Related papers: Binary Jumbled Indexing: Suffix tree histogram
A fringe subtree of a rooted tree is a subtree consisting of one of the nodes and all its descendants. In this paper, we are specifically interested in the number of non-isomorphic trees that appear in the collection of all fringe subtrees…
This paper describes the shortest path problem in weighted graphs and examines the differences in efficiency that occur when using Dijkstra's algorithm with a Fibonacci heap, binary heap, and self-balancing binary tree. Using C++…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…
Considering the worst-case scenario, junction tree algorithm remains the most general solution for exact MAP inference with polynomial run-time guarantees. Unfortunately, its main tractability assumption requires the treewidth of a…
Two strings $x$ and $y$ over $\Sigma \cup \Pi$ of equal length are said to \emph{parameterized match} (\emph{p-match}) if there is a renaming bijection $f:\Sigma \cup \Pi \rightarrow \Sigma \cup \Pi$ that is identity on $\Sigma$ and…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
The subgraph-subgraph matching problem is, given a pair of graphs and a positive integer $K$, to find $K$ vertices in the first graph, $K$ vertices in the second graph, and a bijection between them, so as to minimize the number of adjacency…
In a bipartite graph, a subgraph is an $s$-biplex if each vertex of the subgraph is adjacent to all but at most $s$ vertices on the opposite set. The enumeration of $s$-biplexes from a given graph is a fundamental problem in bipartite graph…
Path planning in robotics often requires finding high-quality solutions to continuously valued and/or high-dimensional problems. These problems are challenging and most planning algorithms instead solve simplified approximations. Popular…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
Augmented B-trees (aB-trees) are a broad class of data structures. The seminal work "succincter" by Patrascu showed that any aB-tree can be stored using only two bits of redundancy, while supporting queries to the tree in time proportional…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
We present an approach to implement binary search trees in the rule-based graph programming language GP 2. Our implementation uses GP 2's rooted graph transformation rules to be fast and supports insertion, deletion and query operations. We…
For a labeled tree on the vertex set $\set{1,2,\ldots,n}$, the local direction of each edge $(i\,j)$ is from $i$ to $j$ if $i<j$. For a rooted tree, there is also a natural global direction of edges towards the root. The number of edges…
We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds…
We revisit the classic border tree data structure [Gu, Farach, Beigel, SODA 1994] that answers the following prefix-suffix queries on a string $T$ of length $n$ over an integer alphabet $\Sigma=[0,\sigma)$: for any $i,j \in [0,n)$ return…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…