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

In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…

A binary word is Sturmian if the occurrences of each letter are balanced, in the sense that in any two factors of the same length, the difference between the number of occurrences of the same letter is at most 1. In digital geometry,…

Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…

Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…

Parameterized complexity theory offers a framework for a refined analysis of hard algorithmic problems. Instead of expressing the running time of an algorithm as a function of the input size only, running times are expressed with respect to…

Compression algorithms and streaming algorithms are both powerful tools for dealing with massive data sets, but many of the best compression algorithms -- e.g., those based on the Burrows-Wheeler Transform -- at first seem incompatible with…

A class of parameter-free online linear optimization algorithms is proposed that harnesses the structure of an adversarial sequence by adapting to some side information. These algorithms combine the reduction technique of Orabona and…

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…

String matching is a fundamental problem in computer science, with critical applications in text retrieval, bioinformatics, and data analysis. Among the numerous solutions that have emerged for this problem in recent decades,…

Words in some natural languages can have a composite structure. Elements of this structure include the root (that could also be composite), prefixes and suffixes with which various nuances and relations to other words can be expressed.…

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 investigate the parameterized complexity of the Isometric Path Partition problem when parameterized by the treewidth ($\mathrm{tw}$) of the input graph, arguably one of the most widely studied parameters. Courcelle's theorem shows that…

Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…

Many problems that can be solved in quadratic time have bit-parallel speed-ups with factor $w$, where $w$ is the computer word size. A classic example is computing the edit distance of two strings of length $n$, which can be solved in…

The usefulness of parameterized algorithmics has often depended on what Niedermeier has called, "the art of problem parameterization". In this paper we introduce and explore a novel but general form of parameterization: the number of…

We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…

Given a word $w$ and a Parikh vector $\mathcal{P}$, an abelian run of period $\mathcal{P}$ in $w$ is a maximal occurrence of a substring of $w$ having abelian period $\mathcal{P}$. Our main result is an online algorithm that, given a word…

Representing texts as fixed-length vectors is central to many language processing tasks. Most traditional methods build text representations based on the simple Bag-of-Words (BoW) representation, which loses the rich semantic relations…

Let two static sequences of strings $P$ and $S$, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string $T$ given…