Avoidability index for binary patterns with reversal

For every pattern $p$ over the alphabet $\{x,y,x^R,y^R\}$, we specify the least $k$ such that $p$ is $k$-avoidable.Comment: 15 pages, 1 figur

Ten Conferences WORDS: Open Problems and Conjectures

In connection to the development of the field of Combinatorics on Words, we present a list of open problems and conjectures that were stated during the ten last meetings WORDS. We wish to continually update the present document by adding informations concerning advances in problems solving

How many double squares can a string contain?

Counting the types of squares rather than their occurrences, we consider the problem of bounding the number of distinct squares in a string. Fraenkel and Simpson showed in 1998 that a string of length n contains at most 2n distinct squares. Ilie presented in 2007 an asymptotic upper bound of 2n - Theta(log n). We show that a string of length n contains at most 5n/3 distinct squares. This new upper bound is obtained by investigating the combinatorial structure of double squares and showing that a string of length n contains at most 2n/3 double squares. In addition, the established structural properties provide a novel proof of Fraenkel and Simpson's result.Comment: 29 pages, 20 figure

Linear-Time Algorithms for Finding Tucker Submatrices and Lekkerkerker-Boland Subgraphs

Lekkerkerker and Boland characterized the minimal forbidden induced subgraphs for the class of interval graphs. We give a linear-time algorithm to find one in any graph that is not an interval graph. Tucker characterized the minimal forbidden submatrices of binary matrices that do not have the consecutive-ones property. We give a linear-time algorithm to find one in any binary matrix that does not have the consecutive-ones property.Comment: A preliminary version of this work appeared in WG13: 39th International Workshop on Graph-Theoretic Concepts in Computer Scienc

Lightweight LCP Construction for Very Large Collections of Strings

The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several applications, especially in biological contexts. Nowadays, the input data for many problems are big collections of strings, for instance the data coming from "next-generation" DNA sequencing (NGS) technologies. In this paper we present the first lightweight algorithm (called extLCP) for the simultaneous computation of the longest common prefix array and the Burrows-Wheeler transform of a very large collection of strings having any length. The computation is realized by performing disk data accesses only via sequential scans, and the total disk space usage never needs more than twice the output size, excluding the disk space required for the input. Moreover, extLCP allows to compute also the suffix array of the strings of the collection, without any other further data structure is needed. Finally, we test our algorithm on real data and compare our results with another tool capable to work in external memory on large collections of strings.Comment: This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ The final version of this manuscript is in press in Journal of Discrete Algorithm

The Non-Archimedean Theory of Discrete Systems

In the paper, we study behavior of discrete dynamical systems (automata) w.r.t. transitivity; that is, speaking loosely, we consider how diverse may be behavior of the system w.r.t. variety of word transformations performed by the system: We call a system completely transitive if, given arbitrary pair $a,b$ of finite words that have equal lengths, the system $\mathfrak A$, while evolution during (discrete) time, at a certain moment transforms $a$ into $b$. To every system $\mathfrak A$, we put into a correspondence a family $\mathcal F_{\mathfrak A}$ of continuous maps of a suitable non-Archimedean metric space and show that the system is completely transitive if and only if the family $\mathcal F_{\mathfrak A}$ is ergodic w.r.t. the Haar measure; then we find easy-to-verify conditions the system must satisfy to be completely transitive. The theory can be applied to analyze behavior of straight-line computer programs (in particular, pseudo-random number generators that are used in cryptography and simulations) since basic CPU instructions (both numerical and logical) can be considered as continuous maps of a (non-Archimedean) metric space $\mathbb Z_2$ of 2-adic integers.Comment: The extended version of the talk given at MACIS-201

The geometry of non-unit Pisot substitutions

Let $\sigma$ be a non-unit Pisot substitution and let $\alpha$ be the associated Pisot number. It is known that one can associate certain fractal tiles, so-called \emph{Rauzy fractals}, with $\sigma$. In our setting, these fractals are subsets of a certain open subring of the ad\`ele ring $\mathbb{A}_{\mathbb{Q}(\alpha)}$. We present several approaches on how to define Rauzy fractals and discuss the relations between them. In particular, we consider Rauzy fractals as the natural geometric objects of certain numeration systems, define them in terms of the one-dimensional realization of $\sigma$ and its dual (in the spirit of Arnoux and Ito), and view them as the dual of multi-component model sets for particular cut and project schemes. We also define stepped surfaces suited for non-unit Pisot substitutions. We provide basic topological and geometric properties of Rauzy fractals associated with non-unit Pisot substitutions, prove some tiling results for them, and provide relations to subshifts defined in terms of the periodic points of $\sigma$, to adic transformations, and a domain exchange. We illustrate our results by examples on two and three letter substitutions.Comment: 29 page

Pisot conjecture and Rauzy fractals

We provide a proof of Pisot conjecture, a classification problem in Ergodic Theory on recurrent sequences generated by irreducible Pisot substitutions.Comment: revise

Invariance: a Theoretical Approach for Coding Sets of Words Modulo Literal (Anti)Morphisms

Let $A$ be a finite or countable alphabet and let $\theta$ be literal (anti)morphism onto $A^*$ (by definition, such a correspondence is determinated by a permutation of the alphabet). This paper deals with sets which are invariant under $\theta$ ($\theta$-invariant for short).We establish an extension of the famous defect theorem. Moreover, we prove that for the so-called thin $\theta$-invariant codes, maximality and completeness are two equivalent notions. We prove that a similar property holds in the framework of some special families of $\theta$-invariant codes such as prefix (bifix) codes, codes with a finite deciphering delay, uniformly synchronized codes and circular codes. For a special class of involutive antimorphisms, we prove that any regular $\theta$-invariant code may be embedded into a complete one.Comment: To appear in Acts of WORDS 201