The Complexity of Rooted Phylogeny Problems

Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary tree that satisfies the formula? If the formulas do not contain disjunctions, the problem becomes the famous rooted triple consistency problem, which can be solved in polynomial time by an algorithm of Aho, Sagiv, Szymanski, and Ullman. If the clauses in the formulas are restricted to disjunctions of negated triples, Ng, Steel, and Wormald showed that the problem remains NP-complete. We systematically study the computational complexity of the problem for all such restrictions of the clauses in the input formula. For certain restricted disjunctions of triples we present an algorithm that has sub-quadratic running time and is asymptotically as fast as the fastest known algorithm for the rooted triple consistency problem. We also show that any restriction of the general rooted phylogeny problem that does not fall into our tractable class is NP-complete, using known results about the complexity of Boolean constraint satisfaction problems. Finally, we present a pebble game argument that shows that the rooted triple consistency problem (and also all generalizations studied in this paper) cannot be solved by Datalog

Querying the Guarded Fragment

Evaluating a Boolean conjunctive query Q against a guarded first-order theory F is equivalent to checking whether "F and not Q" is unsatisfiable. This problem is relevant to the areas of database theory and description logic. Since Q may not be guarded, well known results about the decidability, complexity, and finite-model property of the guarded fragment do not obviously carry over to conjunctive query answering over guarded theories, and had been left open in general. By investigating finite guarded bisimilar covers of hypergraphs and relational structures, and by substantially generalising Rosati's finite chase, we prove for guarded theories F and (unions of) conjunctive queries Q that (i) Q is true in each model of F iff Q is true in each finite model of F and (ii) determining whether F implies Q is 2EXPTIME-complete. We further show the following results: (iii) the existence of polynomial-size conformal covers of arbitrary hypergraphs; (iv) a new proof of the finite model property of the clique-guarded fragment; (v) the small model property of the guarded fragment with optimal bounds; (vi) a polynomial-time solution to the canonisation problem modulo guarded bisimulation, which yields (vii) a capturing result for guarded bisimulation invariant PTIME.Comment: This is an improved and extended version of the paper of the same title presented at LICS 201

A Polynomial Translation of Logic Programs with Nested Expressions into Disjunctive Logic Programs: Preliminary Report

Nested logic programs have recently been introduced in order to allow for arbitrarily nested formulas in the heads and the bodies of logic program rules under the answer sets semantics. Nested expressions can be formed using conjunction, disjunction, as well as the negation as failure operator in an unrestricted fashion. This provides a very flexible and compact framework for knowledge representation and reasoning. Previous results show that nested logic programs can be transformed into standard (unnested) disjunctive logic programs in an elementary way, applying the negation as failure operator to body literals only. This is of great practical relevance since it allows us to evaluate nested logic programs by means of off-the-shelf disjunctive logic programming systems, like DLV. However, it turns out that this straightforward transformation results in an exponential blow-up in the worst-case, despite the fact that complexity results indicate that there is a polynomial translation among both formalisms. In this paper, we take up this challenge and provide a polynomial translation of logic programs with nested expressions into disjunctive logic programs. Moreover, we show that this translation is modular and (strongly) faithful. We have implemented both the straightforward as well as our advanced transformation; the resulting compiler serves as a front-end to DLV and is publicly available on the Web.Comment: 10 pages; published in Proceedings of the 9th International Workshop on Non-Monotonic Reasonin

Survey-propagation decimation through distributed local computations

We discuss the implementation of two distributed solvers of the random K-SAT problem, based on some development of the recently introduced survey-propagation (SP) algorithm. The first solver, called the "SP diffusion algorithm", diffuses as dynamical information the maximum bias over the system, so that variable nodes can decide to freeze in a self-organized way, each variable making its decision on the basis of purely local information. The second solver, called the "SP reinforcement algorithm", makes use of time-dependent external forcing messages on each variable, which let the variables get completely polarized in the direction of a solution at the end of a single convergence. Both methods allow us to find a solution of the random 3-SAT problem in a range of parameters comparable with the best previously described serialized solvers. The simulated time of convergence towards a solution (if these solvers were implemented on a distributed device) grows as log(N).Comment: 18 pages, 10 figure

On QBF Proofs and Preprocessing

QBFs (quantified boolean formulas), which are a superset of propositional formulas, provide a canonical representation for PSPACE problems. To overcome the inherent complexity of QBF, significant effort has been invested in developing QBF solvers as well as the underlying proof systems. At the same time, formula preprocessing is crucial for the application of QBF solvers. This paper focuses on a missing link in currently-available technology: How to obtain a certificate (e.g. proof) for a formula that had been preprocessed before it was given to a solver? The paper targets a suite of commonly-used preprocessing techniques and shows how to reconstruct certificates for them. On the negative side, the paper discusses certain limitations of the currently-used proof systems in the light of preprocessing. The presented techniques were implemented and evaluated in the state-of-the-art QBF preprocessor bloqqer.Comment: LPAR 201

A Survey of Satisfiability Modulo Theory

Satisfiability modulo theory (SMT) consists in testing the satisfiability of first-order formulas over linear integer or real arithmetic, or other theories. In this survey, we explain the combination of propositional satisfiability and decision procedures for conjunctions known as DPLL(T), and the alternative "natural domain" approaches. We also cover quantifiers, Craig interpolants, polynomial arithmetic, and how SMT solvers are used in automated software analysis.Comment: Computer Algebra in Scientific Computing, Sep 2016, Bucharest, Romania. 201

09461 Abstracts Collection -- Algorithms and Applications for Next Generation SAT Solvers

From 8th to 13th November 2009, the Dagstuhl Seminar 09461 "Algorithms and Applications for Next Generation SAT Solvers" was held in Schloss Dagstuhl--Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts, slides or full papers are provided, if available

Evaluating QBF Solvers: Quantifier Alternations Matter

We present an experimental study of the effects of quantifier alternations on the evaluation of quantified Boolean formula (QBF) solvers. The number of quantifier alternations in a QBF in prenex conjunctive normal form (PCNF) is directly related to the theoretical hardness of the respective QBF satisfiability problem in the polynomial hierarchy. We show empirically that the performance of solvers based on different solving paradigms substantially varies depending on the numbers of alternations in PCNFs. In related theoretical work, quantifier alternations have become the focus of understanding the strengths and weaknesses of various QBF proof systems implemented in solvers. Our results motivate the development of methods to evaluate orthogonal solving paradigms by taking quantifier alternations into account. This is necessary to showcase the broad range of existing QBF solving paradigms for practical QBF applications. Moreover, we highlight the potential of combining different approaches and QBF proof systems in solvers.Comment: preprint of a paper to be published at CP 2018, LNCS, Springer, including appendi