Related papers: Computing Matching Statistics on Repetitive Texts
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 introduce the first self-index based on the Lempel-Ziv 1977 compression format (LZ77). It is particularly competitive for highly repetitive text collections such as sequence databases of genomes of related species, software repositories,…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
Given a string $P$ of length $m$, a longer string $T$ of length $n>m$, and two integers $l\geq 0$ and $r\geq 0$, the context of $P$ in $T$ is the set of all string pairs $(L,R)$, with $|L|=l$ and $|R|=r$, such that the string $LPR$ occurs…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
Fast matching of regular expressions with bounded repetition, aka counting, such as (ab){50,100}, i.e., matching linear in the length of the text and independent of the repetition bounds, has been an open problem for at least two decades.…
Computing the LZ factorization (or LZ77 parsing) of a string is a computational bottleneck in many diverse applications, including data compression, text indexing, and pattern discovery. We describe new linear time LZ factorization…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
We consider several types of internal queries, that is, questions about fragments of a given text $T$ specified in constant space by their locations in $T$. Our main result is an optimal data structure for Internal Pattern Matching (IPM)…
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…
Domains like bioinformatics, version control systems, collaborative editing systems (wiki), and others, are producing huge data collections that are very repetitive. That is, there are few differences between the elements of the collection.…
At the present scenario of the internet, there exist many optimization techniques to improve the Web speed but almost expensive in terms of bandwidth. So after a long investigation on different techniques to compress the data without any…
We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…
In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
We investigate the performance of large language models on repetitive deterministic prediction tasks and study how the sequence accuracy rate scales with output length. Each such task involves repeating the same operation n times. Examples…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…