Related papers: Some New Results on Sequence Reconstruction Proble…
Given a threshold $L$ and a set $\mathcal{R} = \{R_1, \ldots, R_m\}$ of $m$ haplotype sequences, each having length $n$, the minimum segmentation problem for founder reconstruction is to partition the sequences into disjoint segments…
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…
We consider the problem of recovering a signal consisting of a superposition of point sources from low-resolution data with a cut-off frequency f. If the distance between the sources is under 1/f, this problem is not well posed in the sense…
The fixed length Levenshtein (FLL) distance between two words $\mathbf{x,y} \in \mathbb{Z}_m^n$ is the smallest integer $t$ such that $\mathbf{x}$ can be transformed to $\mathbf{y}$ by $t$ insertions and $t$ deletions. The size of a ball in…
In parametric sequence alignment, optimal alignments of two sequences are computed as a function of the penalties for mismatches and spaces, producing many different optimal alignments. Here we give a 3/(2^{7/3}\pi^{2/3})n^{2/3} +O(n^{1/3}…
In this work we consider the problem of computing the $(\min, +)$-convolution of two sequences $a$ and $b$ of lengths $n$ and $m$, respectively, where $n \geq m$. We assume that $a$ is arbitrary, but $b_i = f(i)$, where $f(x) \colon [0,m)…
The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction,…
What is the smallest number of pieces that you can cut an n-sided regular polygon into so that the pieces can be rearranged to form a rectangle? Call it r(n). The rectangle may have any proportions you wish, as long as it is a rectangle.…
The problem of computing the cardinality of the intersection of multiple balls in the Hamming space has attracted a lot of attention recently due to their applications in the list reconstruction problem and information retrieval in…
We introduce a new class of problems lying halfway between questions about graph capacity and intersection. We say that two binary sequences x and y of the same length have a skewincidence if there is a coordinate i for which x_i=y_{i+1}=1…
In this paper, we investigate binary reconstruction codes capable of correcting one deletion and one substitution. We define the \emph{single-deletion single-substitution ball} function $ \mathcal{B} $ as a mapping from a sequence to the…
We study the problem of constructing sequences $(x_n)_{n=1}^{\infty}$ on $[0,1]$ in such a way that $$ D_N^* = \sup_{0 \leq x \leq 1} \left| \frac{ \left\{1 \leq i \leq N: x_i \leq x \right\}}{N} - x \right|$$ is uniformly small. A result…
String similarity, longest common subsequence and shortest edit scripts are the triplets of problem that related to each other. There are different algorithms exist to generate edit script by solving longest common subsequence problem. This…
In the longest common substring problem, we are given two strings of length $n$ and must find a substring of maximal length that occurs in both strings. It is well known that the problem can be solved in linear time, but the solution is not…
The tableau reconstruction problem, posed by Monks (2009), asks the following. Starting with a standard Young tableau $T$, a 1-minor of $T$ is a tableau obtained by first deleting any cell of $T$, and then performing jeu de taquin slides to…
Let C be a linear code with length n and minimum distance d. The stopping redundancy of C is defined as the minimum number of rows in a parity-check matrix for C such that the smallest stopping sets in the corresponding Tanner graph have…
Given an image generated by the convolution of point sources with a band-limited function, the deconvolution problem is to reconstruct the source number, positions, and amplitudes. This problem arises from many important applications in…
We describe computer searches that prove the graph reconstruction conjecture for graphs with up to 13 vertices and some limited classes on larger sizes. We also investigate the reconstructibility of tournaments up to 13 vertices, digraphs…
The construction of deletion codes for the Levenshtein metric is reduced to the construction of codes over the integers for the Manhattan metric by run length coding. The latter codes are constructed by expurgation of translates of…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…