相关论文: Finding Approximate Palindromes in Strings Quickly…
We give a 3/2-approximation algorithm for stable matchings that runs in $O(m)$ time. The previously best known algorithm by McDermid has the same approximation ratio but runs in $O(n^{3/2}m)$ time, where $n$ denotes the number of people and…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
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…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
Given a pattern string $P$ of length $n$ consisting of $\delta$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $\Sigma$ of size $\Delta$, the {\em exact string…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
We study a new generalization of palindromes and gapped palindromes called block palindromes. A block palindrome is a string that becomes a palindrome when identical substrings are replaced with a distinct character. We investigate several…
We prove a precise formula for the minimal number K(n) such that every binary word of length $n$ can be divided into K(n) palindromes. Also we estimate the average number $\ol K(n)$ of palindromes composing a random binary word of 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…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…
In the classical interval scheduling type of problems, a set of $n$ jobs, characterized by their start and end time, need to be executed by a set of machines, under various constraints. In this paper we study a new variant in which the jobs…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
We present a randomized algorithm that computes a constant approximation of a graph's arboricity, using $\tilde{O}(n/\lambda)$ queries to adjacency lists and in the same time bound. Here, $n$ and $\lambda$ denote the number of nodes and the…