Related papers: Composite repetition-aware data structures
Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…
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…
Strategic diagrams and co-word analysis are widely employed to examine the conceptual structure of scientific domains and their development over time. Yet a structural inconsistency characterises dominant longitudinal implementations:…
A self-index is a compressed data structure that supports locate queries -- reporting all positions where a given pattern occurs in a string while maintaining the string in compressed form. While many self-indexes have been proposed,…
Compact directed acyclic word graphs (CDAWGs) [Blumer et al. 1987] are a fundamental data structure on strings with applications in text pattern searching, data compression, and pattern discovery. Intuitively, the CDAWG of a string $T$ is…
Similarity measure as a fundamental task in heterogeneous information network analysis has been applied to many areas, e.g., product recommendation, clustering and Web search. Most of the existing metrics depend on the meta-path or…
Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string $T$ of length $n$ in $O(r)$ words of compressed working space, where $r \le n$ is the…
Introduced about thirty years ago in the field of Data Compression, the Burrows-Wheeler Transform (BWT) is a string transformation that, besides being a booster of the performance of memoryless compressors, plays a fundamental role in the…
Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…
Structural measures of graphs, such as treewidth, are central tools in computational complexity resulting in efficient algorithms when exploiting the parameter. It is even known that modern SAT solvers work efficiently on instances of small…
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.…
The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…
Document listing on string collections is the task of finding all documents where a pattern appears. It is regarded as the most fundamental document retrieval problem, and is useful in various applications. Many of the fastest-growing…
The Burrows-Wheeler Transform (BWT) is a fundamental component in many data structures for text indexing and compression, widely used in areas such as bioinformatics and information retrieval. The extended BWT (eBWT) generalizes the…
Bipartite data is common in data engineering and brings unique challenges, particularly when it comes to clustering tasks that impose on strong structural assumptions. This work presents an unsupervised method for assessing similarity in…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
The problem of detecting and measuring the repetitiveness of one-dimensional strings has been extensively studied in data compression and text indexing. Our understanding of these issues has been significantly improved by the introduction…