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

Parallel parameterized complexity theory studies how fixed-parameter tractable (fpt) problems can be solved in parallel. Previous theoretical work focused on parallel algorithms that are very fast in principle, but did not take into account…

The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…

The edit distance of two strings is the minimum number of insertions, deletions, and substitutions of characters needed to transform one string into the other. The textbook dynamic-programming algorithm computes the edit distance of two…

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…

The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…

We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…

We study systems of String Equations where block variables need to be assigned strings so that their concatenation gives a specified target string. We investigate this problem under a multivariate complexity framework, searching for…

This paper studies the unification problem with associative, commutative, and associative-commutative functions mainly from a viewpoint of the parameterized complexity on the number of variables. It is shown that both associative and…

Online bipartite matching is a fundamental problem in online algorithms. The goal is to match two sets of vertices to maximize the sum of the edge weights, where for one set of vertices, each vertex and its corresponding edge weights appear…

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…

Most existing Neural Machine Translation models use groups of characters or whole words as their unit of input and output. We propose a model with a hierarchical char2word encoder, that takes individual characters both as input and output.…

Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…

We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this…

We present the first worst-case linear time algorithm that directly computes the parameterized suffix and LCP arrays for constant sized alphabets. Previous algorithms either required quadratic time or the parameterized suffix tree to be…

In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…

We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…

When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…

Random graph models are widely used to understand network properties and graph algorithms. Key to such analyses are the different parameters of each model, which affect various network features, such as its size, clustering, or degree…

We propose a novel transformer-based styled handwritten text image generation approach, HWT, that strives to learn both style-content entanglement as well as global and local writing style patterns. The proposed HWT captures the long and…

We present efficient combinatorial parameterized algorithms for several classical graph-based counting problems in computational chemistry, including (i) Kekule structures, (ii) the Hosoya index, (iii) the Merrifield-Simmons index, and (iv)…