Related papers: An Algorithm for the Longest Common Subsequence an…
The problem of finding the longest common subsequence (LCS) for a set of sequences is a very interesting and challenging problem in computer science. This problem is NP-complete, but because of its importance, many heuristic algorithms have…
In the Shortest Superstring problem, we are given a set of strings and we are asking for a common superstring, which has the minimum number of characters. The Shortest Superstring problem is NP-hard and several constant-factor approximation…
We generalise a multiple string pattern matching algorithm, recently proposed by Fredriksson and Grabowski [J. Discr. Alg. 7, 2009], to deal with arbitrary dictionaries on an alphabet of size $s$. If $r_m$ is the number of words of length…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Squares (fragments of the form $xx$, for some string $x$) are arguably the most natural type of repetition in strings. The basic algorithmic question concerning squares is to check if a given string of length $n$ is square-free, that is,…
Let us consider the Multiple String Matching Problem. In this problem, we consider a long string, denoted by $t$, of length $n$. This string is referred to as a text. We also consider a sequence of $m$ strings, denoted by $S$, which we…
In the Shortest Superstring problem we are given a set of strings $S=\{s_1, \ldots, s_n\}$ and integer $\ell$ and the question is to decide whether there is a superstring $s$ of length at most $\ell$ containing all strings of $S$ as…
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…
Manacher's algorithm has been shown to be optimal to the longest palindromic substring problem. Many of the existing implementations of this algorithm, however, unanimously required in-memory construction of an augmented string that is…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
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…
We consider the problem of dictionary matching in a stream. Given a set of strings, known as a dictionary, and a stream of characters arriving one at a time, the task is to report each time some string in our dictionary occurs in the…
Given a text and a pattern over an alphabet, the pattern matching problem searches for all occurrences of the pattern in the text. An equivalence relation $\approx$ is called a substring consistent equivalence relation (SCER), if for two…
In this paper, we consider a variant of the classical algorithmic problem of checking whether a given word $v$ is a subsequence of another word $w$. More precisely, we consider the problem of deciding, given a number $p$ (defining a…
In this paper we are dealing with the issue of finding possibly short synchronizing words in automata with weight assigned to each letter in the alphabet $\Sigma$. First we discuss some complexity problems, and then we present new…
In this paper we consider the following problems: how many different subsets of Sigma^n can occur as set of all length-n factors of a finite word? If a subset is representable, how long a word do we need to represent it? How many such…