Query Containment for Highly Expressive Datalog Fragments

The containment problem of Datalog queries is well known to be undecidable. There are, however, several Datalog fragments for which containment is known to be decidable, most notably monadic Datalog and several "regular" query languages on graphs. Monadically Defined Queries (MQs) have been introduced recently as a joint generalization of these query languages. In this paper, we study a wide range of Datalog fragments with decidable query containment and determine exact complexity results for this problem. We generalize MQs to (Frontier-)Guarded Queries (GQs), and show that the containment problem is 3ExpTime-complete in either case, even if we allow arbitrary Datalog in the sub-query. If we focus on graph query languages, i.e., fragments of linear Datalog, then this complexity is reduced to 2ExpSpace. We also consider nested queries, which gain further expressivity by using predicates that are defined by inner queries. We show that nesting leads to an exponentially increasing hierarchy for the complexity of query containment, both in the linear and in the general case. Our results settle open problems for (nested) MQs, and they paint a comprehensive picture of the state of the art in Datalog query containment.Comment: 20 page

A Categorical View on Algebraic Lattices in Formal Concept Analysis

Formal concept analysis has grown from a new branch of the mathematical field of lattice theory to a widely recognized tool in Computer Science and elsewhere. In order to fully benefit from this theory, we believe that it can be enriched with notions such as approximation by computation or representability. The latter are commonly studied in denotational semantics and domain theory and captured most prominently by the notion of algebraicity, e.g. of lattices. In this paper, we explore the notion of algebraicity in formal concept analysis from a category-theoretical perspective. To this end, we build on the the notion of approximable concept with a suitable category and show that the latter is equivalent to the category of algebraic lattices. At the same time, the paper provides a relatively comprehensive account of the representation theory of algebraic lattices in the framework of Stone duality, relating well-known structures such as Scott information systems with further formalisms from logic, topology, domains and lattice theory.Comment: 36 page

Type-elimination-based reasoning for the description logic SHIQbs using decision diagrams and disjunctive datalog

We propose a novel, type-elimination-based method for reasoning in the description logic SHIQbs including DL-safe rules. To this end, we first establish a knowledge compilation method converting the terminological part of an ALCIb knowledge base into an ordered binary decision diagram (OBDD) which represents a canonical model. This OBDD can in turn be transformed into disjunctive Datalog and merged with the assertional part of the knowledge base in order to perform combined reasoning. In order to leverage our technique for full SHIQbs, we provide a stepwise reduction from SHIQbs to ALCIb that preserves satisfiability and entailment of positive and negative ground facts. The proposed technique is shown to be worst case optimal w.r.t. combined and data complexity and easily admits extensions with ground conjunctive queries.Comment: 38 pages, 3 figures, camera ready version of paper accepted for publication in Logical Methods in Computer Scienc

A rule-based ontological framework for the classification of molecules

BACKGROUND: A variety of key activities within life sciences research involves integrating and intelligently managing large amounts of biochemical information. Semantic technologies provide an intuitive way to organise and sift through these rapidly growing datasets via the design and maintenance of ontology-supported knowledge bases. To this end, OWL-a W3C standard declarative language- has been extensively used in the deployment of biochemical ontologies that can be conveniently organised using the classification facilities of OWL-based tools. One of the most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that supplies high quality annotation and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential to grow due to the limited availability of human resources. RESULTS: In this work, we describe a prototype that performs automatic classification of chemical compounds. The software we present implements a sound and complete reasoning procedure of a formalism that extends datalog and builds upon an off-the-shelf deductive database system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. Furthermore, we describe a surface 'less-logician-like' syntax that allows application experts to create ontological descriptions of complex biochemical objects without prior knowledge of logic. In terms of performance, a noticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language suitable for the life sciences domain that exhibits a favourable balance between expressive power and practical feasibility. CONCLUSIONS: Our proposed methodology can form the basis of an ontology-mediated application to assist biocurators in the production of complete and error-free taxonomies. Moreover, such a tool could contribute to a more rapid development of the ChEBI ontology and to the efforts of the ChEBI team to make annotated chemical datasets available to the public. From a modelling point of view, our approach could stimulate the adoption of a different and expressive reasoning paradigm based on rules for which state-of-the-art and highly optimised reasoners are available; it could thus pave the way for the representation of a broader spectrum of life sciences and biomedical knowledge.</p

On the Complexity of Universality for Partially Ordered NFAs

International audiencePartially ordered nondeterminsitic finite automata (poNFAs) are NFAs whose transition relation induces a partial order on states, i.e., for which cycles occur only in the form of self-loops on a single state. A poNFA is universal if it accepts all words over its input alphabet. Deciding universality is PSpace-complete for poNFAs, and we show that this remains true even when restricting to a fixed alphabet. This is nontrivial since standard encodings of alphabet symbols in, e.g., binary can turn self-loops into longer cycles. A lower coNP-complete complexity bound can be obtained if we require that all self-loops in the poNFA are deterministic, in the sense that the symbol read in the loop cannot occur in any other transition from that state. We find that such restricted poNFAs (rpoNFAs) characterise the class of R-trivial languages, and we establish the complexity of deciding if the language of an NFA is R-trivial. Nevertheless, the limitation to fixed alphabets turns out to be essential even in the restricted case: deciding universality of rpoNFAs with unbounded alphabets is PSpace-complete. Our results also prove the complexity of the inclusion and equivalence problems, since universality provides the lower bound, while the upper bound is mostly known or proved in the paper

Revisiting acyclicity and guardedness criteria for decidability of existential rules

Abstract. Existential rules, i.e. Datalog extended with existential quantifiers in rule heads, are currently studied under a variety of names such as Datalog+/-, ∀∃-rules, and tuple-generating dependencies. The renewed interest in this formalism is fuelled by a wealth of recently discovered language fragments for which query answering is decidable. This paper extends and consolidates two of the main approaches in this field -acyclicity and guardedness -by providing (1) complexitypreserving generalisations of weakly acyclic and weakly (frontier-)guarded rules, and (2) a novel formalism of glut-(frontier-)guarded rules that subsumes both. This builds on an insight that acyclicity can be used to extend any existential rule language while retaining decidability. Besides decidability, combined query complexities are established in all cases

A Datalog Hammer for Supervisor Verification Conditions Modulo Simple Linear Arithmetic

The Bernays-Sch\"onfinkel first-order logic fragment over simple linear real arithmetic constraints BS(SLR) is known to be decidable. We prove that BS(SLR) clause sets with both universally and existentially quantified verification conditions (conjectures) can be translated into BS(SLR) clause sets over a finite set of first-order constants. For the Horn case, we provide a Datalog hammer preserving validity and satisfiability. A toolchain from the BS(LRA) prover SPASS-SPL to the Datalog reasoner VLog establishes an effective way of deciding verification conditions in the Horn fragment. This is exemplified by the verification of supervisor code for a lane change assistant in a car and of an electronic control unit for a supercharged combustion engine.Comment: 26 page