Related papers: Indexes for Jumbled Pattern Matching in Strings, T…
The research on indexing repetitive string collections has focused on the same search problems used for regular string collections, though they can make little sense in this scenario. For example, the basic pattern matching query "list all…
Generating trees are a useful technique in the enumeration of various combinatorial objects, particularly restricted permutations. Quite often the generating tree for the set of permutations avoiding a set of patterns requires infinitely…
This paper proposes the use of graph pattern matching for investigative graph search, which is the process of searching for and prioritizing persons of interest who may exhibit part or all of a pattern of suspicious behaviors or…
Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…
Humans recognize object structure from both their appearance and motion; often, motion helps to resolve ambiguities in object structure that arise when we observe object appearance only. There are particular scenarios, however, where…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a…
Given a graph, we can form a spanning forest by first sorting the edges in some order, and then only keep edges incident to a vertex which is not incident to any previous edge. The resulting forest is dependent on the ordering of the edges,…
Determining whether two graphs are structurally identical is a fundamental problem with applications spanning mathematics, computer science, chemistry, and network science. Despite decades of study, graph isomorphism remains a challenging…
String diagrams are a graphical language used to represent processes that can be composed sequentially or in parallel, which correspond graphically to horizontal or vertical juxtaposition. In this paper we demonstrate how to compute the…
Statistical matching aims to integrate two statistical sources. These sources can be two samples or a sample and the entire population. If two samples have been selected from the same population and information has been collected on…
A coloring of a graph G = (V,E) is a partition {V1, V2, . . ., Vk} of V into independent sets or color classes. A vertex v Vi is a Grundy vertex if it is adjacent to at least one vertex in each color class Vj . A coloring is a Grundy…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
We consider algorithms for finding and counting small, fixed graphs in sparse host graphs. In the non-sparse setting, the parameters treedepth and treewidth play a crucial role in fast, constant-space and polynomial-space algorithms…
We study the correspondence between the linear matrix model and the interacting nonlinear string theory. Starting from the simple matrix harmonic oscillator states, we derive in a direct way scattering amplitudes of 2-dimensional strings,…
A hypergraph is a generalization of a graph, in which a hyperedge can connect multiple vertices, modeling complex relationships involving multiple vertices simultaneously. Hypergraph pattern matching, which is to find all isomorphic…