Related papers: Longest Common Substring in Longest Common Subsequ…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
By Emerging huge databases and the need to efficient learning algorithms on these datasets, new problems have appeared and some methods have been proposed to solve these problems by selecting efficient features. Feature selection is a…
Sequence-to-Sequence models were introduced to tackle many real-life problems like machine translation, summarization, image captioning, etc. The standard optimization algorithms are mainly based on example-to-example matching like maximum…
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…
Recently, a novel coded compressed sensing (CCS) approach was proposed in [1] for dealing with the scalability problem for large sensing matrices in massive machine-type communications. The approach is to divide the compressed sensing (CS)…
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…
The minimum common string partition problem is an NP-hard combinatorial optimization problem with applications in computational biology. In this work we propose the first integer linear programming model for solving this problem. Moreover,…
The longest arc-preserving common subsequence problem is an NP-hard combinatorial optimization problem from the field of computational biology. This problem finds applications, in particular, in the comparison of arc-annotated Ribonucleic…
The Longest Common Increasing Subsequence (LCIS) is a variant of the classical Longest Common Subsequence (LCS), in which we additionally require the common subsequence to be strictly increasing. While the well-known "Four Russians"…
We consider the canonical generalization of the well-studied Longest Increasing Subsequence problem to multiple sequences, called $k$-LCIS: Given $k$ integer sequences $X_1,\dots,X_k$ of length at most $n$, the task is to determine the…
This paper shows that a simple algorithm produces the {\em all-prefixes-LCSs-graph} in $O(mn)$ time for two input sequences of size $m$ and $n$. Given any prefix $p$ of the first input sequence and any prefix $q$ of the second input…
Given two equally long, uniformly random binary strings, the expected length of their longest common subsequence (LCS) is asymptotically proportional to the strings' length. Finding the proportionality coefficient $\gamma$, i.e. the limit…
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
For graph learning tasks, many existing methods utilize a message-passing mechanism where vertex features are updated iteratively by aggregation of neighbor information. This strategy provides an efficient means for graph features…
In the area of Pattern Recognition and Matching, finding a Longest Common Subsequence plays an important role. In this paper, we have proposed one algorithm based on parallel computation. We have used OpenMP API package as middleware to…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…