Related papers: A Three-Stage Algorithm for the Closest String Pro…
In the Maximum Duo-Preservation String Mapping problem we are given two strings and wish to map the letters of the former to the letters of the latter so as to maximise the number of duos. A duo is a pair of consecutive letters that is…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
Score-based algorithms that learn Bayesian Network (BN) structures provide solutions ranging from different levels of approximate learning to exact learning. Approximate solutions exist because exact learning is generally not applicable to…
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…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
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,…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
The problem of finding the shortest path for a vehicle visiting a given sequence of target points subject to the motion constraints of the vehicle is an important problem that arises in several monitoring and surveillance applications…
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 problem of similarity search is one of the main problems in computer science. This problem has many applications in text-retrieval, web search, computational biology, bioinformatics and others. Similarity between two data objects can be…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
Constrained optimization problems appear in a wide variety of challenging real-world problems, where constraints often capture the physics of the underlying system. Classic methods for solving these problems rely on iterative algorithms…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
In the Minimum Common String Partition Problem (MCSP), we are given two strings on input, and we want to partition both into the same collection of substrings, minimizing the number of the substrings in the partition. This combinatorial…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
The FAR FROM MOST STRING PROBLEM (FFMSP) is a string selection problem. The objective is to find a string whose distance to other strings in a certain input set is above a given threshold for as many of those strings as possible. This…
In multistage perfect matching problems we are given a sequence of graphs on the same vertex set and asked to find a sequence of perfect matchings, corresponding to the sequence of graphs, such that consecutive matchings are as similar as…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…