Related papers: Succincter Text Indexing with Wildcards

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…

Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…

In the pattern matching with $d$ wildcards problem one is given a text $T$ of length $n$ and a pattern $P$ of length $m$ that contains $d$ wildcard characters, each denoted by a special symbol $'?'$. A wildcard character matches any other…

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find $r$-dominating sets which enable…

In the realm of computer science, the efficiency of text-search algorithms is crucial for processing vast amounts of data in areas such as natural language processing and bioinformatics. Traditional methods like Naive Search, KMP, and…

We introduce the straggler identification problem, in which an algorithm must determine the identities of the remaining members of a set after it has had a large number of insertion and deletion operations performed on it, and now has…

This paper studies the problem of finding an $(1+\epsilon)$-approximate solution to positive semidefinite programs. These are semidefinite programs in which all matrices in the constraints and objective are positive semidefinite and all…

Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…

The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…

We study algorithms for approximating pairwise similarity matrices that arise in natural language processing. Generally, computing a similarity matrix for $n$ data points requires $\Omega(n^2)$ similarity computations. This quadratic…

In-place associative integer sorting technique was proposed for integer lists which requires only constant amount of additional memory replacing bucket sort, distribution counting sort and address calculation sort family of algorithms.…

We present a novel compressed dynamic self-index for highly repetitive text collections. Signature encoding is a compressed dynamic self-index for highly repetitive texts and has a large disadvantage that the pattern search for short…

We show that the compressed suffix array and the compressed suffix tree of a string $T$ can be built in $O(n)$ deterministic time using $O(n\log\sigma)$ bits of space, where $n$ is the string length and $\sigma$ is the alphabet size.…

We consider the problem of encoding two-dimensional arrays, whose elements come from a total order, for answering \topk{} queries. The aim is to obtain encodings that use space close to the information-theoretic lower bound, which can be…

The merging of succinct data structures is a well established technique for the space efficient construction of large succinct indexes. In the first part of the paper we propose a new algorithm for merging succinct representations of de…

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…

We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…

We describe an algorithm for compressing a partially ordered set, or \emph{poset}, so that it occupies space matching the information theory lower bound (to within lower order terms), in the worst case. Using this algorithm, we design a…