Related papers: Compressed Indexing for Consecutive Occurrences
The Parikh vector p(s) of a string s is defined as the vector of multiplicities of the characters. Parikh vector q occurs in s if s has a substring t with p(t)=q. We present two novel algorithms for searching for a query q in a text s. One…
Indexing is an effective way to support efficient query processing in large databases. Recently the concept of learned index, which replaces or complements traditional index structures with machine learning models, has been actively…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
For analysing text algorithms, for computing superstrings, or for testing random number generators, one needs to compute all overlaps between any pairs of words in a given set. The positions of overlaps of a word onto itself, or of two…
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…
Finding the common subsequences of $L$ multiple strings has many applications in the area of bioinformatics, computational linguistics, and information retrieval. A well-known result states that finding a Longest Common Subsequence (LCS)…
Zimin words are very special finite words which are closely related to the pattern-avoidability problem. This problem consists in testing if an instance of a given pattern with variables occurs in almost all words over any finite alphabet.…
While several self-indexes for highly repetitive texts exist, developing a practical self-index applicable to real world repetitive texts remains a challenge. ESP-index is a grammar-based self-index on the notion of edit-sensitive parsing…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
Scaling the amount of compute used to train language models has dramatically improved their capabilities. However, when it comes to inference, we often limit models to making only one attempt at a problem. Here, we explore inference compute…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
Representing sorted integer sequences in small space is a central problem for large-scale retrieval systems such as Web search engines. Efficient query resolution, e.g., intersection or random access, is achieved by carefully partitioning…
For text retrieval systems, the assumption that all data structures reside in main memory is increasingly common. In this context, we present a novel incremental inverted indexing algorithm for web-scale collections that directly constructs…
Important papers have appeared recently on the problem of indexing binary strings for jumbled pattern matching, and further lowering the time bounds in terms of the input size would now be a breakthrough with broad implications. We can…
The data structure at the core of large-scale search engines is the inverted index, which is essentially a collection of sorted integer sequences called inverted lists. Because of the many documents indexed by such engines and stringent…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…
We present an algorithm for searching regular expression matches in compressed text. The algorithm reports the number of matching lines in the uncompressed text in time linear in the size of its compressed version. We define efficient data…
The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…