Related papers: The Sequence Reconstruction of Permutations under …
Let $Q_{n}^{r}$ be the graph with vertex set $\{-1,1\}^{n}$ in which two vertices are joined if their Hamming distance is at most $r$. The edge-isoperimetric problem for $Q_{n}^{r}$ is that: For every $(n,r,M)$ such that $1\le r\le n$ and…
The two-colour Ramsey number $R(m,n)$ is the least natural number $p$ such that any graph of order $p$ must contain either a clique of size $m$ or an independent set of size $n$. We exhibit a method for computing upper bounds for $R(m,n)$…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
An $(n,k)$ sequence covering array is a set of permutations of $[n]$ such that each sequence of $k$ distinct elements of $[n]$ is a subsequence of at least one of the permutations. An $(n,k)$ sequence covering array is perfect if there is a…
Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…
Consider a random graph process with $n$ vertices corresponding to points $v_{i} \sim {Unif}[0,1]$ embedded randomly in the interval, and where edges are inserted between $v_{i}, v_{j}$ independently with probability given by the graphon…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Given $r\geq 3$ and $2^{r-1}+1\leq n< 2^{r}-1$, an $[n,n-r,3]$ shortened Hamming code that can detect a maximal number of double errors is constructed. The optimality of the construction is proven.
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
In this work, we consider the problem of synchronizing two sets of data where the size of the symmetric difference between the sets is small and, in addition, the elements in the symmetric difference are related through the Hamming distance…
This paper examines linear binary codes capable of correcting one or more errors. For the single-error-correcting case, it is shown that the Hamming bound is achieved by a constructive method, and an exact expression for the minimal…
The sequence a_1,...,a_m is a common subsequence in the set of permutations S = {p_1,...,p_k} on [n] if it is a subsequence of p_i(1),...,p_i(n) and p_j(1),...,p_j(n) for some distinct p_i, p_j in S. Recently, Beame and Huynh-Ngoc (2008)…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
An $(r, s)$-formation is a concatenation of $s$ permutations of $r$ letters. If $u$ is a sequence with $r$ distinct letters, then let $\mathit{Ex}(u, n)$ be the maximum length of any $r$-sparse sequence with $n$ distinct letters which has…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common…