Related papers: Computing on Binary Strings
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton…
Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…
Software bugs have caused enormous economic and human loss in recent years. Certified programming seeks to solve this problem by developing languages where we can make demonstrations that guarantee that our programs work properly. However,…
We consider the clustering aggregation problem in which we are given a set of clusterings and want to find an aggregated clustering which minimizes the sum of mismatches to the input clusterings. In the binary case (each clustering is a…
Given a string $w$, another string $v$ is said to be a subsequence of $w$ if $v$ can be obtained from $w$ by removing some of its letters; on the other hand, $v$ is called an absent subsequence of $w$ if $v$ is not a subsequence of $w$. The…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
Given a set of integers W, the Partition problem determines whether W can be divided into two disjoint subsets with equal sums. We model the Partition problem as a system of polynomial equations, and then investigate the complexity of a…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
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…
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…
The Subset Sum problem asks whether a given set of $n$ positive integers contains a subset of elements that sum up to a given target $t$. It is an outstanding open question whether the $O^*(2^{n/2})$-time algorithm for Subset Sum by…
String constraint solving refers to solving combinatorial problems involving constraints over string variables. String solving approaches have become popular over the last years given the massive use of strings in different application…
The modular subset sum problem consists of deciding, given a modulus $m$, a multiset $S$ of $n$ integers in $0..m-1$, and a target integer $t$, whether there exists a subset of $S$ with elements summing to $t \mod m $, and to report such a…
We address the separability problem for straight-line string constraints. The separability problem for languages of a class C by a class S asks: given two languages A and B in C, does there exist a language I in S separating A and B (i.e.,…
Some techniques for the use of bitwise operations are described in the article. As an example, an open problem of isomorphism-free generations of combinatorial objects is discussed. An equivalence relation on the set of square binary…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…
A constant weight binary code consists of $n$-bit binary codewords, each with exactly $w$ bits equal to 1, such that any two codewords are at least Hamming distance $d$ apart. $A(n,d,w)$ is the maximum size of a constant weight binary code…