相关论文: Longest Common Prefix Arrays for Succinct k-Spectr…

An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their…

In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…

Dimensionality reduction, cluster analysis, and sparse representation are basic components in machine learning. However, their relationships have not yet been fully investigated. In this paper, we find that the spectral graph theory…

In this paper, we present a collection of novel and scalable algorithms designed to tackle the challenges inherent in the $k$-clique densest subgraph problem (\kcdsp) within network analysis. We propose \psctl, a novel algorithm based on…

In the reordering buffer problem (RBP), a server is asked to process a sequence of requests lying in a metric space. To process a request the server must move to the corresponding point in the metric. The requests can be processed slightly…

We consider the problem of computing the k-sparse approximation to the discrete Fourier transform of an n-dimensional signal. We show: * An O(k log n)-time randomized algorithm for the case where the input signal has at most k non-zero…

The well-known $k$-disjoint path problem ($k$-DPP) asks for pairwise vertex-disjoint paths between $k$ specified pairs of vertices $(s_i, t_i)$ in a given graph, if they exist. The decision version of the shortest $k$-DPP asks for the…

A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique which we call accelerated sampling. It runs in optimal O(n/p) local computation and communication, and requires a near…

Spectral clustering has found extensive use in many areas. Most traditional spectral clustering algorithms work in three separate steps: similarity graph construction; continuous labels learning; discretizing the learned labels by k-means…

We initiate the study of computational problems on $k$-mers (strings of length $k$) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct $k$-mers found on the walks of a graph. We establish that…

The notions of synchronizing and partitioning sets are recently introduced variants of locally consistent parsings with great potential in problem-solving. In this paper we propose a deterministic algorithm that constructs for a given…

In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…

The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array…

The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…

Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…

The $k$-dimensional Weisfeiler-Leman algorithm ($k$-WL) is a fruitful approach to the Graph Isomorphism problem. 2-WL corresponds to the original algorithm suggested by Weisfeiler and Leman over 50 years ago. 1-WL is the classical color…

A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…

Subexponential parameterized algorithms are known for a wide range of natural problems on planar graphs, but the techniques are usually highly problem specific. The goal of this paper is to introduce a framework for obtaining…

The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…

In this paper, we discuss the development of a sublinear sparse Fourier algorithm for high-dimensional data. In ``Adaptive Sublinear Time Fourier Algorithm" by D. Lawlor, Y. Wang and A. Christlieb (2013), an efficient algorithm with…