相关论文: Parameterized Intractability of Motif Search Probl…
We prove that there is no fpt-algorithm that can approximate the dominating set problem with any constant ratio, unless FPT= W[1]. Our hardness reduction is built on the second author's recent W[1]-hardness proof of the biclique problem.…
We revisit the complexity of the classical $k$-Coloring problem parameterized by clique-width. This is a very well-studied problem that becomes highly intractable when the number of colors $k$ is large. However, much less is known on its…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
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…
In this paper we study the problem of finding a small safe set $S$ in a graph $G$, i.e. a non-empty set of vertices such that no connected component of $G[S]$ is adjacent to a larger component in $G - S$. We enhance our understanding of the…
Recently a strong connection has been shown between the tractability of integer programming (IP) with bounded coefficients on the one side and the structure of its constraint matrix on the other side. To that end, integer linear programming…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
We first give an $\O(2^{n/3})$ quantum algorithm for the 0-1 Knapsack problem with $n$ variables. More generally, for 0-1 Integer Linear Programs with $n$ variables and $d$ inequalities we give an $\O(2^{n/3}n^d)$ quantum algorithm. For $d…
We consider the problem of determining, given x, y in Z^k and a finite set F of affine functions on Z^k, whether y is reachable from x by applying the functions F. We also consider the analogous problem over N^k. These problems are known to…
Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
We classify the complexity of the LTL satisfiability and model checking problems for several standard parameterisations. The investigated parameters are temporal depth, number of propositional variables and formula treewidth, resp.,…
It is well known that sparse approximation problem is \textsf{NP}-hard under general dictionaries. Several algorithms have been devised and analyzed in the past decade under various assumptions on the \emph{coherence} $\mu$ of the…
We propose a quantum algorithm for closest pattern matching which allows us to search for as many distinct patterns as we wish in a given string (database), requiring a query function per symbol of the pattern alphabet. This represents a…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
Given a string $w$ over a finite alphabet $\Sigma$ and an integer $K$, can $w$ be partitioned into strings of length at most $K$, such that there are no \emph{collisions}? We refer to this question as the \emph{string partition} problem and…
Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…