Related papers: The Sequence Reconstruction of Permutations under …
A hamiltonian sequence is a path walk $P$ that can be a hamiltonian path or hamiltonian circuit. Determining whether such hamiltonian sequence exists in a given graph \G is a NP-Complete problem. In this paper, a novel algorithm for…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
A set of $N$ permutations of $\{1,2,\dots,v\}$ is $(N,v,t)$-suitable if each symbol precedes each subset of $t-1$ others in at least one permutation. The central problems are to determine the smallest $N$ for which such a set exists for…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
We study the maximum multiplicity $\mathcal{M}(k,n)$ of a simple transposition $s_k=(k \: k+1)$ in a reduced word for the longest permutation $w_0=n \: n-1 \: \cdots \: 2 \: 1$, a problem closely related to much previous work on sorting…
In the decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), the task is to list the $k$-error occurrences of $P$ in…
Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…
We consider locally recoverable codes (LRCs) and aim to determine the smallest possible length $n=n_q(k,d,r)$ of a linear $[n,k,d]_q$-code with locality $r$. For $k\le 7$ we exactly determine all values of $n_2(k,d,2)$ and for $k\le 6$ we…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Let $\mathcal{B}(\cdot)$ be an error ball function. A set of $q$-ary sequences of length $n$ is referred to as an \emph{$(n,q,N;\mathcal{B})$-reconstruction code} if each sequence $\boldsymbol{x}$ within this set can be uniquely…
Sum-rank Hamming codes are introduced in this work. They are essentially defined as the longest codes (thus of highest information rate) with minimum sum-rank distance at least $ 3 $ (thus one-error-correcting) for a fixed redundancy $ r $,…
A general explicit upper bound is obtained for the proportion $P(n,m)$ of elements of order dividing $m$, where $n-1 \le m \le cn$ for some constant $c$, in the finite symmetric group $S_n$. This is used to find lower bounds for the…
In the beautifully simple-to-state problem of trace reconstruction, the goal is to reconstruct an unknown binary string $x$ given random "traces" of $x$ where each trace is generated by deleting each coordinate of $x$ independently with…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
We study sorting of permutations by random swaps if each comparison gives the wrong result with some fixed probability $p<1/2$. We use this process as prototype for the behaviour of randomized, comparison-based optimization heuristics in…
We introduce alphabet-permutation (AP) codes, a new family of error-correcting codes defined by iteratively applying random coordinate-wise permutations to a fixed initial word. A special case recovers random additive codes and random…
For positive integers $n,r,s$ with $r > s$, the set-coloring Ramsey number $R(n;r,s)$ is the minimum $N$ such that if every edge of the complete graph $K_N$ receives a set of $s$ colors from a palette of $r$ colors, then there is guaranteed…
Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…
We study the classic Text-to-Pattern Hamming Distances problem: given a pattern $P$ of length $m$ and a text $T$ of length $n$, both over a polynomial-size alphabet, compute the Hamming distance between $P$ and $T[i\, .\, . \, i+m-1]$ for…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…