Chaining Test Cases for Reactive System Testing (extended version)

Testing of synchronous reactive systems is challenging because long input sequences are often needed to drive them into a state at which a desired feature can be tested. This is particularly problematic in on-target testing, where a system is tested in its real-life application environment and the time required for resetting is high. This paper presents an approach to discovering a test case chain---a single software execution that covers a group of test goals and minimises overall test execution time. Our technique targets the scenario in which test goals for the requirements are given as safety properties. We give conditions for the existence and minimality of a single test case chain and minimise the number of test chains if a single test chain is infeasible. We report experimental results with a prototype tool for C code generated from Simulink models and compare it to state-of-the-art test suite generators.Comment: extended version of paper published at ICTSS'1

Signatures of arithmetic simplicity in metabolic network architecture

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that several of the properties predicted by the artificial chemistry model hold for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity

Termination of Rewriting with and Automated Synthesis of Forbidden Patterns

We introduce a modified version of the well-known dependency pair framework that is suitable for the termination analysis of rewriting under forbidden pattern restrictions. By attaching contexts to dependency pairs that represent the calling contexts of the corresponding recursive function calls, it is possible to incorporate the forbidden pattern restrictions in the (adapted) notion of dependency pair chains, thus yielding a sound and complete approach to termination analysis. Building upon this contextual dependency pair framework we introduce a dependency pair processor that simplifies problems by analyzing the contextual information of the dependency pairs. Moreover, we show how this processor can be used to synthesize forbidden patterns suitable for a given term rewriting system on-the-fly during the termination analysis.Comment: In Proceedings IWS 2010, arXiv:1012.533

On the Uniform Random Generation of Non Deterministic Automata Up to Isomorphism

In this paper we address the problem of the uniform random generation of non deterministic automata (NFA) up to isomorphism. First, we show how to use a Monte-Carlo approach to uniformly sample a NFA. Secondly, we show how to use the Metropolis-Hastings Algorithm to uniformly generate NFAs up to isomorphism. Using labeling techniques, we show that in practice it is possible to move into the modified Markov Chain efficiently, allowing the random generation of NFAs up to isomorphism with dozens of states. This general approach is also applied to several interesting subclasses of NFAs (up to isomorphism), such as NFAs having a unique initial states and a bounded output degree. Finally, we prove that for these interesting subclasses of NFAs, moving into the Metropolis Markov chain can be done in polynomial time. Promising experimental results constitute a practical contribution.Comment: Frank Drewes. CIAA 2015, Aug 2015, Umea, Sweden. Springer, 9223, pp.12, 2015, Implementation and Application of Automata - 20th International Conferenc

Entanglement Generation of Clifford Quantum Cellular Automata

Clifford quantum cellular automata (CQCAs) are a special kind of quantum cellular automata (QCAs) that incorporate Clifford group operations for the time evolution. Despite being classically simulable, they can be used as basic building blocks for universal quantum computation. This is due to the connection to translation-invariant stabilizer states and their entanglement properties. We will give a self-contained introduction to CQCAs and investigate the generation of entanglement under CQCA action. Furthermore, we will discuss finite configurations and applications of CQCAs.Comment: to appear in the "DPG spring meeting 2009" special issue of Applied Physics

Jabba: hybrid error correction for long sequencing reads using maximal exact matches

Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is that this mapping is constructed with a seed and extend methodology, using maximal exact matches as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of maximal exact matches in the context of third generation reads are presented

Counterexample Generation in Probabilistic Model Checking

Providing evidence for the refutation of a property is an essential, if not the most important, feature of model checking. This paper considers algorithms for counterexample generation for probabilistic CTL formulae in discrete-time Markov chains. Finding the strongest evidence (i.e., the most probable path) violating a (bounded) until-formula is shown to be reducible to a single-source (hop-constrained) shortest path problem. Counterexamples of smallest size that deviate most from the required probability bound can be obtained by applying (small amendments to) k-shortest (hop-constrained) paths algorithms. These results can be extended to Markov chains with rewards, to LTL model checking, and are useful for Markov decision processes. Experimental results show that typically the size of a counterexample is excessive. To obtain much more compact representations, we present a simple algorithm to generate (minimal) regular expressions that can act as counterexamples. The feasibility of our approach is illustrated by means of two communication protocols: leader election in an anonymous ring network and the Crowds protocol