Related papers: Theta palindromes in theta conjugates

We introduce two classes of morphisms over the alphabet $A=\{0,1\}$ whose fixed points contain infinitely many antipalindromic factors. An antipalindrome is a finite word invariant under the action of the antimorphism…

Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement…

Given a set $F$ of words, one associates to each word $w$ in $F$ an undirected graph, called its extension graph, and which describes the possible extensions of $w$ on the left and on the right. We investigate the family of sets of words…

Watson-Crick (WK) finite automata work on a Watson-Crick tape representing a DNA molecule. They have two reading heads. In 5'->3' WK automata, the heads move and read the input in opposite physical directions. In this paper, we consider…

This paper focuses on Watson-Crick languages inspired by DNA computing, their models, and algorithms for deciding the language membership. It analyzes a recently introduced algorithm called WK-CYK and introduces a state space search…

Watson-Crick automata are finite automata working on double strands. Extensive research work has already been done on non-deterministic Watson-Crick automata and on deterministic Watson-Crick automata. In this paper, we introduce a new…

A word $u$ is a scattered factor of $w$ if $u$ can be obtained from $w$ by deleting some of its letters. That is, there exist the (potentially empty) words $u_1,u_2,..., u_n$, and $v_0,v_1,..,v_n$ such that $u = u_1u_2...u_n$ and $w =…

This paper gives a definitive solution to the problem of describing conjugacy classes in arbitrary Coxeter groups in terms of cyclic shifts. Let $(W,S)$ be a Coxeter system. A cyclic shift of an element $w\in W$ is a conjugate of $w$ of the…

Recently, a new characterization of Lyndon words that are also perfectly clustering was proposed by Lapointe and Reutenauer (2024). A word over a ternary alphabet {a,b,c} is called perfectly clustering Lyndon if and only if it is the…

Inspired by multi-head finite automata and Watson-Crick automata in this paper, we introduce new structure namely multi-head Watson-Crick automata where we replace the single tape of multi-head finite automaton by a DNA double strand. The…

Let A be a finite or countable alphabet and let $\theta$ be a literal (anti-)automorphism onto A * (by definition, such a correspondence is determinated by a permutation of the alphabet). This paper deals with sets which are invariant under…

We characterize words which cluster under the Burrows-Wheeler transform as those words $w$ such that $ww$ occurs in a trajectory of an interval exchange transformation, and build examples of clustering words.

A word $u=u_1\dots u_n$ is a scattered factor of a word $w$ if $u$ can be obtained from $w$ by deleting some of its letters: there exist the (potentially empty) words $v_0,v_1,..,v_n$ such that $w = v_0u_1v_1...u_nv_n$. The set of all…

The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…

In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…

We study a new generalization of palindromes and gapped palindromes called block palindromes. A block palindrome is a string that becomes a palindrome when identical substrings are replaced with a distinct character. We investigate several…

This paper contributes to a programme initiated by the first author: `How much information about a graph is revealed in its Potts partition function?'. We show that the $W$-polynomial distinguishes non-isomorphic weighted trees of a…

We study the self-organization of the consonant inventories through a complex network approach. We observe that the distribution of occurrence as well as cooccurrence of the consonants across languages follow a power-law behavior. The…

In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions.…

Models such as Word2Vec and GloVe construct word embeddings based on the co-occurrence probability $P(i,j)$ of words $i$ and $j$ in text corpora. The resulting vectors $W_i$ not only group semantically similar words but also exhibit a…