Related papers: Single and multiple consecutive permutation motif …
We introduce data structures answering queries concerning the occurrences of patterns from a given dictionary $\mathcal{D}$ in fragments of a given string $T$ of length $n$. The dictionary is internal in the sense that each pattern in…
Given a text $T$ and a pattern $P$, the order-preserving matching problem is to find all substrings in $T$ which have the same relative orders as $P$. Order-preserving matching has been an active research area since it was introduced by…
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower…
A pattern p (i.e., a string of variables and terminals) matches a word w, if w can be obtained by uniformly replacing the variables of p by terminal words. The respective matching problem, i.e., deciding whether or not a given pattern…
For any real number $p > 0$, we nearly completely characterize the space complexity of estimating $\|A\|_p^p = \sum_{i=1}^n \sigma_i^p$ for $n \times n$ matrices $A$ in which each row and each column has $O(1)$ non-zero entries and whose…
In this paper, we construct and compare algorithmic approaches to solve the Preference Consistency Problem for preference statements based on hierarchical models. Instances of this problem contain a set of preference statements that are…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
Pollard's rho method finds a prime factor $p$ of an integer $N$ by searching for a collision in a map of the form $x \mapsto x^{2k} + c$ modulo $N$. This search can be parallelized to multiple machines, which may use distinct parameters $k$…
Motif finding is an important step for the detection of rare events occurring in a set of DNA or protein sequences. Extraction of information about these rare events can lead to new biological discoveries. Motifs are some important patterns…
We propose a new indexing structure for parameterized strings, called parameterized position heap. Parameterized position heap is applicable for parameterized pattern matching problem, where the pattern matches a substring of the text if…
The Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
Let $\mathcal{D}$ be a collection of $D$ documents, which are strings over an alphabet of size $\sigma$, of total length $n$. We describe a data structure that uses linear space and and reports $k$ most relevant documents that contain a…
An index for a finite automaton is a powerful data structure that supports locating paths labeled with a query pattern, thus solving pattern matching on the underlying regular language. In this paper, we solve the long-standing problem of…
The text-to-pattern Hamming distances problem asks to compute the Hamming distances between a given pattern of length $m$ and all length-$m$ substrings of a given text of length $n\ge m$. We focus on the $k$-mismatch version of the problem,…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…
Permutation pattern-avoidance is a central concept of both enumerative and extremal combinatorics. In this paper we study the effect of permutation pattern-avoidance on the complexity of optimization problems. In the context of the dynamic…
Given the query string of length $m$, we explore a parallel query in a static suffix tree based data structure for $p \ll n$, where $p$ is the number of processors and $n$ is the length of the text. We present three results on CREW PRAM.…
A natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are $k$ background sequences, and each character in a background sequence is a random…