Related papers: Parameterized Complexity of Superstring Problems
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
Let $S$ be a string of length $n$. In this paper we introduce the notion of \emph{string attractor}: a subset of the string's positions $[1,n]$ such that every distinct substring of $S$ has an occurrence crossing one of the attractor's…
We study sketching and streaming algorithms for the Longest Common Subsequence problem (LCS) on strings of small alphabet size $|\Sigma|$. For the problem of deciding whether the LCS of strings $x,y$ has length at least $L$, we obtain a…
We study the Short Path Packing problem which asks, given a graph $G$, integers $k$ and $\ell$, and vertices $s$ and $t$, whether there exist $k$ pairwise internally vertex-disjoint $s$-$t$ paths of length at most $\ell$. The problem has…
In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…
We introduce a new technique for proving kernelization lower bounds, called cross-composition. A classical problem L cross-composes into a parameterized problem Q if an instance of Q with polynomially bounded parameter value can express the…
The NP-hard Minimum Common String Partition problem asks whether two strings $x$ and $y$ can each be partitioned into at most $k$ substrings, called blocks, such that both partitions use exactly the same blocks in a different order. We…
The Unbounded Subset-Sum Problem (USSP) is defined as: given sum $s$ and a set of integers $W\leftarrow \{p_1,\dots,p_n\}$ output a set of non-negative integers $\{y_1,\dots,y_n\}$ such that $p_1y_1+\dots+p_ny_n=s$. The USSP is an…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
In the {\sc Test Cover} problem we are given a hypergraph $H=(V, \mathcal{E})$ with $|V|=n, |\mathcal{E}|=m$, and we assume that $\mathcal{E}$ is a test cover, i.e. for every pair of vertices $x_i, x_j$, there exists an edge $e \in…
We investigate the parameterized complexity of Vertex Cover parameterized by the difference between the size of the optimal solution and the value of the linear programming (LP) relaxation of the problem. By carefully analyzing the change…
We investigate whether an n-vertex instance (G,k) of Treewidth, asking whether the graph G has treewidth at most k, can efficiently be made sparse without changing its answer. By giving a special form of OR-cross-composition, we prove that…
The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized…
A border of a string is a non-empty proper prefix of the string that is also a suffix. A string is unbordered if it has no border. The longest unbordered factor is a fundamental notion in stringology, closely related to string periodicity.…
Bin Packing with $k$ bins is a fundamental optimisation problem in which we are given a set of $n$ integers and a capacity $T$ and the goal is to partition the set into $k$ subsets, each of total sum at most $T$. Bin Packing is NP-hard…
This paper investigates the complexity of finding secluded paths in graphs. We focus on the \textsc{Short Secluded Path} problem and a natural new variant we introduce, \textsc{Shortest Secluded Path}. Formally, given an undirected graph…
For any $\ell > 0$, we present an algorithm which takes as input a semi-algebraic set, $S$, defined by $P_1 \leq 0,...,P_s \leq 0$, where each $P_i \in \R[X_1,...,X_k]$ has degree $\leq 2,$ and computes the top $\ell$ Betti numbers of $S$,…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…