Related papers: Extending the Burrows-Wheeler Transform for Cartes…
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…
We introduce K-tree in an information retrieval context. It is an efficient approximation of the k-means clustering algorithm. Unlike k-means it forms a hierarchy of clusters. It has been extended to address issues with sparse…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing. First introduced in 1994, it went on to provide the backbone for the first encoding of the classic suffix tree data structure in space close to…
We study data structure problems related to document indexing and pattern matching queries and our main contribution is to show that the pointer machine model of computation can be extremely useful in proving high and unconditional lower…
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
As data volumes continue to grow rapidly, traditional search algorithms, like the red-black tree and B+ Tree, face increasing challenges in performance, especially in big data scenarios with intensive storage access. This paper presents the…
With XML becoming an ubiquitous language for data interoperability purposes in various domains, efficiently querying XML data is a critical issue. This has lead to the design of algebraic frameworks based on tree-shaped patterns akin to the…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
The Burrows-Wheeler Transform (BWT) is among the most influential discoveries in text compression and DNA storage. It is a reversible preprocessing step that rearranges an $n$-letter string into runs of identical characters (by exploiting…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
Given a string of characters, the Burrows-Wheeler Transform rearranges the characters in it so as to produce another string of the same length which is more amenable to compression techniques such as move to front, run-length encoding, and…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…
Index structures are one of the most important tools that DBAs leverage to improve the performance of analytics and transactional workloads. However, building several indexes over large datasets can often become prohibitive and consume…
Overlap is a common phenomenon seen when structural components of a digital object are neither disjoint nor nested inside each other. Overlapping components resist reduction to a structural hierarchy, and tree-based indexing and query…