Related papers: Matching Patterns with Variables under Hamming Dis…
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…
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.…
A string $w$ is called a minimal absent word (MAW) for another string $T$ if $w$ does not occur in $T$ but the proper substrings of $w$ occur in $T$. For example, let $\Sigma = \{\mathtt{a, b, c}\}$ be the alphabet. Then, the set of MAWs…
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 explore worst-case solutions for the problems of single and multiple matching on strings in the word RAM model with word length w. In the first problem, we have to build a data structure based on a pattern p of length m…
The pattern matching problem with swaps is to find all occurrences of a pattern in a text while allowing the pattern to swap adjacent symbols. The goal is to design fast matching algorithm that takes advantage of the bit parallelism of…
The \emph{Hamming distance} $\text{ham}(u,v)$ between two equal-length words $u$, $v$ is the number of positions where $u$ and $v$ differ. The words $u$ and $v$ are said to be \emph{conjugates} if there exist non-empty words $x,y$ such that…
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. In the last two…
The dictionary matching with gaps problem is to preprocess a dictionary $D$ of $d$ gapped patterns $P_1,\ldots,P_d$ over alphabet $\Sigma$, where each gapped pattern $P_i$ is a sequence of subpatterns separated by bounded sequences of don't…
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…
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,…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
In the $k$-mismatch problem, given a pattern and a text of length $n$ and $m$ respectively, we have to find if the text has a sub-string with a Hamming distance of at most $k$ from the pattern. This has been studied in the classical setting…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($\mu$OPPM) is to find all substrings of $t$ that satisfy one of the possible…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
We present theoretical guarantees for an alternating minimization algorithm for the dictionary learning/sparse coding problem. The dictionary learning problem is to factorize vector samples $y^{1},y^{2},\ldots, y^{n}$ into an appropriate…
We present space lower bounds for online pattern matching under a number of different distance measures. Given a pattern of length m and a text that arrives one character at a time, the online pattern matching problem is to report the…
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…
We investigate the problem of deterministic pattern matching in multiple streams. In this model, one symbol arrives at a time and is associated with one of s streaming texts. The task at each time step is to report if there is a new match…