Related papers: Sequence Searching Allowing for Non-Overlapping Ad…
The index coding problem is concerned with broadcasting encoded information to a collection of receivers in a way that enables each receiver to discover its required data based on its side information, which comprises the data required by…
Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
We present a sorting algorithm for the case of recurrent random comparison errors. The algorithm essentially achieves simultaneously good properties of previous algorithms for sorting $n$ distinct elements in this model. In particular, it…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
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…
We consider the problem of finding \textit{semi-matching} in bipartite graphs which is also extensively studied under various names in the scheduling literature. We give faster algorithms for both weighted and unweighted case. For the…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
Submodular maximization is a general optimization problem with a wide range of applications in machine learning (e.g., active learning, clustering, and feature selection). In large-scale optimization, the parallel running time of an…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…
In the String Matching in Labeled Graphs (SMLG) problem, we need to determine whether a pattern string appears on a given labeled graph or a given automaton. Under the Orthogonal Vectors hypothesis, the SMLG problem cannot be solved in…
We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
The problem of determining the correct order of fluctuation of the optimal alignment score of two random strings of length $n$ has been open for several decades. It is known that the biased expected effect of a random letter-change on the…
Encoding data structures store enough information to answer the queries they are meant to support but not enough to recover their underlying datasets. In this paper we give the first encoding data structure for the challenging problem of…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…