Related papers: Burrows-Wheeler transform and LCP array constructi…
Despite the attention that the problem of path planning for tethered robots has garnered in the past few decades, the approaches proposed to solve it typically rely on a discrete representation of the configuration space and do not exploit…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
The move structure represents a permutation $\pi$ of $[0,n)$ as a covering set of $O(r)$ disjoint intervals (contiguous subsets of $[0,n)$), where $r$ is the minimum number of intervals whose values permute together. Formally, $r = 1 +…
The merging of succinct data structures is a well established technique for the space efficient construction of large succinct indexes. In the first part of the paper we propose a new algorithm for merging succinct representations of de…
A weight based dynamic compression method has recently been proposed, which is especially suitable for the encoding of files with locally skewed distributions. Its main idea is to assign larger weights to closer to be encoded symbols by…
We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of…
We present first algorithmic ideas for a practical and lightweight adaption of the DCX suffix array construction algorithm [Sanders et al., 2003] to the distributed-memory setting. Our approach relies on a bucketing technique which enables…
The Fourier Transform is one of the most important linear transformations used in science and engineering. Cooley and Tukey's Fast Fourier Transform (FFT) from 1964 is a method for computing this transformation in time $O(n\log n)$.…
Transformers have emerged as the cornerstone of state-of-the-art natural language processing models, showcasing exceptional performance across a wide range of AI applications. However, the memory demands posed by the self-attention…
Transformer-based models, exemplified by GPT-3, ChatGPT, and GPT-4, have recently garnered considerable attention in both academia and industry due to their promising performance in general language tasks. Nevertheless, these models…
In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these index structures far more complex than a single string, as was originally done with the FM-index…
In this article, a new method, called FWP, is proposed for clustering longitudinal curves. In the proposed method, clusters of mean functions are identified through a weighted concave pairwise fusion method. The EM algorithm and the…
We revisit the longest common extension (LCE) problem, that is, preprocess a string $T$ into a compact data structure that supports fast LCE queries. An LCE query takes a pair $(i,j)$ of indices in $T$ and returns the length of the longest…
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…
We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…
We prove that for every integer $n > 0$ and for every alphabet $\Sigma_k$ of size $k \geq 3$, there exists a necklace of length $n$ whose Burrows-Wheeler Transform (BWT) is completely unclustered, i.e., it consists of exactly $n$ runs with…
When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main…
Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…
Recently, several works have shown that natural modifications of the classical conditional gradient method (aka Frank-Wolfe algorithm) for constrained convex optimization, provably converge with a linear rate when: i) the feasible set is a…
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…