Related papers: Computing Matching Statistics on Repetitive Texts
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
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…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
Annotating large collections of textual data can be time consuming and expensive. That is why the ability to train models with limited annotation budgets is of great importance. In this context, it has been shown that under tight annotation…
We introduce a data structure for counting pattern occurrences in texts compressed with any run-length context-free grammar. Our structure uses space proportional to the grammar size and counts the occurrences of a pattern of length $m$ in…
Search techniques make use of elementary information such as term frequencies and document lengths in computation of similarity weighting. They can also exploit richer statistics, in particular the number of documents in which any two terms…
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 size of the \textit{smallest suffixient set} of positions of a string recently emerged as a new measure of string \textit{repetitiveness} -- a measure reflecting how much of repetitive content the string contains. We study how to…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
The diversity across outputs generated by LLMs shapes perception of their quality and utility. High lexical diversity is often desirable, but there is no standard method to measure this property. Templated answer structures and ``canned''…
We address the problem of counting the number of strings in a collection where a given pattern appears, which has applications in information retrieval and data mining. Existing solutions are in a theoretical stage. We implement these…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
In the Dictionary-based String Matching (DSM) problem, a retrieval system has access to a source sequence and stores the position of a certain number of strings in a posting table. When a user inquires the position of a string, the…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…