Related papers: Approximating LCS and Alignment Distance over Mult…
Approximate Pattern Matching is among the most fundamental string-processing tasks. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to identify the fragments of $T$ that are at distance at most…
Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $\sigma$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a…
Proximity graph-based methods have emerged as a leading paradigm for approximate nearest neighbor (ANN) search in the system community. This paper presents fresh insights into the theoretical foundation of these methods. We describe an…
Analyzing patterns in data streams generated by network traffic, sensor networks, or satellite feeds is a challenge for systems in which the available storage is limited. In addition, real data is noisy, which makes designing data stream…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
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…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
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…
We study the problem of computing a longest increasing subsequence in a sequence $S$ of $n$ distinct elements in the presence of persistent comparison errors. In this model, every comparison between two elements can return the wrong result…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Near MDS (NMDS) codes are closely related to interesting objects in finite geometry and have nice applications in combinatorics and cryptography. But there are many unsolved problems about construction of NMDS codes. In this paper, by using…
Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…
One of the most well-known and simplest models for diversity maximization is the Max-Min Diversification (MMD) model, which has been extensively studied in the data mining and database literature. In this paper, we initiate the study of the…
Approximate nearest-neighbor search is a fundamental algorithmic problem that continues to inspire study due its essential role in numerous contexts. In contrast to most prior work, which has focused on point sets, we consider…
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
The index coding problem is concerned with broadcasting encoded information to a collection of receivers in a way that enables each receiver to discover its required data based on its side information, which comprises the data required by…