Processing SPARQL queries with regular expressions in RDF databases

Background: As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users' requests for extracting information from the RDF data as well as the lack of users' knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results: In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions: Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.X113sciescopu

Language Emptiness of Continuous-Time Parametric Timed Automata

Parametric timed automata extend the standard timed automata with the possibility to use parameters in the clock guards. In general, if the parameters are real-valued, the problem of language emptiness of such automata is undecidable even for various restricted subclasses. We thus focus on the case where parameters are assumed to be integer-valued, while the time still remains continuous. On the one hand, we show that the problem remains undecidable for parametric timed automata with three clocks and one parameter. On the other hand, for the case with arbitrary many clocks where only one of these clocks is compared with (an arbitrary number of) parameters, we show that the parametric language emptiness is decidable. The undecidability result tightens the bounds of a previous result which assumed six parameters, while the decidability result extends the existing approaches that deal with discrete-time semantics only. To the best of our knowledge, this is the first positive result in the case of continuous-time and unbounded integer parameters, except for the rather simple case of single-clock automata

LTL Parameter Synthesis of Parametric Timed Automata

The parameter synthesis problem for parametric timed automata is undecidable in general even for very simple reachability properties. In this paper we introduce restrictions on parameter valuations under which the parameter synthesis problem is decidable for LTL properties. The investigated bounded integer parameter synthesis problem could be solved using an explicit enumeration of all possible parameter valuations. We propose an alternative symbolic zone-based method for this problem which results in a faster computation. Our technique extends the ideas of the automata-based approach to LTL model checking of timed automata. To justify the usefulness of our approach, we provide experimental evaluation and compare our method with explicit enumeration technique.Comment: 23 pages, extended versio

Modeling a Language for Embedded Systems in Timed Automata

We present a compositional method for translating real-timeprograms into networks of timed automata. Programs are written in anassembly like real-time language and translated into models supportedby the tool Uppaal. We have implemented the translation and give anexample of its application on a simple control program for a car. Someproperties of the behavior of the control program are verified using thegenerated model

Modeling a Language for Embedded Systems in Timed Automata

We present a compositional method for translating real-timeprograms into networks of timed automata. Programs are written in anassembly like real-time language and translated into models supportedby the tool Uppaal. We have implemented the translation and give anexample of its application on a simple control program for a car. Someproperties of the behavior of the control program are verified using thegenerated model

New systems for heterogeneous catalytic epoxidation

Epoxides are very useful key intermediates in the construction of synthetically challenging molecules. Owing to their strategic importance in organic synthesis, novel polymer-supported iminium salts were investigated for the catalytic oxidation of unfunctionalised alkenes. A solid-phase methodology was initiated and then developed for the evaluation of several heterogeneous catalysts. In an initial approach, immobilised iminium salts were prepared by condensation of 2-(bromoethyl)benzaldehyde with commercially available aminomethyl resins. These materials were shown to be able to successfully catalyse the epoxidation of 1-phenylcyclohexene. The epoxidation reactions were performed in a triphasic system using Oxone® as the oxidising agent and 25 mol% of the catalyst. For all the resin type employed, namely NovaSyn TG, NovaGel, ArgoGel or PEGA, complete conversion of the alkenes to their respective epoxides was obtained. [Continues.

Optimal infinite scheduling for multi-priced timed automata

This paper is concerned with the derivation of infinite schedules for timed automata that are in some sense optimal. To cover a wide class of optimality criteria we start out by introducing an extension of the (priced) timed automata model that includes both costs and rewards as separate modelling features. A precise definition is then given of what constitutes optimal infinite behaviours for this class of models. We subsequently show that the derivation of optimal non-terminating schedules for such double-priced timed automata is computable. This is done by a reduction of the problem to the determination of optimal mean-cycles in finite graphs with weighted edges. This reduction is obtained by introducing the so-called corner-point abstraction, a powerful abstraction technique of which we show that it preserves optimal schedules

Timed Bisimulation and Open Maps

Formal models for real-time systems have been studied intensively over the past decade. Much of the theory of untimed systems has been lifted to real-time settings. One example is the notion of bisimulation applied to timed transition systems, which is studied here within the general categorical framework of open maps. We define a category of timed transition systems, and show how to characterize standard timed bisimulation in terms of spans of open maps with a natural choice of a path category. This allows us to apply general results from the theory of open maps, e.g. the existence of canonical models and characteristic logics. Also, we obtain here an alternative proof of decidability of bisimulation for finite transition systems, and illustrate the use of open maps in finite presentations of bisimulation