580,440 research outputs found

    Path Checking for MTL and TPTL over Data Words

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    Metric temporal logic (MTL) and timed propositional temporal logic (TPTL) are quantitative extensions of linear temporal logic, which are prominent and widely used in the verification of real-timed systems. It was recently shown that the path checking problem for MTL, when evaluated over finite timed words, is in the parallel complexity class NC. In this paper, we derive precise complexity results for the path-checking problem for MTL and TPTL when evaluated over infinite data words over the non-negative integers. Such words may be seen as the behaviours of one-counter machines. For this setting, we give a complete analysis of the complexity of the path-checking problem depending on the number of register variables and the encoding of constraint numbers (unary or binary). As the two main results, we prove that the path-checking problem for MTL is P-complete, whereas the path-checking problem for TPTL is PSPACE-complete. The results yield the precise complexity of model checking deterministic one-counter machines against formulae of MTL and TPTL

    Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension

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    <p>Abstract</p> <p>Background</p> <p>Model checking approaches were applied to biological pathway validations around 2003. Recently, Fisher <it>et al</it>. have proved the importance of model checking approach by inferring new regulation of signaling crosstalk in <it>C. elegans </it>and confirming the regulation with biological experiments. They took a discrete and state-based approach to explore all possible states of the system underlying vulval precursor cell (VPC) fate specification for desired properties. However, since both discrete and continuous features appear to be an indispensable part of biological processes, it is more appropriate to use quantitative models to capture the dynamics of biological systems. Our key motivation of this paper is to establish a quantitative methodology to model and analyze <it>in silico </it>models incorporating the use of model checking approach.</p> <p>Results</p> <p>A novel method of modeling and simulating biological systems with the use of model checking approach is proposed based on hybrid functional Petri net with extension (HFPNe) as the framework dealing with both discrete and continuous events. Firstly, we construct a quantitative VPC fate model with 1761 components by using HFPNe. Secondly, we employ two major biological fate determination rules – Rule I and Rule II – to VPC fate model. We then conduct 10,000 simulations for each of 48 sets of different genotypes, investigate variations of cell fate patterns under each genotype, and validate the two rules by comparing three simulation targets consisting of fate patterns obtained from <it>in silico </it>and <it>in vivo </it>experiments. In particular, an evaluation was successfully done by using our VPC fate model to investigate one target derived from biological experiments involving hybrid lineage observations. However, the understandings of hybrid lineages are hard to make on a discrete model because the hybrid lineage occurs when the system comes close to certain thresholds as discussed by Sternberg and Horvitz in 1986. Our simulation results suggest that: Rule I that cannot be applied with qualitative based model checking, is more reasonable than Rule II owing to the high coverage of predicted fate patterns (except for the genotype of <it>lin-15ko; lin-12ko </it>double mutants). More insights are also suggested.</p> <p>Conclusion</p> <p>The quantitative simulation-based model checking approach is a useful means to provide us valuable biological insights and better understandings of biological systems and observation data that may be hard to capture with the qualitative one.</p

    Test generation from P systems using model checking

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    This paper presents some testing approaches based on model checking and using different testing criteria. First, test sets are built from different Kripke structure representations. Second, various rule coverage criteria for transitional, non-deterministic, cell-like P systems, are considered in order to generate adequate test sets. Rule based coverage criteria (simple rule coverage, context-dependent rule coverage and variants) are defined and, for each criterion, a set of LTL (Linear Temporal Logic) formulas is provided. A codification of a P system as a Kripke structure and the sets of LTL properties are used in test generation: for each criterion, test cases are obtained from the counterexamples of the associated LTL formulas, which are automatically generated from the Kripke structure codification of the P system. The method is illustrated with an implementation using a specific model checker, NuSMV. (C) 2010 Elsevier Inc. All rights reserved

    Decidability of Divergence for Catalytic P Systems

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    P systems are a biologically inspired model introduced by Gheorghe P¸aun with the aim of representing the structure and the functioning of the cell. Since their introduction, several variants of P systems have been proposed and explored. We concentrate on the class of catalytic P systems without priorities associated to the rules. We show that the divergence problem (i.e., checking for the existence of an infinite computation) is decidable in such a class of P systems. As a corollary, we obtain an alternative proof of the nonuniversality of deterministic catalytic P systems, an open problem recently solved by Ibarra and Yen

    Using A Kernel P System to Solve The 3-Col Problem

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    The newly introduced Kernel P systems offer an unitary and elegant way of integrating established features of existing P system variants with new elements with potential value for formal modelling. This paper presents a case study illustrating the expressive power and efficiency of kernel P systems on the 3-Col problem. The use of model checking (in particular of Spin) for formal verification of kernel P systems is also discussed and illustrated in this case.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08–TIC–0420

    Automated Validation of State-Based Client-Centric Isolation with TLA <sup>+</sup>

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    Clear consistency guarantees on data are paramount for the design and implementation of distributed systems. When implementing distributed applications, developers require approaches to verify the data consistency guarantees of an implementation choice. Crooks et al. define a state-based and client-centric model of database isolation. This paper formalizes this state-based model in, reproduces their examples and shows how to model check runtime traces and algorithms with this formalization. The formalized model in enables semi-automatic model checking for different implementation alternatives for transactional operations and allows checking of conformance to isolation levels. We reproduce examples of the original paper and confirm the isolation guarantees of the combination of the well-known 2-phase locking and 2-phase commit algorithms. Using model checking this formalization can also help finding bugs in incorrect specifications. This improves feasibility of automated checking of isolation guarantees in synthesized synchronization implementations and it provides an environment for experimenting with new designs.</p

    PLTL Partitioned Model Checking for Reactive Systems under Fairness Assumptions

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    We are interested in verifying dynamic properties of finite state reactive systems under fairness assumptions by model checking. The systems we want to verify are specified through a top-down refinement process. In order to deal with the state explosion problem, we have proposed in previous works to partition the reachability graph, and to perform the verification on each part separately. Moreover, we have defined a class, called Bmod, of dynamic properties that are verifiable by parts, whatever the partition. We decide if a property P belongs to Bmod by looking at the form of the Buchi automaton that accepts the negation of P. However, when a property P belongs to Bmod, the property f => P, where f is a fairness assumption, does not necessarily belong to Bmod. In this paper, we propose to use the refinement process in order to build the parts on which the verification has to be performed. We then show that with such a partition, if a property P is verifiable by parts and if f is the expression of the fairness assumptions on a system, then the property f => P is still verifiable by parts. This approach is illustrated by its application to the chip card protocol T=1 using the B engineering design language

    Formal Verification of P Systems with Active Membranes through Model Checking

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    Formal verification of P systems using model checking has attracted a significant amount of research in recent years. However, up to now only P systems with static structure have been considered. This paper makes significant advances in this area by considering P systems with active membranes, in particular P systems with division rules. The paper presents a theoretical framework for addressing this problem and reports on a complex case study involving a well-known NP-complete problem solved using P systems with membrane division rules. This is implemented in Promela and non trivial properties are verified using Spin.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420

    Comparative Analysis of Statistical Model Checking Tools

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    Statistical model checking is a powerful and flexible approach for formal verification of computational models like P systems, which can have very large search spaces. Various statistical model checking tools have been developed, but choosing between them and using the most appropriate one requires a significant degree of experience, not only because different tools have different modelling and property specification languages, but also because they may be designed to support only a certain subset of property types. Furthermore, their performance can vary depending on the property types and membrane systems being verified. In this paper we evaluate the performance of various common statistical model checkers against a pool of biological models. Our aim is to help users select the most suitable SMC tools from among the available options, by comparing their modelling and property specification languages, capabilities and performances

    Extended SNP Systems with States

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    We consider (extended) spiking neural P systems with states, where the applicability of rules in a neuron not only depends on the presence of su ciently many spikes (yet in contrast to the standard de nition, no regular checking sets are used), but also on the current state of the neuron. Moreover, a spiking rule not only sends spikes, but also state information to the connected neurons. We prove that this variant of the original model of extended spiking neural P systems can simulate register machines with only two states, even in the basic non-extended variant
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