Related papers: Optimal prefix-suffix queries with applications
The move structure represents a permutation $\pi$ of $[0,n)$ as a covering set of $O(r)$ disjoint intervals (contiguous subsets of $[0,n)$), where $r$ is the minimum number of intervals whose values permute together. Formally, $r = 1 +…
Encoding data structures store enough information to answer the queries they are meant to support but not enough to recover their underlying datasets. In this paper we give the first encoding data structure for the challenging problem of…
The number of zeros and the number of ones in a binary string are referred to as the composition of the string, and the prefix-suffix compositions of a string are a multiset formed by the compositions of the prefixes and suffixes of all…
Many search engines such as Google, Bing & Yahoo! show search suggestions when users enter search phrases on their interfaces. These suggestions are meant to assist the user in finding what she wants quickly and also suggesting common…
We propose a B tree representation storing $n$ keys, each of $k$ bits, in either (a) $nk + O(nk / \lg n)$ bits or (b) $nk + O(nk \lg \lg n/ \lg n)$ bits of space supporting all B tree operations in either (a) $O(\lg n )$ time or (b) $O(\lg…
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…
Given a string $S$ of $n$ integers in $[0,\sigma)$, a range minimum query RMQ$(i, j)$ asks for the index of the smallest integer in $S[i \dots j]$. It is well known that the problem can be solved with a succinct data structure of size $2n +…
We consider the problem of preprocessing a text $T$ of length $n$ and a dictionary $\mathcal{D}$ in order to be able to efficiently answer queries $CountDistinct(i,j)$, that is, given $i$ and $j$ return the number of patterns from…
Consider observation data, comprised of n observation vectors with values on a set of attributes. This gives us n points in attribute space. Having data structured as a tree, implied by having our observations embedded in an ultrametric…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
Let S be a finite, ordered alphabet, and let x = x_1 x_2 ... x_n be a string over S. A "secondary index" for x answers alphabet range queries of the form: Given a range [a_l,a_r] over S, return the set I_{[a_l;a_r]} = {i |x_i \in [a_l;…
We study leaf-to-ancestor path-minimum queries on a rooted, weighted tree in the oracle model, where the only allowed value operation is a comparison oracle on edge (or node) weights. We give a static data structure that, after O(n log h)…
In this paper, we have developed a fully-dynamic algorithm for maintaining cardinality of maximum-matching in a tree using the construction of top-trees. The time complexities are as follows: 1. Initialization Time: $O(n(log(n)))$ to build…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
For many kinds of prefix-free codes there are efficient and compact alternatives to the traditional tree-based representation. Since these put the codes into canonical form, however, they can only be used when we can choose the order in…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…