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

Kernel methods are powerful tools in machine learning. They have to be computationally efficient. In this paper, we present a novel Geometric-based approach to compute efficiently the string subsequence kernel (SSK). Our main idea is that…

Fast Fourier Transform (FFT) is one of the most important tools in digital signal processing. FFT costs O(N \log N) for transforming a signal of length N. Recently, Sparse Fourier Transform (SFT) has emerged as a critical issue addressing…

Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…

Given integers $k,j$ with $1\le j \le k-1$, we consider the length of the longest $j$-tight path in the binomial random $k$-uniform hypergraph $H^k(n,p)$. We show that this length undergoes a phase transition from logarithmic length to…

Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…

A de Bruijn sequence of order $k$ over a finite alphabet is a cyclic sequence with the property that it contains every possible $k$-sequence as a substring exactly once. Orthogonal de Bruijn sequences are collections of de Bruijn sequences…

Spectral clustering is discussed from many perspectives, by extending it to rectangular arrays and discrepancy minimization too. Near optimal clusters are obtained with singular value decomposition and with the weighted $k$-means algorithm.…

This paper presents a new graph isomorphism invariant, called $\mathfrak{w}$-labeling, that can be used to design a polynomial-time algorithm for solving the graph isomorphism problem for various graph classes. For example, all…

This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under…

We characterize those strings whose suffix arrays are based on arithmetic progressions, in particular, arithmetically progressed permutations where all pairs of successive entries of the permutation have the same difference modulo the…

We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…

The mode of a collection of values (i.e., the most frequent value in the collection) is a key summary statistic. Finding the mode in a given range of an array of values is thus of great importance, and constructing a data structure to solve…

The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…

Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…

Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…

Spectral clustering is a popular and effective algorithm designed to find $k$ clusters in a graph $G$. In the classical spectral clustering algorithm, the vertices of $G$ are embedded into $\mathbb{R}^k$ using $k$ eigenvectors of the graph…

Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…

An efficient algorithm to solve the $k$ shortest non-homotopic path planning ($k$-SNPP) problem in a 2D environment is proposed in this paper. Motivated by accelerating the inefficient exploration of the homotopy-augmented space of the 2D…

Longest common substring (LCS), longest palindrome substring (LPS), and Ulam distance (UL) are three fundamental string problems that can be classically solved in near linear time. In this work, we present sublinear time quantum algorithms…