Related papers: Duplication with transposition distance to the roo…
The discrepancy of a binary string refers to the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. We provide an investigation of the discrepancy of…
We investigate the longest common substring problem for encoded sequences and its asymptotic behaviour. The main result is a strong law of large numbers for a re-scaled version of this quantity, which presents an explicit relation with the…
A family of distance-optimal LRC codes from certain subcodes of $q$-ary Reed-Solomon codes, proposed by I.~Tamo and A.~Barg in 2014, assumes that the code length $n$ is a multiple of $r+1.$ By shortening codes from this family, we show that…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
According to the AdS/CFT correspondence, the maximally supersymmetric SU(N) Yang-Mills theory in 4 dimensions is dual to the type IIB string theory compactified on AdS_5 x S^5. Most of the tests performed so far are confined to the leading…
Let $S_n$ and $S_{n,k}$ be, respectively, the number of subsets and $k$-subsets of $\mathbb{N}_n=\{1,\ldots,n\}$ such that no two subset elements differ by an element of the set $\mathcal{Q}$, the largest element of which is $q$. We prove a…
Recently, it was discovered by several authors that a $q$-ary optimal locally recoverable code, i.e., a locally recoverable code archiving the Singleton-type bound, can have length much bigger than $q+1$. This is quite different from the…
The decomposition of a quasi-abelian code into shorter linear codes over larger alphabets was given in (Jitman, Ling, (2015)), extending the analogous Chinese remainder decomposition of quasi-cyclic codes (Ling, Sol\'e, (2001)). We give a…
A quasi-Gray code of dimension $n$ and length $\ell$ over an alphabet $\Sigma$ is a sequence of distinct words $w_1,w_2,\dots,w_\ell$ from $\Sigma^n$ such that any two consecutive words differ in at most $c$ coordinates, for some fixed…
Alice and Bob want to know if two strings of length n are almost equal. That is, do they differ on \textit{at most} a bits? Let 0\leq a\leq n-1. We show that any deterministic protocol, as well as any error-free quantum protocol (C*…
Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the…
Like classical block codes, a locally repairable code also obeys the Singleton-type bound (we call a locally repairable code {\it optimal} if it achieves the Singleton-type bound). In the breakthrough work of \cite{TB14}, several classes of…
In this paper we present two algorithms for the following problem: given a string and a rational $e > 1$, detect in the online fashion the earliest occurrence of a repetition of exponent $\ge e$ in the string. 1. The first algorithm…
We present an algorithm for approximating the edit distance $\operatorname{ed}(x, y)$ between two strings $x$ and $y$ in time parameterized by the degree to which one of the strings $x$ satisfies a natural pseudorandomness property. The…
We consider the problem of determining the maximum number of moves required to sort a permutation of $[n]$ using cut-and-paste operations, in which a segment is cut out and then pasted into the remaining string, possibly reversed. We give…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
We propose smooth $q$-gram, the first variant of $q$-gram that captures $q$-gram pair within a small edit distance. We apply smooth $q$-gram to the problem of detecting overlapping pairs of error-prone reads produced by single molecule real…
A linear code with parameters $[n, k, n - k + 1]$ is called maximum distance separable (MDS), and one with parameters $[n, k, n - k]$ is called almost MDS (AMDS). A code is near-MDS (NMDS) if both it and its dual are AMDS. NMDS codes…
A recent study by one of the authors has demonstrated the importance of profile vectors in DNA-based data storage. We provide exact values and lower bounds on the number of profile vectors for finite values of alphabet size $q$, read length…