Minimal forbidden words and factor automata

International audienceLet L(M) be the (factorial) language avoiding a given antifactorial language M. We design an automaton accepting L(M) and built from the language M. The construction is eff ective if M is finite. If M is the set of minimal forbidden words of a single word v, the automaton turns out to be the factor automaton of v (the minimal automaton accepting the set of factors of v). We also give an algorithm that builds the trie of M from the factor automaton of a single word. It yields a non-trivial upper bound on the number of minimal forbidden words of a word

Revisiting the Rice Theorem of Cellular Automata

A cellular automaton is a parallel synchronous computing model, which consists in a juxtaposition of finite automata whose state evolves according to that of their neighbors. It induces a dynamical system on the set of configurations, i.e. the infinite sequences of cell states. The limit set of the cellular automaton is the set of configurations which can be reached arbitrarily late in the evolution. In this paper, we prove that all properties of limit sets of cellular automata with binary-state cells are undecidable, except surjectivity. This is a refinement of the classical "Rice Theorem" that Kari proved on cellular automata with arbitrary state sets.Comment: 12 pages conference STACS'1

Decision Problems for Deterministic Pushdown Automata on Infinite Words

The article surveys some decidability results for DPDAs on infinite words (omega-DPDA). We summarize some recent results on the decidability of the regularity and the equivalence problem for the class of weak omega-DPDAs. Furthermore, we present some new results on the parity index problem for omega-DPDAs. For the specification of a parity condition, the states of the omega-DPDA are assigned priorities (natural numbers), and a run is accepting if the highest priority that appears infinitely often during a run is even. The basic simplification question asks whether one can determine the minimal number of priorities that are needed to accept the language of a given omega-DPDA. We provide some decidability results on variations of this question for some classes of omega-DPDAs.Comment: In Proceedings AFL 2014, arXiv:1405.527

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

Entry times in automata with simple defect dynamics

In this paper, we consider a simple cellular automaton with two particles of different speeds that annihilate on contact. Following a previous work by K\r urka et al., we study the asymptotic distribution, starting from a random configuration, of the waiting time before a particle crosses the central column after time n. Drawing a parallel between the behaviour of this automata on a random initial configuration and a certain random walk, we approximate this walk using a Brownian motion, and we obtain explicit results for a wide class of initial measures and other automata with similar dynamics.Comment: In Proceedings AUTOMATA&JAC 2012, arXiv:1208.249