Related papers: Composite repetition-aware data structures
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
Compositional data, which are vectors of proportions constrained to the probability simplex, arise frequently in modern scientific applications, including microbiome relative abundances across body sites and cell-type mixture weights…
The compact directed acyclic word graph (CDAWG) [Blumer et al. 1987] of a string is the minimal compact automaton that recognizes all the suffixes of the string. CDAWGs can be used for various string tasks including text pattern searching,…
We study learning-augmented binary search trees (BSTs) via Treaps with carefully designed priorities. The result is a simple search tree in which the depth of each item $x$ is determined by its predicted weight $w_x$. Specifically, each…
Motivated by applications in polymer-based data storage we introduced the new problem of characterizing the code rate and designing constant-weight binary $B_2$-sequences. Binary $B_2$-sequences are collections of binary strings of length…
Document collections of various domains, e.g., legal, medical, or financial, often share some underlying collection-wide structure, which captures information that can aid both human users and structure-aware models. We propose to identify…
The Lyndon array stores, at each position of a word, the length of the longest maximal Lyndon subword starting at that position, and plays an important role in combinatorics on words, for example in the construction of fundamental data…
An L-system (for lossless compression) is a CPD0L-system extended with two parameters $d$ and $n$, which determines unambiguously a string $w = \tau(\varphi^d(s))[1:n]$, where $\varphi$ is the morphism of the system, $s$ is its axiom, and…
Networked structures arise in a wide array of different contexts such as technological and transportation infrastructures, social phenomena, and biological systems. These highly interconnected systems have recently been the focus of a great…
We introduce a new family of compressed data structures to efficiently store and query large string dictionaries in main memory. Our main technique is a combination of hierarchical Front-coding with ideas from longest-common-prefix…
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
Recurrence plot based methods are highly efficient and widely accepted tools for the investigation of time series or one-dimensional data. We present an extension of the recurrence plots and their quantifications in order to study recurrent…
We study how to obtain concise descriptions of discrete multivariate sequential data. In particular, how to do so in terms of rich multivariate sequential patterns that can capture potentially highly interesting (cor)relations between…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
Burrows-Wheeler transform (BWT) is an invertible text transformation that, given a text $T$ of length $n$, permutes its symbols according to the lexicographic order of suffixes of $T$. BWT is one of the most heavily studied algorithms in…
In the past several years a wide range of methods for the construction of regression trees and other estimators based on the recursive partitioning of samples have appeared in the statistics literature. Many applications involve data…
Temporal graphs represent interactions between entities over time. Deciding whether entities can reach each other through temporal paths is useful for various applications such as in communication networks and epidemiology. Previous works…
The Burrows-Wheeler Transform (BWT) moves characters with similar contexts in a text together, where a character's context consists of the characters immediately following it. We say that a property has contextual locality if characters…
The set of permutations on a finite set can be given a lattice structure (known as the weak Bruhat order). The lattice structure is generalized to the set of words on a fixed alphabet $\Sigma = \{ x, y, z, ... \}$, where each letter has a…
A labeled tree (or a trie) is a natural generalization of a string, which can also be seen as a compact representation of a set of strings. This paper considers the labeled tree indexing problem, and provides a number of new results on…