Related papers: The Gapped $k$-Deck Problem

Given a random binary picture $P_n$ of size $n$, i.e., an $n\times n$ grid filled with zeros and ones uniformly at random, when is it possible to reconstruct $P_n$ from its $k$-deck, i.e., the multiset of all its $k\times k$ subgrids? We…

A Dyck sequence is a sequence of opening and closing parentheses (of various types) that is balanced. The Dyck edit distance of a given sequence of parentheses $S$ is the smallest number of edit operations (insertions, deletions, and…

The longest common substring with $k$-mismatches problem is to find, given two strings $S_1$ and $S_2$, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance between $A_1$ and $A_2$ is $\le k$. We introduce a…

Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…

The densest $k$-subgraph problem is the problem of finding a $k$-vertex subgraph of a graph with the maximum number of edges. In order to solve large instances of the densest $k$-subgraph problem, we introduce two algorithms that are based…

Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…

We examine the open problem of finding the shortest string that contains each of the n! permutations of n symbols as contiguous substrings (i.e., the shortest superpermutation on n symbols). It has been conjectured that the shortest…

String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…

The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…

A modified $k$-deck of a graph is obtained by removing $k$ edges in all possible ways and adding $k$ (not necessarily new) edges in all possible ways. Krasikov and Roditty used these decks to give an independent proof of M\"uller's result…

We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…

String attractors [STOC 2018] are combinatorial objects recently introduced to unify all known dictionary compression techniques in a single theory. A set $\Gamma\subseteq [1..n]$ is a $k$-attractor for a string $S\in[1..\sigma]^n$ if and…

The edge geodesic cover problem of a graph $G$ is to find a smallest number of geodesics that cover the edge set of $G$. The edge $k$-general position problem is introduced as the problem to find a largest set $S$ of edges of $G$ such that…

For a set of positive integers $D$, a $k$-term $D$-diffsequence is a sequence of positive integers $a_1<a_2<\cdots<a_k$ such that $a_i-a_{i-1}\in D$ for $i=2,3,\cdots,k$. For $k\in\mathbb{Z}^+$ and $D\subset \mathbb{Z}^+$, we define…

We consider subsequences with gap constraints, i.e., length-k subsequences p that can be embedded into a string w such that the induced gaps (i.e., the factors of w between the positions to which p is mapped to) satisfy given gap…

Given an action of a group $G$ on a set $S$, the $k$-deck of a subset $T$ of $S$ is the multiset of all subsets of $T$ of size $k$, each given up to translation by $G$. For a given subset $T$, the {\em reconstruction number} of $T$ is the…

In the Manhattan Sequence Consensus problem (MSC problem) we are given $k$ integer sequences, each of length $l$, and we are to find an integer sequence $x$ of length $l$ (called a consensus sequence), such that the maximum Manhattan…

The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…

The subgraph-subgraph matching problem is, given a pair of graphs and a positive integer $K$, to find $K$ vertices in the first graph, $K$ vertices in the second graph, and a bijection between them, so as to minimize the number of adjacency…

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…