Related papers: Indexes for Jumbled Pattern Matching in Strings, T…
An $r$-matching in a graph $G$ is a collection of edges in $G$ such that the distance between any two edges is at least $r$. A $2$-matching is also called an induced matching. In this paper, we estimate the maximum number of $r$-matchings…
We describe indexes for searching large data sets for variable-length-gapped (VLG) patterns. VLG patterns are composed of two or more subpatterns, between each adjacent pair of which is a gap-constraint specifying upper and lower bounds on…
The trie data structure is a good choice for finite maps whose keys are data structures (trees) rather than atomic values. But what if we want the keys to be patterns, each of which matches many lookup keys? Efficient matching of this kind…
We address the correspondence search problem among multiple graphs with complex properties while considering the matching consistency. We describe each pair of graphs by combining multiple attributes, then jointly match them in a unified…
We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using…
In this article, Temperley's bijection between spanning trees of the square grid on the one hand, and perfect matchings (also known as dimer coverings) of the square grid on the other, is extended to the setting of general planar directed…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…
Packing graphs is a combinatorial problem where several given graphs are being mapped into a common host graph such that every edge is used at most once. In the planar tree packing problem we are given two trees T1 and T2 on n vertices and…
Many datasets take the form of a bipartite graph where two types of nodes are connected by relationships, like the movies watched by a user or the tags associated with a file. The partitioning of the bipartite graph could be used to fasten…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
In this paper we propose a family of algorithms combining tree-clustering with conditioning that trade space for time. Such algorithms are useful for reasoning in probabilistic and deterministic networks as well as for accomplishing…
In previous work, the author defined the intersection graph of a chord diagram associated with string links (as in the theory of finite type invariants). In this paper, we classify the trees which can be obtained as intersection graphs of…
The relationship between two important problems in tree pattern matching, the largest common subtree and the smallest common supertree problems, is established by means of simple constructions, which allow one to obtain a largest common…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
We revisit the complexity of building, given a two-dimensional string of size $n$, an indexing structure that allows locating all $k$ occurrences of a two-dimensional pattern of size $m$. While a structure of size $\mathcal{O}(n)$ with…
Although the analysis of rooted tree shape has wide-ranging applications, notions of tree balance have developed independently in different domains. In computer science, a balanced tree is one that enables efficient updating and retrieval…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…