Related papers: Binary Jumbled Indexing: Suffix tree histogram
The suffix array, perhaps the most important data structure in modern string processing, is often augmented with the longest common prefix (LCP) array which stores the lengths of the LCPs for lexicographically adjacent suffixes of a string.…
We present a compressed representation of tries based on top tree compression [ICALP 2013] that works on a standard, comparison-based, pointer machine model of computation and supports efficient prefix search queries. Namely, we show how to…
We consider the following generalization of binary search in sorted arrays to tree domains. In each step of the search, an algorithm is querying a vertex $q$, and as a reply, it receives an answer, which either states that $q$ is the…
A $B$-tree is a type of search tree where every node (except possibly for the root) contains between $m$ and $2m$ keys for some positive integer $m$, and all leaves have the same distance to the root. We study sequences of $B$-trees that…
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…
We present several new results and connections between various extensions of finite automata through the study of vector automata and homing vector automata. We show that homing vector automata outperform extended finite automata when both…
An SPQR-tree is a data structure that efficiently represents all planar embeddings of a biconnected planar graph. It is a key tool in a number of constrained planarity testing algorithms, which seek a planar embedding of a graph subject to…
The Spanning Tree Congestion (STC) problem is the following NP-hard problem: given a graph $G$, construct a spanning tree $T$ of $G$ minimizing its maximum edge congestion where the congestion of an edge $e\in T$ is the number of edges $uv$…
We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…
The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…
We consider a problem of enumerating chemical graphs from given constraints concerning their structures, which has an important application to a novel method for the inverse QSAR/QSPR recently proposed. In this paper, the structure of a…
We initiate the study of tree structures in the context of scenario-based robust optimization. Specifically, we study Binary Search Trees (BSTs) and Huffman coding, two fundamental techniques for efficiently managing and encoding data based…
This paper presents the novel `uniqueness tree' algorithm, as one possible method for determining whether two finite, undirected graphs are isomorphic. We prove that the algorithm has polynomial time complexity in the worst case, and that…
Collective entity disambiguation aims to jointly resolve multiple mentions by linking them to their associated entities in a knowledge base. Previous works are primarily based on the underlying assumption that entities within the same…
Binary search trees (BST) are a popular type of data structure when dealing with ordered data. Indeed, they enable one to access and modify data efficiently, with their height corresponding to the worst retrieval time. From a probabilistic…
We focus on modeling the relationship between an input feature vector and the predicted outcome of a trained decision tree using mixed-integer optimization. This can be used in many practical applications where a decision tree or tree…
We consider the $Parameterized$ $Pattern$ $Matching$ problem, where a pattern $P$ matches some location in a text $\mathsf{T}$ iff there is a one-to-one correspondence between the alphabet symbols of the pattern to those of the text. More…
The mode of a collection of values (i.e., the most frequent value in the collection) is a key summary statistic. Finding the mode in a given range of an array of values is thus of great importance, and constructing a data structure to solve…
We study the Short Path Packing problem which asks, given a graph $G$, integers $k$ and $\ell$, and vertices $s$ and $t$, whether there exist $k$ pairwise internally vertex-disjoint $s$-$t$ paths of length at most $\ell$. The problem has…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…