A árvore de sufixos é uma estrutura dados, que representa em espaço linear todos os fatores de uma palavra, com diversos exemplos de aplicações práticas. Neste trabalho, definimos uma estrutura mais geral: a árvore de Ukkonen. Provamos para ela diversas propriedades combinatórias, dentre quais, a minimalidade em um sentido preciso. Acreditamos que a apresentação aqui oferecida, além de mais geral que as árvores de sufixo, tem a vantagem de oferecer uma descrição explícita da topologia da árvore, de seus vértices, arestas e rótulos, o que não vimos em nenhum outro trabalho. Como aplicações, apresentamos também a árvore esparsa de sufixos (que armazena apenas um subconjunto dos sufixos) e a árvore de k-fatores (que armazena apenas os segmentos de comprimento k, ao invés dos sufixos) definidas como casos particulares das árvores de Ukkonen. Propomos para as árvores esparsas um novo algoritmo de construção com tempo O(n) e espaço O(m), onde n é tamanho da palavra e m é número de sufixos. Para as árvores de k-fatores, propomos um novo algoritmo online com tempo e espaço O(n), onde n é o tamanho da palavra. / The suffix tree is a data structure that represents, in linear space, all factors of a given word, with several examples of practical applications. In this work, we define a more general structure: the Ukkonen\'s tree. We prove many properties for it, among them, its minimality in a precise sense. We believe that this presentation, besides being more general than the suffix trees, has the advantage of offering an explicit description of the tree topology, its vertices, edges and labels, which was not seen in any other work. As applications, we also presents the sparse suffix tree (which stores only a subset of the suffixes) and the k-factor tree (which stores only the substrings of length k, instead of the suffixes), both defined as Ukkonen\'s tree special cases. We propose a new construction algorithm for the sparse suffix trees with time O(n) and space O(m), where n is the size of the word and m is the number of suffixes. For the k-factor trees, we propose a new online algorithm with time and space O(n), where n is the size of the word.

In recent years, combinatorial properties of finite and infinite words have become increasingly important in fields of physics, biology, mathematics, and computer science. In particular, the fascinating family of Sturmian words has become an extremely active subject of research. These infinite binary sequences have numerous applications in various fields of mathematics, such as symbolic dynamics, the study of continued fraction expansion, and also in some domains of physics ( quasicrystal modelling ) and computer science ( pattern recognition, digital straightness ). There has also been a recent surge of interest in a natural generalization of Sturmian words to more than two letters - the so - called episturmian words, which include the well - known Arnoux - Rauzy sequences. This thesis represents a significant contribution to the study of Sturmian and episturmian words, and related objects such as generalized Thue - Morse words and substitutions on a finite alphabet. Specifically, we prove some new properties of certain palindromic factors of the infinite Fibonacci word; establish generalized ' singular ' decompositions of suffixes of certain morphic Sturmian words; completely describe where palindromes occur in characteristic Sturmian words; explicitly determine all integer powers occurring in a certain class of k-strict episturmian words ( including the k-bonacci word ) ; and prove that certain episturmian and generalized Thue - Morse continued fractions are transcendental. Lastly, we begin working towards a proof of a characterization of invertible substitutions on a finite alphabet, which generalizes the fact that invertible substitutions on two letters are exactly the Sturmian morphisms. / Thesis (Ph.D.)--School of Mathematical Sciences, 2006.

In this thesis we present and solve selected problems arising from digital geometry and combinatorics on words. We consider digital straight lines and, equivalently, upper mechanical words with positive irrational slopes a<1 and intercept 0. We formulate a continued fraction (CF) based description of their run-hierarchical structure. Paper I gives a theoretical basis for the CF-description of digital lines. We define for each irrational positive slope less than 1 a sequence of digitization parameters which fully specifies the run-hierarchical construction. In Paper II we use the digitization parameters in order to get a description of runs using only integers. We show that the CF-elements of the slopes contain the complete information about the run-hierarchical structure of the line. The index jump function introduced by the author indicates for each positive integer k the index of the CF-element which determines the shape of the digitization runs on level k. In Paper III we present the results for upper mechanical words and compare our CF-based formula with two well-known methods, one of which was formulated by Johann III Bernoulli and proven by Markov, while the second one is known as the standard sequences method. Due to the special treatment of some CF-elements equal to 1 (essential 1's in Paper IV), our method is currently the only one which reflects the run-hierarchical structure of upper mechanical words by analogy to digital lines. In Paper IV we define two equivalence relations on the set of all digital lines with positive irrational slopes a<1. One of them groups into classes all the lines with the same run length on all digitization levels, the second one groups the lines according to the run construction in terms of long and short runs on all levels. We analyse the equivalence classes with respect to minimal and maximal elements. In Paper V we take another look at the equivalence relation defined by run construction, this time independently of the context, which makes the results more general. In Paper VI we define a run-construction encoding operator, by analogy with the well-known run-length encoding operator. We formulate and present a proof of a fixed-point theorem for Sturmian words. We show that in each equivalence class under the relation based on run length on all digitization levels (as defined in Paper IV), there exists exactly one fixed point of the run-construction encoding operator.

Title: Structure of equality sets Author: Jana Hadravová Department: Department of Algebra Supervisor: doc. Mgr. Štěpán Holub, Ph.D., Dept. of Algebra Abstract: Binary equality set of two morphisms g, h : ⌃⇤ ! A⇤ is a set of all words w over two-letter alphabet ⌃ satisfying g(w) = h(w). Elements of this set are called binary equality words. One of the important results of research on binary equality sets is the proof of the fact that each binary equality set is generated by at most two words provided that both morphisms g and h are non-periodic. Moreover, if a binary equality set is generated by exactly two words, then the structure of both generators, and therefore of the whole set, is uniquely given. This work presents the results of our research on the structure of binary equality sets with a single generator. Importantly, these generators can be decomposed into simpler structures. Generators which can not be further decomposed are called simple equality words. First part of the presented work describes the structure of simple equality words and introduces their detailed classification. The main result of the first part is a precise characterisation of su ciently large simple equality words. In the second part, the work describes the iterative process which transforms a general generator of a binary...

Nous étudions dans cette thèse différents problèmes d'évitabilité des répétitions dans les mots infinis. Soulevée par Thue et motivée par ses travaux sur les mots sans carrés, la problématique s'est développée au cours du XXe siècle, et est aujourd'hui devenue un des grands domaines de recherche en combinatoire des mots. En 1972, Dejean proposa une importante conjecture, dont la validation étape par étape s'est terminée récemment (2009). La conjecture concerne le seuil des répétitions d'un alphabet, i.e., la borne inférieure des exposants évitables sur cet alphabet. La notion de seuil, comme frontière entre évitabilité et non-évitabilité d'un ensemble donné de mots, est le fil directeur de nos travaux. Nous nous intéressons d'abord à une généralisation du seuil des répétitions (nous donnons des encadrements de sa valeur). Cette notion permet d'ajouter, pour décrire l'ensemble des répétitions à éviter, au paramètre de l'exposant, celui de la longueur des répétitions. Puis, nous étudions des problèmes d'existence de mots dans lesquels, simultanément, certaines répétitions sont interdites et d'autres sont forcées. Nous répondons, pour l'alphabet ternaire, à la question : quels réels sont l'exposant critique d'un mot infini sur un alphabet fixé? Nous introduisons ensuite une notion de haute répétitivité, et établissons une description partielle des couples d'exposants paramètrant une double contrainte de haute répétitivité et d'évitabilité. Pour finir, nous utilisons des résultats et techniques issus de ces problématiques pour résoudre une question de coloration de graphes : nous introduisons un seuil des répétitions, calqué sur celui connu pour les mots, et donnons sa valeur pour deux classes de graphes, les arbres et les graphes de subdivisions. / In this thesis we study various problems on repetition avoidance in infinite words. Raised by Thue and motivated by his work on squarefree words, the topic developed during the 20th century, and has nowadays become a principal area of research in combinatorics on words. In 1972, Dejean proposed an important conjecture whose verification in steps was completed recently (2009). The conjecture concerns the repetition threshold for an alphabet, i.e., the infimum of the avoidable exponents for that alphabet. The notion of threshold as a borderline between avoidability and unavoidability for a given set of words is the guiding line of our work. First, we focus on a generalization of the repetition threshold. This concept allows us to include, in addition to the exponent, the length of the repetitions as a parameter in the description of the set of repetitions to avoid. We obtain various bounds in that respect. We then study existence problems for words in which simultaneously some repetitions are forbidden, and others are forced. For the ternary alphabet, we answer the question: what real numbers are the critical exponent of some infinite word over a given alphabet? Also, we introduce a notion of highly repetitive words and give a partial description of the pairs of exponents which parameterize the existence of words both highly repetitive and repetition-free. Finally, we use results and techniques stemming from those problems to solve a question on graph colouring: we introduce a repetition threshold adapted from the thresholds we know for words, and give its value for two classes of graphs, namely, trees and subdivision graphs.

A árvore de sufixos é uma estrutura dados, que representa em espaço linear todos os fatores de uma palavra, com diversos exemplos de aplicações práticas. Neste trabalho, definimos uma estrutura mais geral: a árvore de Ukkonen. Provamos para ela diversas propriedades combinatórias, dentre quais, a minimalidade em um sentido preciso. Acreditamos que a apresentação aqui oferecida, além de mais geral que as árvores de sufixo, tem a vantagem de oferecer uma descrição explícita da topologia da árvore, de seus vértices, arestas e rótulos, o que não vimos em nenhum outro trabalho. Como aplicações, apresentamos também a árvore esparsa de sufixos (que armazena apenas um subconjunto dos sufixos) e a árvore de k-fatores (que armazena apenas os segmentos de comprimento k, ao invés dos sufixos) definidas como casos particulares das árvores de Ukkonen. Propomos para as árvores esparsas um novo algoritmo de construção com tempo O(n) e espaço O(m), onde n é tamanho da palavra e m é número de sufixos. Para as árvores de k-fatores, propomos um novo algoritmo online com tempo e espaço O(n), onde n é o tamanho da palavra. / The suffix tree is a data structure that represents, in linear space, all factors of a given word, with several examples of practical applications. In this work, we define a more general structure: the Ukkonen\'s tree. We prove many properties for it, among them, its minimality in a precise sense. We believe that this presentation, besides being more general than the suffix trees, has the advantage of offering an explicit description of the tree topology, its vertices, edges and labels, which was not seen in any other work. As applications, we also presents the sparse suffix tree (which stores only a subset of the suffixes) and the k-factor tree (which stores only the substrings of length k, instead of the suffixes), both defined as Ukkonen\'s tree special cases. We propose a new construction algorithm for the sparse suffix trees with time O(n) and space O(m), where n is the size of the word and m is the number of suffixes. For the k-factor trees, we propose a new online algorithm with time and space O(n), where n is the size of the word.

In this doctoral dissertation, we studied and solved several questions regarding positional and abstract numeration systems. Each particular problem is the focus of a chapter. The first problem concerns the study of the preservation of recognizability under multiplication by a constant in abstract numeration systems built on polynomial regular languages. We obtained several results generalizing those from P. Lecomte and M. Rigo. The second problem we considered is a decidability problem, which was already studied, most notably, by J. Honkala and A. Muchnik. For our part, we studied this problem for two new cases: the linear positional numeration systems and the abstract numeration systems. Next, we focused on the extension to the multidimensional setting of a result of A. Maes and M.~Rigo regarding S-automatic infinite words. We obtained a characterization of multidimensional S-automatic words in terms of multidimensional (non-necessarily uniform) morphisms. This result can be viewed as the analogous of O. Salon's extension of a theorem of A. Cobham. Finally, generalizing results of P. Lecomte and M. Rigo, we proposed a formalism to represent real numbers in the general framework of abstract numeration systems built on languages that are not necessarily regular. This formalism encompasses in particular the rational base numeration systems, which have been recently introduced by S. Akiyama, Ch. Frougny, and J. Sakarovitch. Finally, we ended with a list of open questions in the continuation of this work./Dans cette dissertation, nous étudions et résolvons plusieurs questions autour des systèmes de numération abstraits. Chaque problème étudié fait l'objet d'un chapitre. Le premier concerne l'étude de la conservation de la reconnaissabilité par la multiplication par une constante dans des systèmes de numération abstraits construits sur des langages réguliers polynomiaux. Nous avons obtenus plusieurs résultats intéressants généralisant ceux de P. Lecomte et M. Rigo. Le deuxième problème auquel je me suis intéressée est un problème de décidabilité déjà étudié notamment par J. Honkala et A. Muchnik et ici décliné en deux nouvelles versions : les systèmes de numération de position linéaires et les systèmes de numération abstraits. Ensuite, nous nous penchons sur l'extension au cas multidimensionnel d'un résultat d'A. Maes et de M. Rigo à propos des mots infinis S-automatiques. Nous avons obtenu une caractérisation des mots S-automatiques multidimensionnels en termes de morphismes multidimensionnels (non nécessairement uniformes). Ce résultat peut être vu comme un analogue de l'extension obtenue par O. Salon d'un théorème de A. Cobham. Finalement, nous proposons un formalisme de la représentation des nombres réels dans le cadre général des systèmes de numération abstraits basés sur des langages qui ne sont pas nécessairement réguliers. Ce formalisme englobe notamment le cas des numérations en bases rationnelles introduits récemment par S. Akiyama, Ch. Frougny et J. Sakarovitch. Nous terminons par une liste de questions ouvertes dans la continuité de ce travail.

Cette dissertation se divise en deux parties, distinctes mais connexes, qui sont le reflet de la cotutelle. Nous étudions et résolvons des problèmes concernant d'une part la combinatoire des mots dans un contexte abélien et d'autre part des problèmes de couverture dans des graphes. Chaque question fait l'objet d'un chapitre. En combinatoire des mots, le premier problème considéré s'intéresse à la régularité des suites au sens défini par Allouche et Shallit. Nous montrons qu'une suite qui satisfait une certaine propriété de symétrie est 2-régulière. Ensuite, nous appliquons ce théorème pour montrer que les fonctions de complexité 2-abélienne du mot de Thue--Morse ainsi que du mot appelé ''period-doubling'' sont 2-régulières. Les calculs et arguments développés dans ces démonstrations s'inscrivent dans un schéma plus général que nous espérons pouvoir utiliser à nouveau pour prouver d'autres résultats de régularité. Le deuxième problème poursuit le développement de la notion de mot de retour abélien introduite par Puzynina et Zamboni. Nous obtenons une caractérisation des mots sturmiens avec un intercepte non nul en termes du cardinal (fini ou non) de l'ensemble des mots de retour abélien par rapport à tous les préfixes. Nous décrivons cet ensemble pour Fibonacci ainsi que pour Thue--Morse (bien que cela ne soit pas un mot sturmien). Nous étudions la relation existante entre la complexité abélienne et le cardinal de cet ensemble. En théorie des graphes, le premier problème considéré traite des codes identifiants dans les graphes. Ces codes ont été introduits par Karpovsky, Chakrabarty et Levitin pour modéliser un problème de détection de défaillance dans des réseaux multiprocesseurs. Le rapport entre la taille optimale d'un code identifiant et la taille optimale du relâchement fractionnaire d'un code identifiant est comprise entre 1 et 2 ln(|V|)+1 où V est l'ensemble des sommets du graphe. Nous nous concentrons sur les graphes sommet-transitifs, car nous pouvons y calculer précisément la solution fractionnaire. Nous exhibons des familles infinies, appelées quadrangles généralisés, de graphes sommet-transitifs pour lesquelles les solutions entière et fractionnaire sont de l'ordre |V|^k avec k dans {1/4, 1/3, 2/5}. Le second problème concerne les (r,a,b)-codes couvrants de la grille infinie déjà étudiés par Axenovich et Puzynina. Nous introduisons la notion de 2-coloriages constants de graphes pondérés et nous les étudions dans le cas de quatre cycles pondérés particuliers. Nous présentons une méthode permettant de lier ces 2-coloriages aux codes couvrants. Enfin, nous déterminons les valeurs exactes des constantes a et b de tout (r,a,b)-code couvrant de la grille infinie avec |a-b|>4. Il s'agit d'une extension d'un théorème d'Axenovich. / This dissertation is divided into two (distinct but connected) parts that reflect the joint PhD. We study and we solve several questions regarding on the one hand combinatorics on words in an abelian context and on the other hand covering problems in graphs. Each particular problem is the topic of a chapter. In combinatorics on words, the first problem considered focuses on the 2-regularity of sequences in the sense of Allouche and Shallit. We prove that a sequence satisfying a certain symmetry property is 2-regular. Then we apply this theorem to show that the 2-abelian complexity functions of the Thue--Morse word and the period-doubling word are 2-regular. The computation and arguments leading to these results fit into a quite general scheme that we hope can be used again to prove additional regularity results. The second question concerns the notion of return words up to abelian equivalence, introduced by Puzynina and Zamboni. We obtain a characterization of Sturmian words with non-zero intercept in terms of the finiteness of the set of abelian return words to all prefixes. We describe this set of abelian returns for the Fibonacci word but also for the Thue-Morse word (which is not Sturmian). We investigate the relationship existing between the abelian complexity and the finiteness of this set. In graph theory, the first problem considered deals with identifying codes in graphs. These codes were introduced by Karpovsky, Chakrabarty and Levitin to model fault-diagnosis in multiprocessor systems. The ratio between the optimal size of an identifying code and the optimal size of a fractional relaxation of an identifying code is between 1 and 2 ln(|V|)+1 where V is the vertex set of the graph. We focus on vertex-transitive graphs, since we can compute the exact fractional solution for them. We exhibit infinite families, called generalized quadrangles, of vertex-transitive graphs with integer and fractional identifying codes of order |V|^k with k in {1/4,1/3,2/5}. The second problem concerns (r,a,b)-covering codes of the infinite grid already studied by Axenovich and Puzynina. We introduce the notion of constant 2-labellings of weighted graphs and study them in four particular weighted cycles. We present a method to link these labellings with covering codes. Finally, we determine the precise values of the constants a and b of any (r,a,b)-covering code of the infinite grid with |a-b|>4. This is an extension of a theorem of Axenovich.

Cette dissertation se divise en deux parties, distinctes mais connexes, qui sont le reflet de la cotutelle. Nous étudions et résolvons des problèmes concernant d'une part la combinatoire des mots dans un contexte abélien et d'autre part des problèmes de couverture dans des graphes. Chaque question fait l'objet d'un chapitre. En combinatoire des mots, le premier problème considéré s'intéresse à la régularité des suites au sens défini par Allouche et Shallit. Nous montrons qu'une suite qui satisfait une certaine propriété de symétrie est 2-régulière. Ensuite, nous appliquons ce théorème pour montrer que les fonctions de complexité 2-abélienne du mot de Thue--Morse ainsi que du mot appelé ''period-doubling'' sont 2-régulières. Les calculs et arguments développés dans ces démonstrations s'inscrivent dans un schéma plus général que nous espérons pouvoir utiliser à nouveau pour prouver d'autres résultats de régularité. Le deuxième problème poursuit le développement de la notion de mot de retour abélien introduite par Puzynina et Zamboni. Nous obtenons une caractérisation des mots sturmiens avec un intercepte non nul en termes du cardinal (fini ou non) de l'ensemble des mots de retour abélien par rapport à tous les préfixes. Nous décrivons cet ensemble pour Fibonacci ainsi que pour Thue--Morse (bien que cela ne soit pas un mot sturmien). Nous étudions la relation existante entre la complexité abélienne et le cardinal de cet ensemble. En théorie des graphes, le premier problème considéré traite des codes identifiants dans les graphes. Ces codes ont été introduits par Karpovsky, Chakrabarty et Levitin pour modéliser un problème de détection de défaillance dans des réseaux multiprocesseurs. Le rapport entre la taille optimale d'un code identifiant et la taille optimale du relâchement fractionnaire d'un code identifiant est comprise entre 1 et 2 ln(|V|)+1 où V est l'ensemble des sommets du graphe. Nous nous concentrons sur les graphes sommet-transitifs, car nous pouvons y calculer précisément la solution fractionnaire. Nous exhibons des familles infinies, appelées quadrangles généralisés, de graphes sommet-transitifs pour lesquelles les solutions entière et fractionnaire sont de l'ordre |V|^k avec k dans {1/4, 1/3, 2/5}. Le second problème concerne les (r,a,b)-codes couvrants de la grille infinie déjà étudiés par Axenovich et Puzynina. Nous introduisons la notion de 2-coloriages constants de graphes pondérés et nous les étudions dans le cas de quatre cycles pondérés particuliers. Nous présentons une méthode permettant de lier ces 2-coloriages aux codes couvrants. Enfin, nous déterminons les valeurs exactes des constantes a et b de tout (r,a,b)-code couvrant de la grille infinie avec |a-b|>4. Il s'agit d'une extension d'un théorème d'Axenovich. / This dissertation is divided into two (distinct but connected) parts that reflect the joint PhD. We study and we solve several questions regarding on the one hand combinatorics on words in an abelian context and on the other hand covering problems in graphs. Each particular problem is the topic of a chapter. In combinatorics on words, the first problem considered focuses on the 2-regularity of sequences in the sense of Allouche and Shallit. We prove that a sequence satisfying a certain symmetry property is 2-regular. Then we apply this theorem to show that the 2-abelian complexity functions of the Thue--Morse word and the period-doubling word are 2-regular. The computation and arguments leading to these results fit into a quite general scheme that we hope can be used again to prove additional regularity results. The second question concerns the notion of return words up to abelian equivalence, introduced by Puzynina and Zamboni. We obtain a characterization of Sturmian words with non-zero intercept in terms of the finiteness of the set of abelian return words to all prefixes. We describe this set of abelian returns for the Fibonacci word but also for the Thue-Morse word (which is not Sturmian). We investigate the relationship existing between the abelian complexity and the finiteness of this set. In graph theory, the first problem considered deals with identifying codes in graphs. These codes were introduced by Karpovsky, Chakrabarty and Levitin to model fault-diagnosis in multiprocessor systems. The ratio between the optimal size of an identifying code and the optimal size of a fractional relaxation of an identifying code is between 1 and 2 ln(|V|)+1 where V is the vertex set of the graph. We focus on vertex-transitive graphs, since we can compute the exact fractional solution for them. We exhibit infinite families, called generalized quadrangles, of vertex-transitive graphs with integer and fractional identifying codes of order |V|^k with k in {1/4,1/3,2/5}. The second problem concerns (r,a,b)-covering codes of the infinite grid already studied by Axenovich and Puzynina. We introduce the notion of constant 2-labellings of weighted graphs and study them in four particular weighted cycles. We present a method to link these labellings with covering codes. Finally, we determine the precise values of the constants a and b of any (r,a,b)-covering code of the infinite grid with |a-b|>4. This is an extension of a theorem of Axenovich.