相关论文: Wheeler maps

Graph rewriting is a popular tool for the optimisation and modification of graph expressions in domains such as compilers, machine learning and quantum computing. The underlying data structures are often port graphs - graphs with labels at…

In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…

The $k$-dimensional Weisfeiler-Leman algorithm is a powerful tool in graph isomorphism testing. For an input graph $G$, the algorithm determines a canonical coloring of $s$-tuples of vertices of $G$ for each $s$ between 1 and $k$. We say…

A foundation model like GPT elicits many emergent abilities, owing to the pre-training with broad inclusion of data and the use of the powerful Transformer architecture. While foundation models in natural languages are prevalent, can we…

We consider a variation of the spectral sparsification problem where we are required to keep a subgraph of the original graph. Formally, given a union of two weighted graphs $G$ and $W$ and an integer $k$, we are asked to find a $k$-edge…

We introduce a novel multivariate approach for solving weighted parameterized problems. In our model, given an instance of size $n$ of a minimization (maximization) problem, and a parameter $W \geq 1$, we seek a solution of weight at most…

Supervised learning with tabular data presents unique challenges, including low data sizes, the absence of structural cues, and heterogeneous features spanning both categorical and continuous domains. Unlike vision and language tasks, where…

We present linear-space data structures for several frequency queries on trees, namely: path mode, path least frequent element, and path $\alpha$-minority queries. We present the first linear-space data structures, requiring $O(n…

Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings, however, since this introduction, it has been used more generally to describe any BWT of a collection of strings and the fundamental…

Let $t$ be a permutation (that shall play the role of the {\em text}) on $[n]$ and a pattern $p$ be a sequence of $m$ distinct integer(s) of $[n]$, $m\leq n$. The pattern $p$ occurs in $t$ in position $i$ if and only if $p_1... p_m$ is…

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…

Recently, Conte et al. generalized the longest-common prefix (LCP) array from strings to Wheeler DFAs, and they showed that it can be used to efficiently determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the LCP…

Subgraph counting is a fundamental task for analyzing structural patterns in graph-structured data, with important applications in domains such as computational biology and social network analysis, where recurring motifs reveal functional…

Given an unlabeled road map, we consider, from an algorithmic perspective, the cartographic problem to place non-overlapping road labels embedded in their roads. We first decompose the road network into logically coherent road sections,…

Chart constraints, which specify at which string positions a constituent may begin or end, have been shown to speed up chart parsers for PCFGs. We generalize chart constraints to more expressive grammar formalisms and describe a neural…

The dynamic shortest paths problem on planar graphs asks us to preprocess a planar graph $G$ such that we may support insertions and deletions of edges in $G$ as well as distance queries between any two nodes $u,v$ subject to the constraint…

The transversal hypergraph problem is the task of enumerating the minimal hitting sets of a hypergraph. It is a long-standing open question whether this can be done in output-polynomial time. For hypergraphs whose solutions have bounded…

Given a string of characters, the Burrows-Wheeler Transform rearranges the characters in it so as to produce another string of the same length which is more amenable to compression techniques such as move to front, run-length encoding, and…

We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…

There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…