A set-based reasoner for the description logic \shdlssx (Extended Version)

We present a \ke-based implementation of a reasoner for a decidable fragment of (stratified) set theory expressing the description logic \dlssx (\shdlssx, for short). Our application solves the main TBox and ABox reasoning problems for \shdlssx. In particular, it solves the consistency problem for \shdlssx-knowledge bases represented in set-theoretic terms, and a generalization of the \emph{Conjunctive Query Answering} problem in which conjunctive queries with variables of three sorts are admitted. The reasoner, which extends and optimizes a previous prototype for the consistency checking of \shdlssx-knowledge bases (see \cite{cilc17}), is implemented in \textsf{C++}. It supports \shdlssx-knowledge bases serialized in the OWL/XML format, and it admits also rules expressed in SWRL (Semantic Web Rule Language).Comment: arXiv admin note: text overlap with arXiv:1804.11222, arXiv:1707.07545, arXiv:1702.0309

E-Generalization Using Grammars

We extend the notion of anti-unification to cover equational theories and present a method based on regular tree grammars to compute a finite representation of E-generalization sets. We present a framework to combine Inductive Logic Programming and E-generalization that includes an extension of Plotkin's lgg theorem to the equational case. We demonstrate the potential power of E-generalization by three example applications: computation of suggestions for auxiliary lemmas in equational inductive proofs, computation of construction laws for given term sequences, and learning of screen editor command sequences.Comment: 49 pages, 16 figures, author address given in header is meanwhile outdated, full version of an article in the "Artificial Intelligence Journal", appeared as technical report in 2003. An open-source C implementation and some examples are found at the Ancillary file

Set Unification

The unification problem in algebras capable of describing sets has been tackled, directly or indirectly, by many researchers and it finds important applications in various research areas--e.g., deductive databases, theorem proving, static analysis, rapid software prototyping. The various solutions proposed are spread across a large literature. In this paper we provide a uniform presentation of unification of sets, formalizing it at the level of set theory. We address the problem of deciding existence of solutions at an abstract level. This provides also the ability to classify different types of set unification problems. Unification algorithms are uniformly proposed to solve the unification problem in each of such classes. The algorithms presented are partly drawn from the literature--and properly revisited and analyzed--and partly novel proposals. In particular, we present a new goal-driven algorithm for general ACI1 unification and a new simpler algorithm for general (Ab)(Cl) unification.Comment: 58 pages, 9 figures, 1 table. To appear in Theory and Practice of Logic Programming (TPLP

Verifying the Interplay of Authorization Policies and Workflow in Service-Oriented Architectures (Full version)

A widespread design approach in distributed applications based on the service-oriented paradigm, such as web-services, consists of clearly separating the enforcement of authorization policies and the workflow of the applications, so that the interplay between the policy level and the workflow level is abstracted away. While such an approach is attractive because it is quite simple and permits one to reason about crucial properties of the policies under consideration, it does not provide the right level of abstraction to specify and reason about the way the workflow may interfere with the policies, and vice versa. For example, the creation of a certificate as a side effect of a workflow operation may enable a policy rule to fire and grant access to a certain resource; without executing the operation, the policy rule should remain inactive. Similarly, policy queries may be used as guards for workflow transitions. In this paper, we present a two-level formal verification framework to overcome these problems and formally reason about the interplay of authorization policies and workflow in service-oriented architectures. This allows us to define and investigate some verification problems for SO applications and give sufficient conditions for their decidability.Comment: 16 pages, 4 figures, full version of paper at Symposium on Secure Computing (SecureCom09

Bayesian models for syndrome- and gene-specific probabilities of novel variant pathogenicity

BACKGROUND: With the advent of affordable and comprehensive sequencing technologies, access to molecular genetics for clinical diagnostics and research applications is increasing. However, variant interpretation remains challenging, and tools that close the gap between data generation and data interpretation are urgently required. Here we present a transferable approach to help address the limitations in variant annotation. METHODS: We develop a network of Bayesian logistic regression models that integrate multiple lines of evidence to evaluate the probability that a rare variant is the cause of an individual's disease. We present models for genes causing inherited cardiac conditions, though the framework is transferable to other genes and syndromes. RESULTS: Our models report a probability of pathogenicity, rather than a categorisation into pathogenic or benign, which captures the inherent uncertainty of the prediction. We find that gene- and syndrome-specific models outperform genome-wide approaches, and that the integration of multiple lines of evidence performs better than individual predictors. The models are adaptable to incorporate new lines of evidence, and results can be combined with familial segregation data in a transparent and quantitative manner to further enhance predictions. Though the probability scale is continuous, and innately interpretable, performance summaries based on thresholds are useful for comparisons. Using a threshold probability of pathogenicity of 0.9, we obtain a positive predictive value of 0.999 and sensitivity of 0.76 for the classification of variants known to cause long QT syndrome over the three most important genes, which represents sufficient accuracy to inform clinical decision-making. A web tool APPRAISE [http://www.cardiodb.org/APPRAISE] provides access to these models and predictions. CONCLUSIONS: Our Bayesian framework provides a transparent, flexible and robust framework for the analysis and interpretation of rare genetic variants. Models tailored to specific genes outperform genome-wide approaches, and can be sufficiently accurate to inform clinical decision-making

Predicate Abstraction with Indexed Predicates

Predicate abstraction provides a powerful tool for verifying properties of infinite-state systems using a combination of a decision procedure for a subset of first-order logic and symbolic methods originally developed for finite-state model checking. We consider models containing first-order state variables, where the system state includes mutable functions and predicates. Such a model can describe systems containing arbitrarily large memories, buffers, and arrays of identical processes. We describe a form of predicate abstraction that constructs a formula over a set of universally quantified variables to describe invariant properties of the first-order state variables. We provide a formal justification of the soundness of our approach and describe how it has been used to verify several hardware and software designs, including a directory-based cache coherence protocol.Comment: 27 pages, 4 figures, 1 table, short version appeared in International Conference on Verification, Model Checking and Abstract Interpretation (VMCAI'04), LNCS 2937, pages = 267--28

Transforming specifications of observable behaviour into programs

A methodology for deriving programs from specifications of observable behaviour is described. The class of processes to which this methodology is applicable includes those whose state changes are fully definable by labelled transition systems, for example communicating processes without internal state changes. A logic program representation of such labelled transition systems is proposed, interpreters based on path searching techniques are defined, and the use of partial evaluation techniques to derive the executable programs is described