with complete functions and Herbrand models, recently proposed in the literature. We argue that this choice yields some counterintuitive effects from a logic programming and knowledge representation point of view. We then propose a variant called QELF where the set of functions is partitioned into partial and Herbrand functions (we also call constructors). In the rest of the paper, we show a direct connection to Scott's Logic of Existence and present a practical application, proposing an extension of normal logic programs to deal with partial functions and equality, so that they can be translated into function-free normal programs, being possible in this way to compute their answer sets with any standard ASP solver.
Fages' Theorem and Answer Set Programming  [PDF]
Yuliya Babovich,Esra Erdem,Vladimir Lifschitz
Computer Science , 2000,
Abstract: We generalize a theorem by Francois Fages that describes the relationship between the completion semantics and the answer set semantics for logic programs with negation as failure. The study of this relationship is important in connection with the emergence of answer set programming. Whenever the two semantics are equivalent, answer sets can be computed by a satisfiability solver, and the use of answer set solvers such as smodels and dlv is unnecessary. A logic programming representation of the blocks world due to Ilkka Niemelae is discussed as an example.
Constructing majority-rule supertrees
Jianrong Dong, David Fernández-Baca, FR McMorris
Algorithms for Molecular Biology , 2010, DOI: 10.1186/1748-7188-5-2
Abstract: We study a variant of one of Cotton and Wilkinson's methods, called majority-rule (+) supertrees. After proving that a key underlying problem for constructing majority-rule (+) supertrees is NP-hard, we develop a polynomial-size exact integer linear programming formulation of the problem. We then present a data reduction heuristic that identifies smaller subproblems that can be solved independently. While this technique is not guaranteed to produce optimal solutions, it can achieve substantial problem-size reduction. Finally, we report on a computational study of our approach on various real data sets, including the 121-taxon, 7-tree Seabirds data set of Kennedy and Page.The results indicate that our exact method is computationally feasible for moderately large inputs. For larger inputs, our data reduction heuristic makes it feasible to tackle problems that are well beyond the range of the basic integer programming approach. Comparisons between the results obtained by our heuristic and exact solutions indicate that the heuristic produces good answers. Our results also suggest that the majority-rule (+) approach, in both its basic form and with data reduction, yields biologically meaningful phylogenies.A supertree method begins with a collection of phylogenetic trees with possibly different leaf (taxon) sets, and assembles them into a larger phylogenetic tree, a supertree, whose taxon set is the union of the taxon sets of the input trees. Interest in supertrees was sparked by Gordon's paper [1]. Since then, particularly during the past decade, there has been a flurry of activity with many supertree methods proposed and studied from the algorithmic, theoretical, and biological points of view. The appeal of supertree synthesis is that it can combine disparate data to provide a high-level perspective that is harder to attain from individual trees. A recent example of the use of this approach is the species-level phylogeny of nearly all extant Mammalia constructed by Bin
Possibilistic Answer Set Programming Revisited  [PDF]
Kim Bauters,Steven Schockaert,Martine De Cock,Dirk Vermeir
Computer Science , 2012,
Abstract: Possibilistic answer set programming (PASP) extends answer set programming (ASP) by attaching to each rule a degree of certainty. While such an extension is important from an application point of view, existing semantics are not well-motivated, and do not always yield intuitive results. To develop a more suitable semantics, we first introduce a characterization of answer sets of classical ASP programs in terms of possibilistic logic where an ASP program specifies a set of constraints on possibility distributions. This characterization is then naturally generalized to define answer sets of PASP programs. We furthermore provide a syntactic counterpart, leading to a possibilistic generalization of the well-known Gelfond-Lifschitz reduct, and we show how our framework can readily be implemented using standard ASP solvers.
Symmetry Breaking for Answer Set Programming  [PDF]
Christian Drescher
Computer Science , 2010,
Abstract: In the context of answer set programming, this work investigates symmetry detection and symmetry breaking to eliminate symmetric parts of the search space and, thereby, simplify the solution process. We contribute a reduction of symmetry detection to a graph automorphism problem which allows to extract symmetries of a logic program from the symmetries of the constructed coloured graph. We also propose an encoding of symmetry-breaking constraints in terms of permutation cycles and use only generators in this process which implicitly represent symmetries and always with exponential compression. These ideas are formulated as preprocessing and implemented in a completely automated flow that first detects symmetries from a given answer set program, adds symmetry-breaking constraints, and can be applied to any existing answer set solver. We demonstrate computational impact on benchmarks versus direct application of the solver. Furthermore, we explore symmetry breaking for answer set programming in two domains: first, constraint answer set programming as a novel approach to represent and solve constraint satisfaction problems, and second, distributed nonmonotonic multi-context systems. In particular, we formulate a translation-based approach to constraint answer set solving which allows for the application of our symmetry detection and symmetry breaking methods. To compare their performance with a-priori symmetry breaking techniques, we also contribute a decomposition of the global value precedence constraint that enforces domain consistency on the original constraint via the unit-propagation of an answer set solver. We evaluate both options in an empirical analysis. In the context of distributed nonmonotonic multi-context system, we develop an algorithm for distributed symmetry detection and also carry over symmetry-breaking constraints for distributed answer set programming.
Complex Optimization in Answer Set Programming  [PDF]
Martin Gebser,Roland Kaminski,Torsten Schaub
Computer Science , 2011,
Abstract: Preference handling and optimization are indispensable means for addressing non-trivial 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-programming, 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.
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