arXiv subjects

Giuseppa Castiglione

Publications and source records attributed to Giuseppa Castiglione.

7 recordsLinked to original sources

arXiv2025

Universally Wheeler Languages

The notion of Wheeler languages is rooted in the Burrows-Wheeler transform (BWT), one of the most central concepts in data compression and indexing. The BWT has been generalized to finite automata, the so-called Wheeler automata, by Gagie et al. [Theor. Comput. Sci. 2017]. Wheeler languages have subsequently been defined as the class of regular languages for which there exists a Wheeler automaton accepting them. Besides their advantages in data indexing, these Wheelerlanguages also satisfy many interesting properties from a language theoretic point of view [Alanko et al., Inf. Comput. 2021]. A characteristic yet unsatisfying feature of Wheeler languages however is that their definition depends on a fixed order of the alphabet. In this paper we introduce the Universally Wheeler languages UW, i.e., the regular languages that are Wheeler with respect to all orders of a given alphabet. Our first main contribution is to relate UW to some very well known regular language classes. We first show that the Striclty Locally Testable languages are strictly included in UW. After noticing that UW is not closed under taking the complement, we prove that the class of languages for which both the language and its complement are in UW exactly coincides with those languages that are Definite or Reverse Definite. Secondly, we prove that deciding if a regular language given by a DFA is in UW can be done in quadratic time. We also show that this is optimal unless the Strong Exponential Time Hypothesis (SETH) fails.

cs.FL↗

arXiv2023

Hypercubes and Isometric Words based on Swap and Mismatch Distance

The hypercube of dimension n is the graph whose vertices are the 2^n binary words of length n, and there is an edge between two of them if they have Hamming distance 1. We consider an edit distance based on swaps and mismatches, to which we refer as tilde-distance, and define the tilde-hypercube with edges linking words at tilde-distance 1. Then, we introduce and study some isometric subgraphs of the tilde-hypercube obtained by using special words called tilde-isometric words. The subgraphs keep only the vertices that avoid a given tilde-isometric word as a factor. In the case of word 11, the subgraph is called tilde-Fibonacci cube, as a generalization of the classical Fibonacci cube. The tilde-hypercube and the tilde-Fibonacci cube can be recursively defined; the same holds for the number of their edges. This allows an asymptotic estimation of the number of edges in the tilde-Fibonacci cube, in comparison to the total number in the tilde-hypercube.

math.CO↗

arXiv2023

Isometric Words based on Swap and Mismatch Distance

An edit distance is a metric between words that quantifies how two words differ by counting the number of edit operations needed to transform one word into the other one. A word f is said isometric with respect to an edit distance if, for any pair of f-free words u and v, there exists a transformation of minimal length from u to v via the related edit operations such that all the intermediate words are also f-free. The adjective 'isometric' comes from the fact that, if the Hamming distance is considered (i.e., only mismatches), then isometric words are connected with definitions of isometric subgraphs of hypercubes. We consider the case of edit distance with swap and mismatch. We compare it with the case of mismatch only and prove some properties of isometric words that are related to particular features of their overlaps.

cs.FL↗

arXiv2021

A new distance based on minimal absent words and applications to biological sequences

A minimal absent word of a sequence x, is a sequence yt hat is not a factorof x, but all of its proper factors are factors of x as well. The set of minimal absent words uniquely defines the sequence itself. In recent times minimal absent words have been used in order to compare sequences. In fact, to do this, one can compare the sets of their minimal absent words. Chairungasee and Crochemorein [2] define a distance between pairs of sequences x and y, where the symmetric difference of the sets of minimal absent words of x and y is involved. Here, weconsider a different distance, introduced in [1], based on a specific subset of such symmetric difference that, in our opinion, better capture the different features ofthe considered sequences. We show the result of some experiments where the distance is tested on a dataset of genetic sequences by 11 living species, in order to compare the new distance with the ones existing in literature.

cs.FL↗

arXiv2020

The Intersection of $3$-Maximal Submonids

Very little is known about the structure of the intersection of two $k$-generated monoids of words, even for $k=3$. Here we investigate the case of $k$-maximal monoids, that is, monoids whose basis of cardinality $k$ cannot be non-trivially decomposed into at most $k$ words. We characterize the intersection in the case of two $3$-maximal monoids.

cs.FL↗

arXiv2020

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 $Y$ a {\em primitive root} of $X$. As a main result, we prove that if a set has rank $2$, then it has a unique primitive root. To obtain this result, we prove that the intersection of two $2$-maximal submonoids is either the empty word or a submonoid generated by one single primitive word. For a single word $w$, we say that the set $\{x,y\}$ is a {\em bi-root} of $w$ if $w$ can be written as a concatenation of copies of $x$ and $y$ and $\{x,y\}$ is a primitive set. We prove that every primitive word $w$ has at most one bi-root $\{x,y\}$ such that $|x|+|y|<\sqrt{|w|}$. That is, the bi-root of a word is unique provided the word is sufficiently long with respect to the size (sum of lengths) of the root. Our results are also compared to previous approaches that investigate pseudo-repetitions, where a morphic involutive function $θ$ is defined on $A^*$. In this setting, the notions of $θ$-power, $θ$-primitive and $θ$-root are defined, and it is shown that any word has a unique $θ$-primitive root. This result can be obtained with our approach by showing that a word $w$ is $θ$-primitive if and only if $\{w, θ(w)\}$ is a primitive set.

cs.FL↗

arXiv2019

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 $X \subseteq F^*$. 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 $X \subseteq A^*$ 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 $X \subseteq Y^*$. 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 root. This result cannot be extended to sets of rank larger than 2. For a single word $w$, we say that the set $\{x,y\}$ is a {\em binary root} of $w$ if $w$ can be written as a concatenation of copies of $x$ and $y$ and $\{x,y\}$ is a primitive set. We prove that every primitive word $w$ has at most one binary root $\{x,y\}$ such that $|x|+|y|<\sqrt{|w|}$. That is, the binary root of a word is unique provided the length of the word is sufficiently large with respect to the size of the root. Our results are also compared to previous approaches that investigate pseudo-repetitions, where a morphic involutive function $θ$ is defined on $A^*$. In this setting, the notions of $θ$-power, $θ$-primitive and $θ$-root are defined, and it is shown that any word has a unique $θ$-primitive root. This result can be obtained with our approach by showing that a word $w$ is $θ$-primitive if and only if $\{w, θ(w)\}$ is a primitive set.

cs.FL↗