A Short Counterexample Property for Safety and Liveness Verification of Fault-tolerant Distributed Algorithms

Distributed algorithms have many mission-critical applications ranging from embedded systems and replicated databases to cloud computing. Due to asynchronous communication, process faults, or network failures, these algorithms are difficult to design and verify. Many algorithms achieve fault tolerance by using threshold guards that, for instance, ensure that a process waits until it has received an acknowledgment from a majority of its peers. Consequently, domain-specific languages for fault-tolerant distributed systems offer language support for threshold guards. We introduce an automated method for model checking of safety and liveness of threshold-guarded distributed algorithms in systems where the number of processes and the fraction of faulty processes are parameters. Our method is based on a short counterexample property: if a distributed algorithm violates a temporal specification (in a fragment of LTL), then there is a counterexample whose length is bounded and independent of the parameters. We prove this property by (i) characterizing executions depending on the structure of the temporal formula, and (ii) using commutativity of transitions to accelerate and shorten executions. We extended the ByMC toolset (Byzantine Model Checker) with our technique, and verified liveness and safety of 10 prominent fault-tolerant distributed algorithms, most of which were out of reach for existing techniques.Comment: 16 pages, 11 pages appendi

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013

A Quantum Game of Life

This research describes a three dimensional quantum cellular automaton (QCA) which can simulate all other 3D QCA. This intrinsically universal QCA belongs to the simplest subclass of QCA: Partitioned QCA (PQCA). PQCA are QCA of a particular form, where incoming information is scattered by a fixed unitary U before being redistributed and rescattered. Our construction is minimal amongst PQCA, having block size 2 x 2 x 2 and cell dimension 2. Signals, wires and gates emerge in an elegant fashion.Comment: 13 pages, 10 figures. Final version, accepted by Journ\'ees Automates Cellulaires (JAC 2010)

A Unifying Approach to Decide Relations for Timed Automata and their Game Characterization

In this paper we present a unifying approach for deciding various bisimulations, simulation equivalences and preorders between two timed automata states. We propose a zone based method for deciding these relations in which we eliminate an explicit product construction of the region graphs or the zone graphs as in the classical methods. Our method is also generic and can be used to decide several timed relations. We also present a game characterization for these timed relations and show that the game hierarchy reflects the hierarchy of the timed relations. One can obtain an infinite game hierarchy and thus the game characterization further indicates the possibility of defining new timed relations which have not been studied yet. The game characterization also helps us to come up with a formula which encodes the separation between two states that are not timed bisimilar. Such distinguishing formulae can also be generated for many relations other than timed bisimilarity.Comment: In Proceedings EXPRESS/SOS 2013, arXiv:1307.690

A process-algebraic semantics for generalised nonblocking.

Generalised nonblocking is a weak liveness property to express the ability of a system to terminate under given preconditions. This paper studies the notions of equivalence and refinement that preserve generalised nonblocking and proposes a semantic model that characterises generalised nonblocking equivalence. The model can be constructed from the transition structure of an automaton, and has a finite representation for every finite-state automaton. It is used to construct a unique automaton representation for all generalised nonblocking equivalent automata. This gives rise to effective decision procedures to verify generalised nonblocking equivalence and refinement, and to a method to simplify automata while preserving generalised nonblocking equivalence. The results of this paper provide for better understanding of nonblocking in a compositional framework, with possible applications in compositional verification

On the Number of Synchronizing Colorings of Digraphs

We deal with $k$-out-regular directed multigraphs with loops (called simply \emph{digraphs}). The edges of such a digraph can be colored by elements of some fixed $k$-element set in such a way that outgoing edges of every vertex have different colors. Such a coloring corresponds naturally to an automaton. The road coloring theorem states that every primitive digraph has a synchronizing coloring. In the present paper we study how many synchronizing colorings can exist for a digraph with $n$ vertices. We performed an extensive experimental investigation of digraphs with small number of vertices. This was done by using our dedicated algorithm exhaustively enumerating all small digraphs. We also present a series of digraphs whose fraction of synchronizing colorings is equal to $1-1/k^d$, for every $d \ge 1$ and the number of vertices large enough. On the basis of our results we state several conjectures and open problems. In particular, we conjecture that $1-1/k$ is the smallest possible fraction of synchronizing colorings, except for a single exceptional example on 6 vertices for $k=2$.Comment: CIAA 2015. The final publication is available at http://link.springer.com/chapter/10.1007/978-3-319-22360-5_1