The growth rate over trees of any family of set defined by a monadic second order formula is semi-computable

Monadic second order logic can be used to express many classical notions of sets of vertices of a graph as for instance: dominating sets, induced matchings, perfect codes, independent sets or irredundant sets. Bounds on the number of sets of any such family of sets are interesting from a combinatorial point of view and have algorithmic applications. Many such bounds on different families of sets over different classes of graphs are already provided in the literature. In particular, Rote recently showed that the number of minimal dominating sets in trees of order $n$ is at most $95^{\frac{n}{13}}$ and that this bound is asymptotically sharp up to a multiplicative constant. We build on his work to show that what he did for minimal dominating sets can be done for any family of sets definable by a monadic second order formula. We first show that, for any monadic second order formula over graphs that characterizes a given kind of subset of its vertices, the maximal number of such sets in a tree can be expressed as the \textit{growth rate of a bilinear system}. This mostly relies on well known links between monadic second order logic over trees and tree automata and basic tree automata manipulations. Then we show that this "growth rate" of a bilinear system can be approximated from above.We then use our implementation of this result to provide bounds on the number of independent dominating sets, total perfect dominating sets, induced matchings, maximal induced matchings, minimal perfect dominating sets, perfect codes and maximal irredundant sets on trees. We also solve a question from D. Y. Kang et al. regarding $r$-matchings and improve a bound from G\'orska and Skupie\'n on the number of maximal matchings on trees. Remark that this approach is easily generalizable to graphs of bounded tree width or clique width (or any similar class of graphs where tree automata are meaningful)

Limit sets of stable Cellular Automata

We study limit sets of stable cellular automata standing from a symbolic dynamics point of view where they are a special case of sofic shifts admitting a steady epimorphism. We prove that there exists a right-closing almost-everywhere steady factor map from one irreducible sofic shift onto another one if and only if there exists such a map from the domain onto the minimal right-resolving cover of the image. We define right-continuing almost-everywhere steady maps and prove that there exists such a steady map between two sofic shifts if and only if there exists a factor map from the domain onto the minimal right-resolving cover of the image. In terms of cellular automata, this translates into: A sofic shift can be the limit set of a stable cellular automaton with a right-closing almost-everywhere dynamics onto its limit set if and only if it is the factor of a fullshift and there exists a right- closing almost-everywhere factor map from the sofic shift onto its minimal right- resolving cover. A sofic shift can be the limit set of a stable cellular automaton reaching its limit set with a right-continuing almost-everywhere factor map if and only if it is the factor of a fullshift and there exists a factor map from the sofic shift onto its minimal right-resolving cover. Finally, as a consequence of the previous results, we provide a characterization of the Almost of Finite Type shifts (AFT) in terms of a property of steady maps that have them as range.Comment: 18 pages, 3 figure

Nondeterministic State Complexity for Suffix-Free Regular Languages

We investigate the nondeterministic state complexity of basic operations for suffix-free regular languages. The nondeterministic state complexity of an operation is the number of states that are necessary and sufficient in the worst-case for a minimal nondeterministic finite-state automaton that accepts the language obtained from the operation. We consider basic operations (catenation, union, intersection, Kleene star, reversal and complementation) and establish matching upper and lower bounds for each operation. In the case of complementation the upper and lower bounds differ by an additive constant of two.Comment: In Proceedings DCFS 2010, arXiv:1008.127

Revisiting Waiting Times in DNA evolution

Transcription factors are short stretches of DNA (or $k$-mers) mainly located in promoters sequences that enhance or repress gene expression. With respect to an initial distribution of letters on the DNA alphabet, Behrens and Vingron consider a random sequence of length $n$ that does not contain a given $k$-mer or word of size $k$. Under an evolution model of the DNA, they compute the probability $\mathfrak{p}_n$ that this $k$-mer appears after a unit time of 20 years. They prove that the waiting time for the first apparition of the $k$-mer is well approximated by $T_n=1/\mathfrak{p}_n$. Their work relies on the simplifying assumption that the $k$-mer is not self-overlapping. They observe in particular that the waiting time is mostly driven by the initial distribution of letters. Behrens et al. use an approach by automata that relaxes the assumption related to words overlaps. Their numerical evaluations confirms the validity of Behrens and Vingron approach for non self-overlapping words, but provides up to 44% corrections for highly self-overlapping words such as $\mathtt{AAAAA}$. We devised an approach of the problem by clump analysis and generating functions; this approach leads to prove a quasi-linear behaviour of $\mathfrak{p}_n$ for a large range of values of $n$, an important result for DNA evolution. We present here this clump analysis, first by language decomposition, and next by an automaton construction; finally, we describe an equivalent approach by construction of Markov automata.Comment: 19 pages, 3 Figures, 2 Table

On Nonnegative Integer Matrices and Short Killing Words

Let $n$ be a natural number and $\mathcal{M}$ a set of $n \times n$-matrices over the nonnegative integers such that the joint spectral radius of $\mathcal{M}$ is at most one. We show that if the zero matrix $0$ is a product of matrices in $\mathcal{M}$, then there are $M_1, \ldots, M_{n^5} \in \mathcal{M}$ with $M_1 \cdots M_{n^5} = 0$. This result has applications in automata theory and the theory of codes. Specifically, if $X \subset \Sigma^*$ is a finite incomplete code, then there exists a word $w \in \Sigma^*$ of length polynomial in $\sum_{x \in X} |x|$ such that $w$ is not a factor of any word in $X^*$. This proves a weak version of Restivo's conjecture.Comment: This version is a journal submission based on a STACS'19 paper. It extends the conference version as follows. (1) The main result has been generalized to apply to monoids generated by finite sets whose joint spectral radius is at most 1. (2) The use of Carpi's theorem is avoided to make the paper more self-contained. (3) A more precise result is offered on Restivo's conjecture for finite code

Learning Moore Machines from Input-Output Traces

The problem of learning automata from example traces (but no equivalence or membership queries) is fundamental in automata learning theory and practice. In this paper we study this problem for finite state machines with inputs and outputs, and in particular for Moore machines. We develop three algorithms for solving this problem: (1) the PTAP algorithm, which transforms a set of input-output traces into an incomplete Moore machine and then completes the machine with self-loops; (2) the PRPNI algorithm, which uses the well-known RPNI algorithm for automata learning to learn a product of automata encoding a Moore machine; and (3) the MooreMI algorithm, which directly learns a Moore machine using PTAP extended with state merging. We prove that MooreMI has the fundamental identification in the limit property. We also compare the algorithms experimentally in terms of the size of the learned machine and several notions of accuracy, introduced in this paper. Finally, we compare with OSTIA, an algorithm that learns a more general class of transducers, and find that OSTIA generally does not learn a Moore machine, even when fed with a characteristic sample

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

On the Minimal Uncompletable Word Problem

Let S be a finite set of words over an alphabet Sigma. The set S is said to be complete if every word w over the alphabet Sigma is a factor of some element of S*, i.e. w belongs to Fact(S*). Otherwise if S is not complete, we are interested in finding bounds on the minimal length of words in Sigma* which are not elements of Fact(S*) in terms of the maximal length of words in S.Comment: 5 pages; added references, corrected typo