Keijo Heljanko

Linear Encodings of Bounded LTL Model Checking

We consider the problem of bounded model checking (BMC) for linear tempo- ral logic (LTL). We present several efficient encodings that have size linear in the bound. Furthermore, we show how the encodings can be extended to LTL with past operators (PLTL). The generalised encoding is still of linear size, but cannot detect minimal length counterexamples. By using the virtual unrolling technique minimal length counterexam- ples can be captured, however, the size of the encoding is quadratic in the specification. We also extend virtual unrolling to Buchi automata, enabling them to accept minimal length counterexamples. Our BMC encodings can be made incremental in order to benefit from incremental SAT technology. With fairly small modifications the incremental encoding can be further enhanced with a termination check, allowing us to prove properties with BMC. An analysis of the liveness-to-safety transformation reveals many similarities to the BMC encodings in this paper. We conduct experiments to determine the advantage of em- ploying dedicated BMC encodings for PLTL over combining more general but potentially less efficient approaches with BMC: the liveness-to-safety t with invariant checking and Buchi automata with fair cycle detection. Experiments clearly show that our new encodings improve performance of BMC con- siderably, particularly in the case of the incremental encoding, and that they are very competitive for finding bugs. Dedicated encodings seem to have an advantage over using more general methods with BMC. Using the liveness-to-safety translation with BDD-based invariant checking results in an efficient method to find shortest counterexamples that com- plements the BMC-based approach. For proving complex properties BDD-based methods still tend to perform better.

Planning as satisfiability: parallel plans and algorithms for plan search

We address two aspects of constructing plans efficiently by means of satisfiability testing: efficient encoding of the problem of existence of plans of a given number t of time points in the propositional logic and strategies for finding plans, given these formulae for different values of t. For the first problem we consider three semantics for plans with parallel operator application in order to make the search for plans more efficient. The standard semantics requires that parallel operators are independent and can therefore be executed in any order. We consider a more relaxed definition of parallel plans which was first proposed by Dimopoulos et al., as well as a normal form for parallel plans that requires every operator to be executed as early as possible. We formalize the semantics of parallel plans emerging in this setting and present translations of these semantics into the propositional logic. The sizes of the translations are asymptotically optimal. Each of the semantics is constructed in such a way that there is a plan following the semantics exactly when there is a sequential plan, and moreover, the existence of a parallel plan implies the existence of a sequential plan with as many operators as in the parallel one. For the second problem we consider strategies based on testing the satisfiability of several formulae representing plans of n time steps for several values of n concurrently by several processes. We show that big efficiency gains can be obtained in comparison to the standard strategy of sequentially testing the satisfiability of formulae for an increasing number of time steps.

Bounded LTL model checking with stable models

In this paper, bounded model checking of asynchronous concurrent systems is introduced as a promising application area for answer set programming. As the model of asynchronous systems a generalisation of communicating automata, 1-safe Petri nets, are used. It is shown how a 1-safe Petri net and a requirement on the behaviour of the net can be translated into a logic program such that the bounded model checking problem for the net can be solved by computing stable models of the corresponding program. The use of the stable model semantics leads to compact encodings of bounded reachability and deadlock detection tasks as well as the more general problem of bounded model checking of linear temporal logic. Correctness proofs of the devised translations are given, and some experimental results using the translation and the Smodels system are presented.

Using logic programs with stable model semantics to solve deadlock and reachability problems for 1-safe petri nets

McMillan has presented a deadlock detection method for Petri nets based on finite complete prefixes (i.e. net unfoldings). The basic idea is to transform the PSPACE-complete deadlock detection problem for a 1-safe Petri net into a potentially exponentially larger NP-complete problem of deadlock detection for a finite complete prefix. McMillan suggested a branch-and-bound algorithm for deadlock detection in prefixes. Recently, Melzer and Rmer have presented another approach, which is based on solving mixed integer programming problems. In this work it is shown that instead of using mixed integer programming, a constraint-based logic programming framework can be employed, and a linear-size translation from deadlock detection in prefixes into the problem of finding a stable model of a logic program is presented. As a side result also such a translation for solving the reachability problem is devised. Experimental results are given from an implementation combining the prefix generator of the PEP-tool, the translation, and an implementation of a constraint-based logic programming framework, the smodels system. The experiments show the proposed approach to be quite competitive, when compared to the approaches of McMillan and Melzer/Rmer.

Incremental and complete bounded model checking for full PLTL

Bounded model checking is an efficient method for finding bugs in system designs. The major drawback of the basic method is that it cannot prove properties, only disprove them. Recently, some progress has been made towards proving properties of LTL. We present an incremental and complete bounded model checking method for the full linear temporal logic with past (PLTL). Compared to previous works, our method both improves and extends current results in many ways: (i) our encoding is incremental, resulting in improvements in performance, (ii) we can prove non-existence of a counterexample at shallower depths in many cases, and (iii) we support full PLTL. We have implemented our method in the NuSMV2 model checker and report encouraging experimental results.

Simple Bounded LTL Model Checking

We present a new and very simple translation of the bounded model checking problem which is linear both in the size of the formula and the length of the bound. The resulting CNF-formula has a linear number of variables and clauses.

Bounded LTL Model Checking with Stable Models

In this paper bounded model checking of asynchronous concurrent systems is introduced as a promising application area for answer set programming. As the model of asynchronous systems a generalization of communicating automata, 1-safe Petri nets, are used. It is shown how a 1-safe Petri net and a requirement on the behavior of the net can be translated into a logic program such that the bounded model checking problem for the net can be solved by computing stable models of the corresponding program. The use of the stable model semantics leads to compact encodings of bounded reachability and deadlock detection tasks as well as the more general problem of bounded model checking of linear temporal logic. Some experimental results on solving deadlock detection problems using the translation and the Smodels system are presented.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop

Summary: Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts. Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/ Contact: andre.schumacher@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.

Implementing LTL model checking with net unfoldings

We report on an implementation of the unfolding approach to model-checking LTL-X recently presented by the authors. Contrary to that work, we consider an state-based version of LTL-X, which is more used in practice. We improve on the checking algorithm; the new version allows to reuse code much more efficiently. We present results on a set of case studies.

Bounded Reachability Checking with Process Semantics

Bounded model checking has been recently introduced as an efficient verification method for reactive systems. In this work we apply bounded model checking to asynchronous systems. More specifically, we translate the bounded reachability problem for 1-safe Petri nets into constrained Boolean circuit satisfiability. We consider three semantics: process, step, and interleaving semantics. We show that process semantics has often the best performance for bounded reachability checking.