Related papers: $LCSk$++: Practical similarity metric for long str…
The Longest Common Substring (LCS) and Longest Palindromic Substring (LPS) are classical problems in computer science, representing fundamental challenges in string processing. Both problems can be solved in linear time using a classical…
The problem of finding a longest common subsequence of two main sequences with some constraint that must be a substring of the result (STR-IC-LCS) was formulated recently. It is a variant of the constrained longest common subsequence…
This paper reformulates the problem of finding a longest common increasing subsequence of the two given input sequences in a very succinct way. An extremely simple linear space algorithm based on the new formula can find a longest common…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
In this paper, we propose a novel leaky least mean square (leaky LMS, LLMS) algorithm which employs a p-norm-like constraint to force the solution to be sparse in the application of system identification. As an extension of the LMS…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…
At CPM 2017, Castelli et al. define and study a new variant of the Longest Common Subsequence Problem, termed the Longest Filled Common Subsequence Problem (LFCS). For the LFCS problem, the input consists of two strings $A$ and $B$ and a…
We study the problem of computing similarity joins under edit distance on a set of strings. Edit similarity joins is a fundamental problem in databases, data mining and bioinformatics. It finds important applications in data cleaning and…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
The Longest Common Subsequence (LCS) problem is a very important problem in math- ematics, which has a broad application in scheduling problems, physics and bioinformatics. It is known that the given two random sequences of infinite…
The Universal Similarity Metric (USM) has been demonstrated to give practically useful measures of "similarity" between sequence data. Here we have used the USM as an alternative distance metric in a K-Nearest Neighbours (K-NN) learner to…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
Given the vast reservoirs of data stored worldwide, efficient mining of data from a large information store has emerged as a great challenge. Many databases like that of intrusion detection systems, web-click records, player statistics,…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
We raise the question of approximating the compressibility of a string with respect to a fixed compression scheme, in sublinear time. We study this question in detail for two popular lossless compression schemes: run-length encoding (RLE)…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
Let $A$ and $B$ be two number sequences of length $n$ and $m$, respectively, where $m\le n$. Given a positive number $\delta$, a common almost increasing sequence $s_1\ldots s_k$ is a common subsequence for both $A$ and $B$ such that for…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
We consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…