Related papers: String Attractors
Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…
Inspired by artistic practices such as beadwork and himmeli, we study the problem of threading a single string through a set of tubes, so that pulling the string forms a desired graph. More precisely, given a connected graph (where edges…
We study the concept of \emph{compactor}, which may be seen as a counting-analogue of kernelization in counting parameterized complexity. For a function $F:\Sigma^*\to \Bbb{N}$ and a parameterization $\kappa: \Sigma^*\to \Bbb{N}$, a…
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…
Traditionally, data compression deals with the problem of concisely representing a data source, e.g. a sequence of letters, for the purpose of eventual reproduction (either exact or approximate). In this work we are interested in the case…
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…
A maximal repetition, or run, in a string, is a maximal periodic substring whose smallest period is at most half the length of the substring. In this paper, we consider runs that correspond to a path on a trie, or in other words, on a…
The basic problem of semantic compression is to minimize the length of a message while preserving its meaning. This differs from classical notions of compression in that the distortion is not measured directly at the level of bits, but…
Shannon's entropy is a clear lower bound for statistical compression. The situation is not so well understood for dictionary-based compression. A plausible lower bound is $b$, the least number of phrases of a general bidirectional parse of…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
In this paper, we describe minimal string attractors (of size two) of pseudopalindromic prefixes of standard complementary-symmetric Rote sequences. Such a class of Rote sequences forms a subclass of binary generalized pseudostandard…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
String-averaging is an algorithmic structure used when handling a family of operators in situations where the algorithm at hand requires to employ the operators in a specific order. Sequential orderings are well-known and a simultaneous…
Minimizers are sampling schemes with numerous applications in computational biology. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a linear order $\rho$ on strings of length $k$ (also…
Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…
We introduce the problem of computing a parsing where each phrase is of length at most $m$ and which minimizes the zeroth order entropy of parsing. Based on the recent theoretical results we devise a heuristic for this problem. The solution…
The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…
Tensor network contraction is central to problems ranging from many-body physics to computer science. We describe how to approximate tensor network contraction through bond compression on arbitrary graphs. In particular, we introduce a…