Related papers: Efficient Computation of Sequence Mappability
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
We study the classic Text-to-Pattern Hamming Distances problem: given a pattern $P$ of length $m$ and a text $T$ of length $n$, both over a polynomial-size alphabet, compute the Hamming distance between $P$ and $T[i\, .\, . \, i+m-1]$ for…
We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…
We revisit the $k$-mismatch problem in the streaming model on a pattern of length $m$ and a streaming text of length $n$, both over a size-$\sigma$ alphabet. The current state-of-the-art algorithm for the streaming $k$-mismatch problem, by…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
The recently introduced longest common substring with $k$-mismatches ($k$-LCF) problem is to find, given two sequences $S_1$ and $S_2$ of length $n$ each, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
We present space efficient Monte Carlo algorithms that solve Subset Sum and Knapsack instances with $n$ items using $O^*(2^{0.86n})$ time and polynomial space, where the $O^*(\cdot)$ notation suppresses factors polynomial in the input size.…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
In the $k$-mismatch problem, given a pattern and a text of length $n$ and $m$ respectively, we have to find if the text has a sub-string with a Hamming distance of at most $k$ from the pattern. This has been studied in the classical setting…
Detecting and counting copies of permutation patterns are fundamental algorithmic problems, with applications in the analysis of rankings, nonparametric statistics, and property testing tasks such as independence and quasirandomness…
The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…
In this work, we obtain the following new results. 1. Given a sequence $D=((h_1,s_1), (h_2,s_2) ..., (h_n,s_n))$ of number pairs, where $s_i>0$ for all $i$, and a number $L_h$, we propose an O(n)-time algorithm for finding an index interval…
In the $k$-Edit Circular Pattern Matching ($k$-Edit CPM) problem, we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a positive integer threshold $k$, and we are to report all starting positions of the substrings of $T$ that…
Sequence partition problems arise in many fields, such as sequential data analysis, information transmission, and parallel computing. In this paper, we study the following partition problem variant: given a sequence of $n$ items…
In the \emph{$k$-Diameter-Optimally Augmenting Tree Problem} we are given a tree $T$ of $n$ vertices as input. The tree is embedded in an unknown \emph{metric} space and we have unlimited access to an oracle that, given two distinct…
In this paper, we present and study the \emph{Hamming distance oracle problem}. In this problem, the task is to preprocess two strings $S$ and $T$ of lengths $n$ and $m$, respectively, to obtain a data-structure that is able to answer…
We consider online algorithms for the $k$-server problem on trees. Chrobak and Larmore proposed a $k$-competitive algorithm for this problem that has the optimal competitive ratio. However, a naive implementation of their algorithm has…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
The Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…