Related papers: Indexes for Jumbled Pattern Matching in Strings, T…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
The primary objective of graph pattern matching is to find all appearances of an input graph pattern query in a large data graph. Such appearances are called matches. In this paper, we are interested in finding matches of interaction…
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…
Position heaps are index structures of text strings used for the string matching problem. They are rooted trees whose edges and nodes are labeled and numbered, respectively. This paper is concerned with variants of the inverse problem of…
Graph pattern matching is a fundamental operation for the analysis and exploration ofdata graphs. In thispaper, we presenta novel approachfor efficiently finding homomorphic matches for hybrid graph patterns, where each pattern edge may be…
We study strategies of approximate pattern matching that exploit bidirectional text indexes, extending and generalizing ideas of Lam et al. We introduce a formalism, called search schemes, to specify search strategies of this type, then…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…
Let $S_1, S_2 \in \Sigma^*$ strings, we say that $S_1$ {\em jumble match} $S_2$ if they are permutations of each other. Given a text $T$ of size $N$ and a string $S \in \Sigma^*$, the problem of \emph{Jumbled Pattern Matching} (JPM) is to…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
New applications of data mining, such as in biology, bioinformatics, or sociology, are faced with large datasetsstructured as graphs. We introduce a novel class of tree-shapedpatterns called tree queries, and present algorithms for…
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 closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…
Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
We consider the classical exact multiple string matching problem. Our solution is based on $q$-grams combined with pattern superimposition, bit-parallelism and alphabet size reduction. We discuss the pros and cons of the various…
We describe simple linear time algorithms for coloring the squares of balanced and unbalanced quadtrees so that no two adjacent squares are given the same color. If squares sharing sides are defined as adjacent, we color balanced quadtrees…
Geometric graphs appear in many real-world data sets, such as road networks, sensor networks, and molecules. We investigate the notion of distance between embedded graphs and present a metric to measure the distance between two geometric…