Related papers: Computing alignment plots efficiently
We show tight bounds for online Hamming distance computation in the cell-probe model with word size w. The task is to output the Hamming distance between a fixed string of length n and the last n symbols of a stream. We give a lower bound…
An algorithm (bliss) is proposed to speed up the construction of slow adaptive walks. Slow adaptive walks are adaptive walks biased towards closer points or smaller move steps. They were previously introduced to explore a search space, e.g.…
Uniform sampling of simple graphs having a given degree sequence is a known problem with exponential complexity in the square of the mean degree. For undirected graphs, randomised approximation algorithms have nonetheless been shown to…
Computing an accurate mean of a set of time series is a critical task in applications like nearest-neighbor classification and clustering of time series. While there are many distance functions for time series, the most popular distance…
The Swap-Insert Correction distance from a string $S$ of length $n$ to another string $L$ of length $m\geq n$ on the alphabet $[1..d]$ is the minimum number of insertions, and swaps of pairs of adjacent symbols, converting $S$ into $L$.…
In many modern data sets, High dimension low sample size (HDLSS) data is prevalent in many fields of studies. There has been an increased focus recently on using machine learning and statistical methods to mine valuable information out of…
In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…
This article presents effective (dynamic) algorithm for solving a problem of counting the number of substrings of given string which are also substrings of second string. Presented algorithm can be used for example for quick calculation of…
Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
Previous work has shown the effectiveness of random walk hitting times as a measure of dissimilarity in a variety of graph-based learning problems such as collaborative filtering, query suggestion or finding paraphrases. However,…
It was recently proved that any SLP generating a given string $w$ can be transformed in linear time into an equivalent balanced SLP of the same asymptotic size. We show that this result also holds for RLSLPs, which are SLPs extended with…
We introduce the natural notion of a matching frame in a $2$-dimensional string. A matching frame in a $2$-dimensional $n\times m$ string $M$, is a rectangle such that the strings written on the horizontal sides of the rectangle are…
The traditional approach to fault tolerant computing involves replicating computation units and applying a majority vote operation on individual result bits. This approach, however, has several limitations; the most severe is the resource…
Within many real-world networks the links between pairs of nodes change over time. Thus, there has been a recent boom in studying temporal graphs. Recognizing patterns in temporal graphs requires a proximity measure to compare different…
We study variants of the mean problem under the $p$-Dynamic Time Warping ($p$-DTW) distance, a popular and robust distance measure for sequential data. In our setting we are given a set of finite point sequences over an arbitrary metric…
As an essential operation in data cleaning, the similarity join has attracted considerable attention from the database community. In this paper, we study string similarity joins with edit-distance constraints, which find similar string…
Pairwise sequence comparison is one of the most fundamental problems in string processing. The most common metric to quantify the similarity between sequences S and T is edit distance, d(S,T), which corresponds to the number of characters…
This paper considers the problems of detecting a change point and estimating the location in the correlation matrices of a sequence of high-dimensional vectors, where the dimension is large enough to be comparable to the sample size or even…
In this work, we discuss low-parametric approaches for approximating SimRank matrices, which estimate the similarity between pairs of nodes in a graph. Although SimRank matrices and their computation require a significant amount of memory,…