Related papers: Matching Patterns with Variables Under Edit Distan…
High order networks are weighted hypergraphs col- lecting relationships between elements of tuples, not necessarily pairs. Valid metric distances between high order networks have been defined but they are difficult to compute when the…
We generalize the concept of synchronizing words for finite automata, which map all states of the automata to the same state, to deterministic visibly push-down automata. Here, a synchronizing word w does not only map all states to the same…
Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used…
Dependent pattern matching is a key feature in dependently typed programming. However, there is a theory-practice disconnect: while many proof assistants implement pattern matching as primitive, theoretical presentations give semantics to…
In combinatorics on words, a word $w$ over an alphabet $\Sigma$ is said to avoid a pattern $p$ over an alphabet $\Delta$ if there is no factor $f$ of $w$ such that $f= (p)$ where $h: \Delta^*\to\Sigma^*$ is a non-erasing morphism. A pattern…
Given a pattern $w$ and a text $t$, the speed of a pattern matching algorithm over $t$ with regard to $w$, is the ratio of the length of $t$ to the number of text accesses performed to search $w$ into $t$. We first propose a general method…
The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…
Edit distance is a fundamental measure of distance between strings and has been widely studied in computer science. While the problem of estimating edit distance has been studied extensively, the equally important question of actually…
Fixed-parameter tractability analysis and scheduling are two core domains of combinatorial optimization which led to deep understanding of many important algorithmic questions. However, even though fixed-parameter algorithms are appealing…
We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…
This paper studies the unification problem with associative, commutative, and associative-commutative functions mainly from a viewpoint of the parameterized complexity on the number of variables. It is shown that both associative and…
The problem DFA-Intersection-Nonemptiness asks if a given number of deterministic automata accept a common word. In general, this problem is PSPACE-complete. Here, we investigate this problem for the subclasses of commutative automata and…
Given an LZW/LZ78 compressed text, we want to find an approximate occurrence of a given pattern of length m. The goal is to achieve time complexity depending on the size n of the compressed representation of the text instead of its length.…
We study parameterized Constraint Satisfaction Problem for infinite constraint languages. The parameters that we study are weight of the satisfying assignment, number of constraints, maximum number of occurrences of a variable in the…
Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. A simple dynamic…
The edit distance between two words $w_1, w_2$ is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform $w_1$ to $w_2$. The edit distance generalizes to languages $\mathcal{L}_1,…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
In his 1987 paper entitled "Generalized String Matching", Abrahamson introduced {\em pattern matching with character classes} and provided the first efficient algorithm to solve it. The best known solution to date is due to Linhart and…
We say that a word $w$ on a totally ordered alphabet avoids the word $v$ if there are no subsequences in $w$ order-equivalent to $v$. In this paper we suggest a new approach to the enumeration of words on at most $k$ letters avoiding a…