Clustering and Arnoux-Rauzy words

We characterize the clustering of a word under the Burrows-Wheeler transform in terms of the resolution of a bounded number of bispecial factors belonging to the language generated by all its powers. We use this criterion to compute, in every given Arnoux-Rauzy language on three letters, an explicit bound $K$ such that each word of length at least $K$ is not clustering; this bound is sharp for a set of Arnoux-Rauzy languages including the Tribonacci one. In the other direction, we characterize all standard Arnoux-Rauzy clustering words, and all perfectly clustering Arnoux-Rauzy words. We extend some results to episturmian languages, characterizing those which produce infinitely many clustering words, and to larger alphabets

String attractors and combinatorics on words

The notion of string attractor has recently been introduced in [Prezza, 2017] and studied in [Kempa and Prezza, 2018] to provide a unifying framework for known dictionary-based compressors. A string attractor for a word w = w[1]w[2] · · · w[n] is a subset Γ of the positions 1, . . ., n, such that all distinct factors of w have an occurrence crossing at least one of the elements of Γ. While finding the smallest string attractor for a word is a NP-complete problem, it has been proved in [Kempa and Prezza, 2018] that dictionary compressors can be interpreted as algorithms approximating the smallest string attractor for a given word. In this paper we explore the notion of string attractor from a combinatorial point of view, by focusing on several families of finite words. The results presented in the paper suggest that the notion of string attractor can be used to define new tools to investigate combinatorial properties of the words

Around the Fibonacci Numeration System

Let 1, 2, 3, 5, 8, … denote the Fibonacci sequence beginning with 1 and 2, and then setting each subsequent number to the sum of the two previous ones. Every positive integer n can be expressed as a sum of distinct Fibonacci numbers in one or more ways. Setting R(n) to be the number of ways n can be written as a sum of distinct Fibonacci numbers, we exhibit certain regularity properties of R(n), one of which is connected to the Euler φ-function. In addition, using a theorem of Fine and Wilf, we give a formula for R(n) in terms of binomial coefficients modulo two

Privileged Words and Sturmian Words

This dissertation has two almost unrelated themes: privileged words and Sturmian words. Privileged words are a new class of words introduced recently. A word is privileged if it is a complete first return to a shorter privileged word, the shortest privileged words being letters and the empty word. Here we give and prove almost all results on privileged words known to date. On the other hand, the study of Sturmian words is a well-established topic in combinatorics on words. In this dissertation, we focus on questions concerning repetitions in Sturmian words, reproving old results and giving new ones, and on establishing completely new research directions. The study of privileged words presented in this dissertation aims to derive their basic properties and to answer basic questions regarding them. We explore a connection between privileged words and palindromes and seek out answers to questions on context-freeness, computability, and enumeration. It turns out that the language of privileged words is not context-free, but privileged words are recognizable by a linear-time algorithm. A lower bound on the number of binary privileged words of given length is proven. The main interest, however, lies in the privileged complexity functions of the Thue-Morse word and Sturmian words. We derive recurrences for computing the privileged complexity function of the Thue-Morse word, and we prove that Sturmian words are characterized by their privileged complexity function. As a slightly separate topic, we give an overview of a certain method of automated theorem-proving and show how it can be applied to study privileged factors of automatic words. The second part of this dissertation is devoted to Sturmian words. We extensively exploit the interpretation of Sturmian words as irrational rotation words. The essential tools are continued fractions and elementary, but powerful, results of Diophantine approximation theory. With these tools at our disposal, we reprove old results on powers occurring in Sturmian words with emphasis on the fractional index of a Sturmian word. Further, we consider abelian powers and abelian repetitions and characterize the maximum exponents of abelian powers with given period occurring in a Sturmian word in terms of the continued fraction expansion of its slope. We define the notion of abelian critical exponent for Sturmian words and explore its connection to the Lagrange spectrum of irrational numbers. The results obtained are often specialized for the Fibonacci word; for instance, we show that the minimum abelian period of a factor of the Fibonacci word is a Fibonacci number. In addition, we propose a completely new research topic: the square root map. We prove that the square root map preserves the language of any Sturmian word. Moreover, we construct a family of non-Sturmian optimal squareful words whose language the square root map also preserves.This construction yields examples of aperiodic infinite words whose square roots are periodic.Siirretty Doriast

On the k-Abelian Equivalence Relation of Finite Words

This thesis is devoted to the so-called k-abelian equivalence relation of sequences of symbols, that is, words. This equivalence relation is a generalization of the abelian equivalence of words. Two words are abelian equivalent if one is a permutation of the other. For any positive integer k, two words are called k-abelian equivalent if each word of length at most k occurs equally many times as a factor in the two words. The k-abelian equivalence defines an equivalence relation, even a congruence, of finite words. A hierarchy of equivalence classes in between the equality relation and the abelian equivalence of words is thus obtained. Most of the literature on the k-abelian equivalence deals with infinite words. In this thesis we consider several aspects of the equivalence relations, the main objective being to build a fairly comprehensive picture on the structure of the k-abelian equivalence classes themselves. The main part of the thesis deals with the structural aspects of k-abelian equivalence classes. We also consider aspects of k-abelian equivalence in infinite words. We survey known characterizations of the k-abelian equivalence of finite words from the literature and also introduce novel characterizations. For the analysis of structural properties of the equivalence relation, the main tool is the characterization by the rewriting rule called the k-switching. Using this rule it is straightforward to show that the language comprised of the lexicographically least elements of the k-abelian equivalence classes is regular. Further word-combinatorial analysis of the lexicographically least elements leads us to describe the deterministic finite automata recognizing this language. Using tools from formal language theory combined with our analysis, we give an optimal expression for the asymptotic growth rate of the number of k-abelian equivalence classes of length n over an m-letter alphabet. Explicit formulae are computed for small values of k and m, and these sequences appear in Sloane’s Online Encyclopedia of Integer Sequences. Due to the fact that the k-abelian equivalence relation is a congruence of the free monoid, we study equations over the k-abelian equivalence classes. The main result in this setting is that any system of equations of k-abelian equivalence classes is equivalent to one of its finite subsystems, i.e., the monoid defined by the k-abelian equivalence relation possesses the compactness property. Concerning infinite words, we mainly consider the (k-)abelian complexity function. We complete a classification of the asymptotic abelian complexities of pure morphic binary words. In other words, given a morphism which has an infinite binary fixed point, the limit superior asymptotic abelian complexity of the fixed point can be computed (in principle). We also give a new proof of the fact that the k-abelian complexity of a Sturmian word is n + 1 for length n 2k. In fact, we consider several aspects of the k-abelian equivalence relation in Sturmian words using a dynamical interpretation of these words. We reprove the fact that any Sturmian word contains arbitrarily large k-abelian repetitions. The methods used allow to analyze the situation in more detail, and this leads us to define the so-called k-abelian critical exponent which measures the ratio of the exponent and the length of the root of a k-abelian repetition. This notion is connected to a deep number theoretic object called the Lagrange spectrum

Algorithms and Data Structures for Coding, Indexing, and Mining of Sequential Data

In recent years, the production of sequential data has been rapidly increasing. This requires solving challenging problems about how to represent information, how to retrieve information, and how to extract knowledge, from sequential data. These questions belong to the areas of coding, indexing, and mining, respectively. In this thesis, we investigate problems from those three areas. Coding refers to the way in which information is represented. Coding aims at generating optimal codes, that are codes having a minimum expected length. Codes can be generated for different purposes, from data compression to error detection/correction. The Lempel-Ziv 77 parsing produces an asymptotically optimal code in terms of compression. We study algorithms to efficiently decompress strings from the Lempel-Ziv 77 parsing, using memory proportional to the size of the parsing itself. We provide the first implementation of an algorithm by Bille et al., the only work we are aware of on this problem. We present a practical evaluation of this approach and several optimizations which improve the performance on all datasets we tested. Through the Ulam-R{'e}nyi game, it is possible to provide optimal adaptive error-correcting codes. The game consists of discovering an unknown $m$-bit number by asking membership questions the answers to which can be erroneous. Questions are formulated knowing the answers to all previous ones. We want to find an optimal strategy, i.e., a strategy that can identify any $m$-bit number using the theoretical minimum number of questions. We studied the case where questions are a union of up to a fixed number of intervals, and up to three answers can be erroneous. We first show that for any sufficiently large $m$, there exists a strategy to identify an initially unknown $m$-bit number which uses at most four intervals per question. We further refine our main tool to turn the above asymptotic result into a complete characterization of those instances of the Ulam-R{'e}nyi game that admit optimal strategies. Indexing refers to the way in which information is retrieved. An index for texts permits finding all occurrences of any substring, without traversing the whole text. Many applications require to look for approximate substrings. One of these is the problem of jumbled pattern matching, where two strings match if one is a permutation of the other. We study combinatorial aspects of prefix normal words, a class of binary words introduced in this context. These words can be used as indices for the Indexed Binary Jumbled Pattern Matching problem. We present a new recursive generation algorithm for prefix normal words that is competitive with the previous one but allows to list all prefix normal words sharing the same prefix. This sheds lights on novel insights that may help solving the problem of counting the number of prefix normal words of a given length. We then introduce infinite prefix normal words, and we show that one of the operations used by the algorithm, when repeatedly applied to extend a word, produces an infinite prefix normal word. This motivates the seeking for other operations that produce infinite prefix normal words. We found that one of these operations establishes a connection between prefix normal words and Sturmian words. We also explored the relationship between prefix normal words and Abelian complexity, as well as between prefix normal words and lexicographic order. Mining refers to the way in which information is converted into knowledge. The process of knowledge discovery covers several processing steps, including knowledge extraction. We analyze the problem of mining assertions for an embedded system from its simulation traces. This problem can be modeled as a pattern discovery problem on colored strings. We present two problems of pattern discovery on colored strings: patterns for one color only, or for all colors at the same time. We present two suffix tree-based algorithms. The first algorithm solves both the one color problem and the all colors problem. We then, introduce modifications which improve performance of the algorithm both on synthetic and on real data. We implemented and evaluated the proposed approaches, highlighting time trade-offs that can be obtained. A different way of knowledge extraction is based on the information-theoretic perspective of Pearl's model of causality. It has been postulated that the true causality direction between two phenomena A and B is related to the problem of finding the minimum entropy joint distribution between A and B. This problem is known to be NP-hard, and greedy algorithms have recently been proposed. We provide a novel analysis of one of the proposed heuristic showing that this algorithm guarantees an additive approximation of 1 bit. We then, provide a general criterion for guaranteeing an additive approximation factor of 1. This criterion may be of independent interest in other contexts where couplings are used