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We study the impact that string reversal can have on several repetitiveness measures. First, we exhibit an infinite family of strings where the number, $r$, of runs in the run-length encoding of the Burrows--Wheeler transform (BWT) can…
Given integers $k\geq 2$ and $a_1,\ldots,a_k\geq 1$, let $\boldsymbol{a}:=(a_1,\ldots,a_k)$ and $n:=a_1+\cdots+a_k$. An $\boldsymbol{a}$-multiset permutation is a string of length $n$ that contains exactly $a_i$ symbols $i$ for each…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
Codes over trees were introduced recently to bridge graph theory and coding theory with diverse applications in computer science and beyond. A central challenge lies in determining the maximum number of labelled trees over $n$ nodes with…
We continue the study of Adin, Alon and Roichman [arXiv:2502.14398, 2025] on the number of steps required to sort $n$ labelled points on a circle by transpositions. Imagine that the vertices of a cycle of length $n$ are labelled by the…
We consider $q$-ary (linear and nonlinear) block codes with exactly two distances: $d$ and $d+\delta$. Several combinatorial constructions of optimal such codes are given. In the linear (but not necessary projective) case, we prove that…
We prove that there exists an absolute constant $\delta>0$ such any binary code $C\subset\{0,1\}^N$ tolerating $(1/2-\delta)N$ adversarial deletions must satisfy $|C|\le 2^{\text{poly}\log N}$ and thus have rate asymptotically approaching…
In graph theory, a tree is one of the more popular families of graphs with a wide range of applications in computer science as well as many other related fields. While there are several distance measures over the set of all trees, we…
Due to the wide applications in consumer electronics, data storage systems and communication systems, cyclic codes have been an interesting research topic in coding theory. In this paper, let $p$ be a prime with $p\ge 7$. We determine the…
We study the problem of identifying an n-bit string using a single quantum query to an oracle that computes the Hamming distance between the query and hidden strings. The standard action of the oracle on a response register of dimension r…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
A number of fields, including the study of genome rearrangements and the design of interconnection networks, deal with the connected problems of sorting permutations in "as few moves as possible", using a given set of allowed operations, or…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
Given a generator set $S$ of the symmetric group ${\rm{Sym}}_n$, every permutation $\pi\in {\rm{Sym}_n}$ is a word (product of elements) of $S$. A positive integer $d(\pi)$ is associated with each $\pi\in{\rm{Sym}_n}$ taking the length of…
In this paper, we present and study the \emph{Hamming distance oracle problem}. In this problem, the task is to preprocess two strings $S$ and $T$ of lengths $n$ and $m$, respectively, to obtain a data-structure that is able to answer…
Edit distance similarity search, also called approximate pattern matching, is a fundamental problem with widespread database applications. The goal of the problem is to preprocess $n$ strings of length $d$, to quickly answer queries $q$ of…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
Constructions of quantum MDS codes have been studied by many authors. We refer to the table in page 1482 of [3] for known constructions. However there are only few $q$-ary quantum MDS $[[n,n-2d+2,d]]_q$ codes with minimum distances…
Let $A_2(n,d)$ be the maximum size of a binary code of length $n$ and minimum distance $d$. In this paper we present the following new lower bounds: $A_2(18,4) \ge 5632$, $A_2(21,4) \ge 40960$, $A_2(22,4) \ge 81920$, $A_2(23,4) \ge 163840$,…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…