Related papers: All-Pairs Suffix-Prefix on Fully Dynamic Set of St…
Given a string $S$ over an alphabet $\Sigma$, the 'string indexing problem' is to preprocess $S$ to subsequently support efficient pattern matching queries, i.e., given a pattern string $P$ report all the occurrences of $P$ in $S$. In this…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
For a partial word $w$ the longest common compatible prefix of two positions $i,j$, denoted $lccp(i,j)$, is the largest $k$ such that $w[i,i+k-1]\uparrow w[j,j+k-1]$, where $\uparrow$ is the compatibility relation of partial words (it is…
We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…
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…
Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to…
A weighted string, also known as a position weight matrix, is a sequence of probability distributions over some alphabet. We revisit the Weighted Shortest Common Supersequence (WSCS) problem, introduced by Amir et al. [SPIRE 2011], that is,…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
We give a simple algorithm for the dynamic approximate All-Pairs Shortest Paths (APSP) problem. Given a graph $G = (V, E, l)$ with polynomially bounded edge lengths, our data structure processes $|E|$ edge insertions and deletions in total…
Given a directed weighted graph $G=(V,E)$ undergoing vertex insertions \emph{and} deletions, the All-Pairs Shortest Paths (APSP) problem asks to maintain a data structure that processes updates efficiently and returns after each update the…
Applications in domains ranging from bioinformatics to advertising feature strings that come with numerical scores (utilities). The utilities quantify the importance, interest, profit, or risk of the letters occurring at every position of a…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
Given a directed graph $G = (V,E)$, undergoing an online sequence of edge deletions with $m$ edges in the initial version of $G$ and $n = |V|$, we consider the problem of maintaining all-pairs shortest paths (APSP) in $G$. Whilst this…
Abelian string matching problems are becoming an object of considerable interest in last years. Very recently, Alatabbi et al. \cite{AILR2015} presented the first solution for the longest common Abelian factor problem for a pair of strings,…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
Stemming or suffix stripping, an important part of the modern Information Retrieval systems, is to find the root word (stem) out of a given cluster of words. Existing algorithms targeting this problem have been developed in a haphazard…
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…