相关论文: Computing the Parameterized Burrows--Wheeler Trans…

In 1994, Burrows and Wheeler developed a data compression algorithm which performs significantly better than Lempel-Ziv based algorithms. Since then, a lot of work has been done in order to improve their algorithm, which is based on a…

We consider the problem of implementing linearizable objects that support both read and read-modify-write (RMW) operations in message-passing systems with process crashes. Since in many systems read operations vastly outnumber RMW…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

We study the influence of a graph parameter called modular-width on the time complexity for optimally solving well-known polynomial problems such as Maximum Matching, Triangle Counting, and Maximum $s$-$t$ Vertex-Capacitated Flow. The…

Given a text and a pattern over two types of symbols called constants and variables, the parameterized pattern matching problem is to find all occurrences of substrings of the text that the pattern matches by substituting a variable in the…

In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the…

A mathematical characterization of serially-pruned permutations (SPPs) employed in variable-length permuters and their associated fast pruning algorithms and architectures are proposed. Permuters are used in many signal processing systems…

A strength of parameterized algorithmics is that each problem can be parameterized by an essentially inexhaustible set of parameters. Usually, the choice of the considered parameter is informed by the theoretical relations between…

The Positional Burrows-Wheeler Transform (PBWT) is a fundamental data structure for the efficient representation and analysis of large-scale haplotype panels. For a panel of $h$ sequences $\{S_1, \dots, S_h\}$ over $m$ sites, a key…

Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…

Computing all-pairs shortest paths is a fundamental and much-studied problem with many applications. Unfortunately, despite intense study, there are still no significantly faster algorithms for it than the $\mathcal{O}(n^3)$ time algorithm…

Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…

Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit…

Microarrays are research tools used in gene discovery as well as disease and cancer diagnostics. Two prominent but challenging problems related to microarrays are the Border Minimization Problem (BMP) and the Border Minimization Problem…

The Extended Burrows Wheeler transform (EBWT) helps to find the distance between two sequences. Implementation of an existing algorithm takes considerable amount of time for small size sequences. In this paper, we give a parallel…

In this paper we propose a flexible and lightweight technique for merging compressed indices based on variants of Burrows-Wheeler transform (BWT), thus addressing the need for algorithms that compute compressed indices over large…

Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…

The tree-cut width of a graph is a graph parameter defined by Wollan [J. Comb. Theory, Ser. B, 110:47-66, 2015] with the help of tree-cut decompositions. In certain cases, tree-cut width appears to be more adequate than treewidth as an…

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…

It is known that a number of natural graph problems which are FPT parameterized by treewidth become W-hard when parameterized by clique-width. It is therefore desirable to find a different structural graph parameter which is as general as…