Binary jumbled string matching for highly run-length compressible texts

The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s. Previous solutions created an index of size O(n) in a pre-processing step, which was then used to answer queries in constant time. The fastest algorithms for construction of this index have running time $O(n^2/\log n)$ [Burcsi et al., FUN 2010; Moosa and Rahman, IPL 2010], or $O(n^2/\log^2 n)$ in the word-RAM model [Moosa and Rahman, JDA 2012]. We propose an index constructed directly from the run-length encoding of $s$. The construction time of our index i…

Alignment-free sequence comparison using absent words

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as $q$-gram distance, are usually computed in time linear with respect to the length of the sequences. In this paper, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an {\em absent word} of some sequence if it does not oc…

Marked systems and circular splicing

Splicing systems are generative devices of formal languages, introduced by Head in 1987 to model biological phenomena on linear and circular DNA molecules. In this paper we introduce a special class of finite circular splicing systems named marked systems. We prove that a marked system S generates a regular circular language if and only if S satisfies a special (decidable) property. As a consequence, we show that we can decide whether a regular circular language is generated by a marked system and we characterize the structure of these regular circular languages.

On Combinatorial Generation of Prefix Normal Words

A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present an efficient algorithm for exhaustively listing the prefix normal words with a fixed length. The algorithm is based on the fact that the language of prefix normal words is a bubble language, a class of binary languages with the property that, for any word w in the language, exchanging the first occurrence of 01 by 10 in w results in another word in the language. We prove that each prefix normal word is produced in O(n) amortized time, and conjecture, based on expe…

A Classification of Trapezoidal Words

Trapezoidal words are finite words having at most n+1 distinct factors of length n, for every n>=0. They encompass finite Sturmian words. We distinguish trapezoidal words into two disjoint subsets: open and closed trapezoidal words. A trapezoidal word is closed if its longest repeated prefix has exactly two occurrences in the word, the second one being a suffix of the word. Otherwise it is open. We show that open trapezoidal words are all primitive and that closed trapezoidal words are all Sturmian. We then show that trapezoidal palindromes are closed (and therefore Sturmian). This allows us to characterize the special factors of Sturmian palindromes. We end with several open problems.

On Combinatorial Generation of Prefix Normal Words

A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present an efficient algorithm for exhaustively listing the prefix normal words with a fixed length. The algorithm is based on the fact that the language of prefix normal words is a bubble language, a class of binary languages with the property that, for any word w in the language, exchanging the first occurrence of 01 by 10 in w results in another word in the language. We prove that each prefix normal word is produced in O(n) amortized time, and conjecture, based on expe…

A Characterization of Bispecial Sturmian Words

A finite Sturmian word w over the alphabet {a,b} is left special (resp. right special) if aw and bw (resp. wa and wb) are both Sturmian words. A bispecial Sturmian word is a Sturmian word that is both left and right special. We show as a main result that bispecial Sturmian words are exactly the maximal internal factors of Christoffel words, that are words coding the digital approximations of segments in the Euclidean plane. This result is an extension of the known relation between central words and primitive Christoffel words. Our characterization allows us to give an enumerative formula for bispecial Sturmian words. We also investigate the minimal forbidden words for the set of Sturmian wo…

Reverse-safe data structures for text indexing

We introduce the notion of reverse-safe data structures. These are data structures that prevent the reconstruction of the data they encode (i.e., they cannot be easily reversed). A data structure D is called z-reverse-safe when there exist at least z datasets with the same set of answers as the ones stored by D. The main challenge is to ensure that D stores as many answers to useful queries as possible, is constructed efficiently, and has size close to the size of the original dataset it encodes. Given a text of length n and an integer z, we propose an algorithm which constructs a z-reverse-safe data structure that has size O(n) and answers pattern matching queries of length at most d optim…

Constructing Antidictionaries of Long Texts in Output-Sensitive Space

AbstractA wordxthat is absent from a wordyis calledminimalif all its proper factors occur iny. Given a collection ofkwordsy1, … ,ykover an alphabetΣ, we are asked to compute the set$\mathrm {M}^{\ell }_{\{y_1,\ldots ,y_k\}}$M{y1,…,yk}ℓof minimal absent words of length at mostℓof the collection {y1, … ,yk}. The set$\mathrm {M}^{\ell }_{\{y_1,\ldots ,y_k\}}$M{y1,…,yk}ℓcontains all the wordsxsuch thatxis absent from all the words of the collection while there existi,j, such that the maximal proper suffix ofxis a factor ofyiand the maximal proper prefix ofxis a factor ofyj. In data compression, this corresponds to computing the antidictionary ofkdocuments. In bioinformatics, it corresponds to c…

Abelian-Square-Rich Words

An abelian square is the concatenation of two words that are anagrams of one another. A word of length $n$ can contain at most $\Theta(n^2)$ distinct factors, and there exist words of length $n$ containing $\Theta(n^2)$ distinct abelian-square factors, that is, distinct factors that are abelian squares. This motivates us to study infinite words such that the number of distinct abelian-square factors of length $n$ grows quadratically with $n$. More precisely, we say that an infinite word $w$ is {\it abelian-square-rich} if, for every $n$, every factor of $w$ of length $n$ contains, on average, a number of distinct abelian-square factors that is quadratic in $n$; and {\it uniformly abelian-sq…

Maximal Closed Substrings

A string is closed if it has length 1 or has a nonempty border without internal occurrences. In this paper we introduce the definition of a maximal closed substring (MCS), which is an occurrence of a closed substring that cannot be extended to the left nor to the right into a longer closed substring. MCSs with exponent at least 2 are commonly called runs; those with exponent smaller than 2, instead, are particular cases of maximal gapped repeats. We show that a string of length n contains O(n1.5) MCSs. We also provide an output-sensitive algorithm that, given a string of length n over a constant-size alphabet, locates all m MCSs the string contains in O(nlog n+ m) time.

Enumeration and Structure of Trapezoidal Words

Trapezoidal words are words having at most $n+1$ distinct factors of length $n$ for every $n\ge 0$. They therefore encompass finite Sturmian words. We give combinatorial characterizations of trapezoidal words and exhibit a formula for their enumeration. We then separate trapezoidal words into two disjoint classes: open and closed. A trapezoidal word is closed if it has a factor that occurs only as a prefix and as a suffix; otherwise it is open. We investigate open and closed trapezoidal words, in relation with their special factors. We prove that Sturmian palindromes are closed trapezoidal words and that a closed trapezoidal word is a Sturmian palindrome if and only if its longest repeated …

Presentations of constrained systems with unconstrained positions

International audience; We give a polynomial-time construction of the set of sequences that satisfy a finite-memory constraint defined by a finite list of forbidden blocks, with a specified set of bit positions unconstrained. Such a construction can be used to build modulation/error-correction codes (ECC codes) like the ones defined by the Immink-Wijngaarden scheme in which certain bit positions are reserved for ECC parity. We give a lineartime construction of a finite-state presentation of a constrained system defined by a periodic list of forbidden blocks. These systems, called periodic-finite-type systems, were introduced by Moision and Siegel. Finally, we present a linear-time algorithm for con…

ALGORITHMS FOR JUMBLED PATTERN MATCHING IN STRINGS

The Parikh vector p(s) of a string s is defined as the vector of multiplicities of the characters. Parikh vector q occurs in s if s has a substring t with p(t)=q. We present two novel algorithms for searching for a query q in a text s. One solves the decision problem over a binary text in constant time, using a linear size index of the text. The second algorithm, for a general finite alphabet, finds all occurrences of a given Parikh vector q and has sub-linear expected time complexity; we present two variants, which both use a linear size index of the text.

A note on easy and efficient computation of full abelian periods of a word

Constantinescu and Ilie (Bulletin of the EATCS 89, 167-170, 2006) introduced the idea of an Abelian period with head and tail of a finite word. An Abelian period is called full if both the head and the tail are empty. We present a simple and easy-to-implement $O(n\log\log n)$-time algorithm for computing all the full Abelian periods of a word of length $n$ over a constant-size alphabet. Experiments show that our algorithm significantly outperforms the $O(n)$ algorithm proposed by Kociumaka et al. (Proc. of STACS, 245-256, 2013) for the same problem.

Constructing Antidictionaries in Output-Sensitive Space

A word $x$ that is absent from a word $y$ is called minimal if all its proper factors occur in $y$. Given a collection of $k$ words $y_1,y_2,\ldots,y_k$ over an alphabet $\Sigma$, we are asked to compute the set $\mathrm{M}^{\ell}_{y_{1}\#\ldots\#y_{k}}$ of minimal absent words of length at most $\ell$ of word $y=y_1\#y_2\#\ldots\#y_k$, $\#\notin\Sigma$. In data compression, this corresponds to computing the antidictionary of $k$ documents. In bioinformatics, it corresponds to computing words that are absent from a genome of $k$ chromosomes. This computation generally requires $\Omega(n)$ space for $n=|y|$ using any of the plenty available $\mathcal{O}(n)$-time algorithms. This is because a…

Generating a Gray code for prefix normal words in amortized polylogarithmic time per word

A prefix normal word is a binary word with the property that no substring has more $1$s than the prefix of the same length. By proving that the set of prefix normal words is a bubble language, we can exhaustively list all prefix normal words of length $n$ as a combinatorial Gray code, where successive strings differ by at most two swaps or bit flips. This Gray code can be generated in $\Oh(\log^2 n)$ amortized time per word, while the best generation algorithm hitherto has $\Oh(n)$ running time per word. We also present a membership tester for prefix normal words, as well as a novel characterization of bubble languages.

Fragment assembly through minimal forbidden words

Online Computation of Abelian Runs

Given a word $w$ and a Parikh vector $\mathcal{P}$, an abelian run of period $\mathcal{P}$ in $w$ is a maximal occurrence of a substring of $w$ having abelian period $\mathcal{P}$. We give an algorithm that finds all the abelian runs of period $\mathcal{P}$ in a word of length $n$ in time $O(n\times |\mathcal{P}|)$ and space $O(\sigma+|\mathcal{P}|)$.

Topological properties of cellular automata on trees

We prove that there do not exist positively expansive cellular automata defined on the full k-ary tree shift (for k>=2). Moreover, we investigate some topological properties of these automata and their relationships, namely permutivity, surjectivity, preinjectivity, right-closingness and openness.

Preface

Adaptive learning of compressible strings

Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm needs to ask the oracle $\sigma n/4 -O(n)$ queries in order to be able to reconstruct the hidden string, where $\sigma$ is the size of the alphabet of $S$ and $n$ its length, and gave an algorithm that spends $(\sigma-1)n+O(\sigma \sqrt{n})$ queries to reconstruct $S$. The main contribution of our paper is to improve the above upper-bound in the context where the string is compressible. We first present a universal algorithm that, given a (computable) compre…

Automata and differentiable words

We exhibit the construction of a deterministic automaton that, given k > 0, recognizes the (regular) language of k-differentiable words. Our approach follows a scheme of Crochemore et al. based on minimal forbidden words. We extend this construction to the case of C\infinity-words, i.e., words differentiable arbitrary many times. We thus obtain an infinite automaton for representing the set of C\infinity-words. We derive a classification of C\infinity-words induced by the structure of the automaton. Then, we introduce a new framework for dealing with \infinity-words, based on a three letter alphabet. This allows us to define a compacted version of the automaton, that we use to prove that ev…

Searching for Jumbled Patterns in Strings

On The Maximum Number of Abelian Squares in a Word

Strings (aka sequences or words) form the most basic and natural data structure. They occur whenever information is electronically transmitted (as bit streams), when natural language text is spoken or written down (as words over, for example, the Latin alphabet), in the process of heredity transmission in living cells (through DNA sequences) or the protein synthesis (assequence of amino acids), and in many more different contexts

Special factors and the combinatorics of suffix and factor automata

AbstractThe suffix automaton (resp. factor automaton) of a finite word w is the minimal deterministic automaton recognizing the set of suffixes (resp. factors) of w. We study the relationships between the structure of the suffix and factor automata and classical combinatorial parameters related to the special factors of w. We derive formulae for the number of states of these automata. We also characterize the languages LSA and LFA of words having respectively suffix automaton and factor automaton with the minimal possible number of states.

Algorithms for Anti-Powers in Strings

Abstract A string S [ 1 , n ] is a power (or tandem repeat) of order k and period n / k if it can be decomposed into k consecutive equal-length blocks of letters. Powers and periods are fundamental to string processing, and algorithms for their efficient computation have wide application and are heavily studied. Recently, Fici et al. (Proc. ICALP 2016) defined an anti-power of order k to be a string composed of k pairwise-distinct blocks of the same length ( n / k , called anti-period). Anti-powers are a natural converse to powers, and are objects of combinatorial interest in their own right. In this paper we initiate the algorithmic study of anti-powers. Given a string S, we describe an op…

On Prefix Normal Words

We present a new class of binary words: the prefix normal words. They are defined by the property that for any given length $k$, no factor of length $k$ has more $a$'s than the prefix of the same length. These words arise in the context of indexing for jumbled pattern matching (a.k.a. permutation matching or Parikh vector matching), where the aim is to decide whether a string has a factor with a given multiplicity of characters, i.e., with a given Parikh vector. Using prefix normal words, we give the first non-trivial characterization of binary words having the same set of Parikh vectors of factors. We prove that the language of prefix normal words is not context-free and is strictly contai…

Minimal Absent Words in Rooted and Unrooted Trees

We extend the theory of minimal absent words to (rooted and unrooted) trees, having edges labeled by letters from an alphabet \(\varSigma \) of cardinality \(\sigma \). We show that the set \(\text {MAW}(T)\) of minimal absent words of a rooted (resp. unrooted) tree T with n nodes has cardinality \(O(n\sigma )\) (resp. \(O(n^{2}\sigma )\)), and we show that these bounds are realized. Then, we exhibit algorithms to compute all minimal absent words in a rooted (resp. unrooted) tree in output-sensitive time \(O(n+|\text {MAW}(T)|)\) (resp. \(O(n^{2}+|\text {MAW}(T)|)\) assuming an integer alphabet of size polynomial in n.

On The Least Number of Palindromes in an Infinite Word

A characterization of regular circular languages generated by marked splicing systems

AbstractSplicing systems are generative devices of formal languages, introduced by Head in 1987 to model biological phenomena on linear and circular DNA molecules. A splicing system is defined by giving an initial set I and a set R of rules. Some unanswered questions are related to the computational power of circular splicing systems. In particular, a still open question is to find a characterization of circular languages generated by finite circular splicing systems (i.e., circular splicing systems with both I and R finite sets). In this paper we introduce a special class of the latter systems named marked systems. We prove that a marked system S generates a regular circular language if an…

Cyclic Complexity of Words

We introduce and study a complexity function on words $c_x(n),$ called \emph{cyclic complexity}, which counts the number of conjugacy classes of factors of length $n$ of an infinite word $x.$ We extend the well-known Morse-Hedlund theorem to the setting of cyclic complexity by showing that a word is ultimately periodic if and only if it has bounded cyclic complexity. Unlike most complexity functions, cyclic complexity distinguishes between Sturmian words of different slopes. We prove that if $x$ is a Sturmian word and $y$ is a word having the same cyclic complexity of $x,$ then up to renaming letters, $x$ and $y$ have the same set of factors. In particular, $y$ is also Sturmian of slope equ…

On the Lie complexity of Sturmian words

Bell and Shallit recently introduced the Lie complexity of an infinite word $s$ as the function counting for each length the number of conjugacy classes of words whose elements are all factors of $s$. They proved, using algebraic techniques, that the Lie complexity is bounded above by the first difference of the factor complexity plus one; hence, it is uniformly bounded for words with linear factor complexity, and, in particular, it is at most 2 for Sturmian words, which are precisely the words with factor complexity $n+1$ for every $n$. In this note, we provide an elementary combinatorial proof of the result of Bell and Shallit and give an exact formula for the Lie complexity of any Sturmi…

Combinatorics of Finite Words and Suffix Automata

The suffix automaton of a finite word is the minimal deterministic automaton accepting the language of its suffixes. The states of the suffix automaton are the classes of an equivalence relation defined on the set of factors. We explore the relationship between the combinatorial properties of a finite word and the structural properties of its suffix automaton. We give formulas for expressing the total number of states and the total number of edges of the suffix automaton in terms of special factors of the word.

On the regularity of circular splicing languages : A survey and new developments

Circular splicing has been introduced to model a specific recombinant behaviour of circular DNA, continuing the investigation initiated with linear splicing. In this paper we focus on the relationship between regular circular languages and languages generated by finite circular splicing systems. We survey the known results towards a characterization of the intersection between these two classes and provide new contributions on the open problem of finding this characterization. First, we exhibit a non-regular circular language generated by a circular simple system thus disproving a known result in this area. Then we give new results related to a restrictive class of circular splicing systems…

Open and Closed Prefixes of Sturmian Words

A word is closed if it contains a proper factor that occurs both as a prefix and as a suffix but does not have internal occurrences, otherwise it is open. We deal with the sequence of open and closed prefixes of Sturmian words and prove that this sequence characterizes every finite or infinite Sturmian word up to isomorphisms of the alphabet. We then characterize the combinatorial structure of the sequence of open and closed prefixes of standard Sturmian words. We prove that every standard Sturmian word, after swapping its first letter, can be written as an infinite product of squares of reversed standard words.

Abelian Powers and Repetitions in Sturmian Words

Richomme, Saari and Zamboni (J. Lond. Math. Soc. 83: 79-95, 2011) proved that at every position of a Sturmian word starts an abelian power of exponent $k$ for every $k > 0$. We improve on this result by studying the maximum exponents of abelian powers and abelian repetitions (an abelian repetition is an analogue of a fractional power) in Sturmian words. We give a formula for computing the maximum exponent of an abelian power of abelian period $m$ starting at a given position in any Sturmian word of rotation angle $\alpha$. vAs an analogue of the critical exponent, we introduce the abelian critical exponent $A(s_\alpha)$ of a Sturmian word $s_\alpha$ of angle $\alpha$ as the quantity $A(s_\a…

On the Structure of Bispecial Sturmian Words

A balanced word is one in which any two factors of the same length contain the same number of each letter of the alphabet up to one. Finite binary balanced words are called Sturmian words. A Sturmian word is bispecial if it can be extended to the left and to the right with both letters remaining a Sturmian word. There is a deep relation between bispecial Sturmian words and Christoffel words, that are the digital approximations of Euclidean segments in the plane. In 1997, J. Berstel and A. de Luca proved that \emph{palindromic} bispecial Sturmian words are precisely the maximal internal factors of \emph{primitive} Christoffel words. We extend this result by showing that bispecial Sturmian wo…

On prefix normal words and prefix normal forms

A $1$-prefix normal word is a binary word with the property that no factor has more $1$s than the prefix of the same length; a $0$-prefix normal word is defined analogously. These words arise in the context of indexed binary jumbled pattern matching, where the aim is to decide whether a word has a factor with a given number of $1$s and $0$s (a given Parikh vector). Each binary word has an associated set of Parikh vectors of the factors of the word. Using prefix normal words, we provide a characterization of the equivalence class of binary words having the same set of Parikh vectors of their factors. We prove that the language of prefix normal words is not context-free and is strictly contai…

On Table Arrangements, Scrabble Freaks, and Jumbled Pattern Matching

Given a string s, the Parikh vector of s, denoted p(s), counts the multiplicity of each character in s. Searching for a match of Parikh vector q (a “jumbled string”) in the text s requires to find a substring t of s with p(t) = q. The corresponding decision problem is to verify whether at least one such match exists. So, for example for the alphabet Σ = {a, b, c}, the string s = abaccbabaaa has Parikh vector p(s) = (6,3,2), and the Parikh vector q = (2,1,1) appears once in s in position (1,4). Like its more precise counterpart, the renown Exact String Matching, Jumbled Pattern Matching has ubiquitous applications, e.g., string matching with a dyslectic word processor, table rearrangements, …

On Sets of Words of Rank Two

Given a (finite or infinite) subset X of the free monoid A∗ over a finite alphabet A, the rank of X is the minimal cardinality of a set F such that X⊆ F∗. A submonoid M generated by k elements of A∗ is k-maximal if there does not exist another submonoid generated by at most k words containing M. We call a set X⊆ A∗ primitive if it is the basis of a |X|-maximal submonoid. This extends the notion of primitive word: indeed, w is a primitive set if and only if w is a primitive word. By definition, for any set X, there exists a primitive set Y such that X⊆ Y∗. The set Y is therefore called a primitive root of X. As a main result, we prove that if a set has rank 2, then it has a unique primitive …

Factorizations of the Fibonacci Infinite Word

The aim of this note is to survey the factorizations of the Fibonacci infinite word that make use of the Fibonacci words and other related words, and to show that all these factorizations can be easily derived in sequence starting from elementary properties of the Fibonacci numbers.

On the least number of palindromes contained in an infinite word

We investigate the least number of palindromic factors in an infinite word. We first consider general alphabets, and give answers to this problem for periodic and non-periodic words, closed or not under reversal of factors. We then investigate the same problem when the alphabet has size two.

Fast computation of abelian runs

Given a word $w$ and a Parikh vector $\mathcal{P}$, an abelian run of period $\mathcal{P}$ in $w$ is a maximal occurrence of a substring of $w$ having abelian period $\mathcal{P}$. Our main result is an online algorithm that, given a word $w$ of length $n$ over an alphabet of cardinality $\sigma$ and a Parikh vector $\mathcal{P}$, returns all the abelian runs of period $\mathcal{P}$ in $w$ in time $O(n)$ and space $O(\sigma+p)$, where $p$ is the norm of $\mathcal{P}$, i.e., the sum of its components. We also present an online algorithm that computes all the abelian runs with periods of norm $p$ in $w$ in time $O(np)$, for any given norm $p$. Finally, we give an $O(n^2)$-time offline randomi…

Properties of a Class of Toeplitz Words

We study the properties of the uncountable set of Stewart words. These are Toeplitz words specified by infinite sequences of Toeplitz patterns of the form $\alpha\beta\gamma$, where $\alpha,\beta,\gamma$ is any permutation of the symbols 0,1,?. We determine the critical exponent of the Stewart words, prove that they avoid the pattern $xxyyxx$, find all factors that are palindromes, and determine their subword complexity. An interesting aspect of our work is that we use automata-theoretic methods and a decision procedure for automata to carry out the proofs.

On Approximate Jumbled Pattern Matching in Strings

Given a string s, the Parikh vector of s, denoted p(s), counts the multiplicity of each character in s. Searching for a match of a Parikh vector q in the text s requires finding a substring t of s with p(t) = q. This can be viewed as the task of finding a jumbled (permuted) version of a query pattern, hence the term Jumbled Pattern Matching. We present several algorithms for the approximate version of the problem: Given a string s and two Parikh vectors u, v (the query bounds), find all maximal occurrences in s of some Parikh vector q such that u <= q <= v. This definition encompasses several natural versions of approximate Parikh vector search. We present an algorithm solving this problem …

Some Remarks on Differentiable Sequences and Recursivity

International audience; We investigate the recursive structure of differentiable sequences over the alphabet {1, 2}. We derive a recursive formula for the (n + 1)-th symbol of a differentiable sequence, which yields to a new recursive formula for the Kolakoski sequence. Finally, we show that the sequence of absolute differences of consecutive symbols of a differentiable sequence u is a morphic image of the run-length encoding of u.

Word assembly through minimal forbidden words

AbstractWe give a linear-time algorithm to reconstruct a finite word w over a finite alphabet A of constant size starting from a finite set of factors of w verifying a suitable hypothesis. We use combinatorics techniques based on the minimal forbidden words, which have been introduced in previous papers. This improves a previous algorithm which worked under the assumption of stronger hypothesis.

A subquadratic algorithm for minimum palindromic factorization

We give an $\mathcal{O}(n \log n)$-time, $\mathcal{O}(n)$-space algorithm for factoring a string into the minimum number of palindromic substrings. That is, given a string $S [1..n]$, in $\mathcal{O}(n \log n)$ time our algorithm returns the minimum number of palindromes $S_1,\ldots, S_\ell$ such that $S = S_1 \cdots S_\ell$. We also show that the time complexity is $\mathcal{O}(n)$ on average and $\Omega(n\log n)$ in the worst case. The last result is based on a characterization of the palindromic structure of Zimin words.

Anti-powers in infinite words

In combinatorics of words, a concatenation of $k$ consecutive equal blocks is called a power of order $k$. In this paper we take a different point of view and define an anti-power of order $k$ as a concatenation of $k$ consecutive pairwise distinct blocks of the same length. As a main result, we show that every infinite word contains powers of any order or anti-powers of any order. That is, the existence of powers or anti-powers is an unavoidable regularity. Indeed, we prove a stronger result, which relates the density of anti-powers to the existence of a factor that occurs with arbitrary exponent. As a consequence, we show that in every aperiodic uniformly recurrent word, anti-powers of ev…

Universal Lyndon Words

A word w over an alphabet Σ is a Lyndon word if there exists an order defined on Σ for which w is lexicographically smaller than all of its conjugates (other than itself). We introduce and study universal Lyndon words, which are words over an n-letter alphabet that have length n! and such that all the conjugates are Lyndon words. We show that universal Lyndon words exist for every n and exhibit combinatorial and structural properties of these words. We then define particular prefix codes, which we call Hamiltonian lex-codes, and show that every Hamiltonian lex-code is in bijection with the set of the shortest unrepeated prefixes of the conjugates of a universal Lyndon word. This allows us t…

Abelian antipowers in infinite words

Abstract An abelian antipower of order k (or simply an abelian k-antipower) is a concatenation of k consecutive words of the same length having pairwise distinct Parikh vectors. This definition generalizes to the abelian setting the notion of a k-antipower, as introduced in Fici et al. (2018) [7] , that is a concatenation of k pairwise distinct words of the same length. We aim to study whether a word contains abelian k-antipowers for arbitrarily large k. S. Holub proved that all paperfolding words contain abelian powers of every order (Holub, 2013 [8] ). We show that they also contain abelian antipowers of every order.

Reverse-Safe Text Indexing

We introduce the notion of reverse-safe data structures. These are data structures that prevent the reconstruction of the data they encode (i.e., they cannot be easily reversed). A data structure D is called z - reverse-safe when there exist at least z datasets with the same set of answers as the ones stored by D . The main challenge is to ensure that D stores as many answers to useful queries as possible, is constructed efficiently, and has size close to the size of the original dataset it encodes. Given a text of length n and an integer z , we propose an algorithm that constructs a z -reverse-safe data structure ( z -RSDS) that has size O(n) and answers decision and counting pattern matc…

Abelian combinatorics on words: A survey

We survey known results and open problems in abelian combinatorics on words. Abelian combinatorics on words is the extension to the commutative setting of the classical theory of combinatorics on words. The extension is based on \emph{abelian equivalence}, which is the equivalence relation defined in the set of words by having the same Parikh vector, that is, the same number of occurrences of each letter of the alphabet. In the past few years, there was a lot of research on abelian analogues of classical definitions and properties in combinatorics on words. This survey aims to gather these results.

Computing abelian periods in words

International audience

Linear-time sequence comparison using minimal absent words & applications

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as q-gram distance, are usually computed in time linear with respect to the length of the sequences. In this article, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an absent word of some sequence if it does not occur in…

Substring Complexity in Sublinear Space

Shannon's entropy is a definitive lower bound for statistical compression. Unfortunately, no such clear measure exists for the compressibility of repetitive strings. Thus, ad-hoc measures are employed to estimate the repetitiveness of strings, e.g., the size $z$ of the Lempel-Ziv parse or the number $r$ of equal-letter runs of the Burrows-Wheeler transform. A more recent one is the size $\gamma$ of a smallest string attractor. Unfortunately, Kempa and Prezza [STOC 2018] showed that computing $\gamma$ is NP-hard. Kociumaka et al. [LATIN 2020] considered a new measure that is based on the function $S_T$ counting the cardinalities of the sets of substrings of each length of $T$, also known as …

Abelian Repetitions in Sturmian Words

We investigate abelian repetitions in Sturmian words. We exploit a bijection between factors of Sturmian words and subintervals of the unitary segment that allows us to study the periods of abelian repetitions by using classical results of elementary Number Theory. We prove that in any Sturmian word the superior limit of the ratio between the maximal exponent of an abelian repetition of period $m$ and $m$ is a number $\geq\sqrt{5}$, and the equality holds for the Fibonacci infinite word. We further prove that the longest prefix of the Fibonacci infinite word that is an abelian repetition of period $F_j$, $j&gt;1$, has length $F_j(F_{j+1}+F_{j-1} +1)-2$ if $j$ is even or $F_j(F_{j+1}+F_{j-1}…

On the Greedy Algorithm for the Shortest Common Superstring Problem with Reversals

We study a variation of the classical Shortest Common Superstring (SCS) problem in which a shortest superstring of a finite set of strings $S$ is sought containing as a factor every string of $S$ or its reversal. We call this problem Shortest Common Superstring with Reversals (SCS-R). This problem has been introduced by Jiang et al., who designed a greedy-like algorithm with length approximation ratio $4$. In this paper, we show that a natural adaptation of the classical greedy algorithm for SCS has (optimal) compression ratio $\frac12$, i.e., the sum of the overlaps in the output string is at least half the sum of the overlaps in an optimal solution. We also provide a linear-time implement…

Minimal forbidden factors of circular words

Minimal forbidden factors are a useful tool for investigating properties of words and languages. Two factorial languages are distinct if and only if they have different (antifactorial) sets of minimal forbidden factors. There exist algorithms for computing the minimal forbidden factors of a word, as well as of a regular factorial language. Conversely, Crochemore et al. [IPL, 1998] gave an algorithm that, given the trie recognizing a finite antifactorial language $M$, computes a DFA recognizing the language whose set of minimal forbidden factors is $M$. In the same paper, they showed that the obtained DFA is minimal if the input trie recognizes the minimal forbidden factors of a single word.…

On the Number of Closed Factors in a Word

A closed word (a.k.a. periodic-like word or complete first return) is a word whose longest border does not have internal occurrences, or, equivalently, whose longest repeated prefix is not right special. We investigate the structure of closed factors of words. We show that a word of length $n$ contains at least $n+1$ distinct closed factors, and characterize those words having exactly $n+1$ closed factors. Furthermore, we show that a word of length $n$ can contain $\Theta(n^{2})$ many distinct closed factors.

The sequence of open and closed prefixes of a Sturmian word

A finite word is closed if it contains a factor that occurs both as a prefix and as a suffix but does not have internal occurrences, otherwise it is open. We are interested in the {\it oc-sequence} of a word, which is the binary sequence whose $n$-th element is $0$ if the prefix of length $n$ of the word is open, or $1$ if it is closed. We exhibit results showing that this sequence is deeply related to the combinatorial and periodic structure of a word. In the case of Sturmian words, we show that these are uniquely determined (up to renaming letters) by their oc-sequence. Moreover, we prove that the class of finite Sturmian words is a maximal element with this property in the class of binar…

Normal, Abby Normal, Prefix Normal

A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present results about the number $pnw(n)$ of prefix normal words of length $n$, showing that $pnw(n) =\Omega\left(2^{n - c\sqrt{n\ln n}}\right)$ for some $c$ and $pnw(n) = O \left(\frac{2^n (\ln n)^2}{n}\right)$. We introduce efficient algorithms for testing the prefix normal property and a "mechanical algorithm" for computing prefix normal forms. We also include games which can be played with prefix normal words. In these games Alice wishes to stay normal but Bob wants t…

Vertical Representation of C∞-words

International audience; We present a new framework for dealing with C∞-words, based on their left and right frontiers. Thisallows us to give a compact representation of them, and to describe the set of C∞-words throughan infinite directed acyclic graph G. This graph is defined by a map acting on the frontiers ofC∞-words. We show that this map can be defined recursively and with no explicit reference toC∞-words. We then show that some important conjectures on C∞-words follow from analogousstatements on the structure of the graph G.

Minimal Forbidden Factors of Circular Words

Minimal forbidden factors are a useful tool for investigating properties of words and languages. Two factorial languages are distinct if and only if they have different (antifactorial) sets of minimal forbidden factors. There exist algorithms for computing the minimal forbidden factors of a word, as well as of a regular factorial language. Conversely, Crochemore et al. [IPL, 1998] gave an algorithm that, given the trie recognizing a finite antifactorial language M, computes a DFA of the language having M as set of minimal forbidden factors. In the same paper, they showed that the obtained DFA is minimal if the input trie recognizes the minimal forbidden factors of a single word. We gener…

Normal, Abby Normal, Prefix Normal

A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present results about the number \(\textit{pnw}(n)\) of prefix normal words of length n, showing that \(\textit{pnw}(n) =\Omega\left(2^{n - c\sqrt{n\ln n}}\right)\) for some c and \(\textit{pnw}(n) = O \left(\frac{2^n (\ln n)^2}{n}\right)\). We introduce efficient algorithms for testing the prefix normal property and a “mechanical algorithm” for computing prefix normal forms. We also include games which can be played with prefix normal words. In these games Alice wishes t…

Primitive sets of words

Given a (finite or infinite) subset $X$ of the free monoid $A^*$ over a finite alphabet $A$, the rank of $X$ is the minimal cardinality of a set $F$ such that $X \subseteq F^*$. We say that a submonoid $M$ generated by $k$ elements of $A^*$ is {\em $k$-maximal} if there does not exist another submonoid generated by at most $k$ words containing $M$. We call a set $X \subseteq A^*$ {\em primitive} if it is the basis of a $|X|$-maximal submonoid. This definition encompasses the notion of primitive word -- in fact, $\{w\}$ is a primitive set if and only if $w$ is a primitive word. By definition, for any set $X$, there exists a primitive set $Y$ such that $X \subseteq Y^*$. We therefore call $Y$…

Bacteria classification using minimal absent words

Bacteria classification has been deeply investigated with different tools for many purposes, such as early diagnosis, metagenomics, phylogenetics. Classification methods based on ribosomal DNA sequences are considered a reference in this area. We present a new classificatier for bacteria species based on a dissimilarity measure of purely combinatorial nature. This measure is based on the notion of Minimal Absent Words, a combinatorial definition that recently found applications in bioinformatics. We can therefore incorporate this measure into a probabilistic neural network in order to classify bacteria species. Our approach is motivated by the fact that there is a vast literature on the com…

Splicing Systems from Past to Future: Old and New Challenges

A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing systems, introduced by P\u{a}un and subsequently developed by many researchers in both linear and circular case of splicing definition. In particular, we will present recent results on this topic and how they stimulate new challenging investigations.

Algorithms for Computing Abelian Periods of Words

Constantinescu and Ilie (Bulletin EATCS 89, 167--170, 2006) introduced the notion of an \emph{Abelian period} of a word. A word of length $n$ over an alphabet of size $\sigma$ can have $\Theta(n^{2})$ distinct Abelian periods. The Brute-Force algorithm computes all the Abelian periods of a word in time $O(n^2 \times \sigma)$ using $O(n \times \sigma)$ space. We present an off-line algorithm based on a $\sel$ function having the same worst-case theoretical complexity as the Brute-Force one, but outperforming it in practice. We then present on-line algorithms that also enable to compute all the Abelian periods of all the prefixes of $w$.

Words with the Maximum Number of Abelian Squares

An abelian square is the concatenation of two words that are anagrams of one another. A word of length n can contain \(\varTheta (n^2)\) distinct factors that are abelian squares. We study infinite words such that the number of abelian square factors of length n grows quadratically with n.

Vertical representation of C∞-words

We present a new framework for dealing with C ∞ -words, based on their left and right frontiers. This allows us to give a compact representation of them, and to describe the set of C ∞ -words through an infinite directed acyclic graph G. This graph is defined by a map acting on the frontiers of C ∞ -words. We show that this map can be defined recursively and with no explicit reference to C ∞ -words. We then show that some important conjectures on C ∞ -words follow from analogous statements on the structure of the graph G.