Related papers: Two simple full-text indexes based on the suffix a…
The linear-size suffix tries (LSTries) [Crochemore et al., TCS 2016] are a version of suffix trees in which the edge labels are single characters, yet are able to perform pattern matching queries in optimal time. Instead of explicitly…
A compressed full-text self-index occupies space close to that of the compressed text and simultaneously allows fast pattern matching and random access to the underlying text. Among the best compressed self-indexes, in theory and in…
Document listing on string collections is the task of finding all documents where a pattern appears. It is regarded as the most fundamental document retrieval problem, and is useful in various applications. Many of the fastest-growing…
FastText has established itself as a fundamental algorithm for learning word representations, demonstrating exceptional capability in handling out-of-vocabulary words through character-level n-gram embeddings. However, its hash-based…
Efficient construction of the suffix tree given an input text is an active area of research from the time it was first introduced. Both theoretical computer scientists and engineers tackled the problem. In this paper we focus on the fastest…
Transformer models rely heavily on the scaled dot-product attention (SDPA) operation, typically implemented as FlashAttention. Characterized by its frequent interleaving of matrix multiplications and softmax operations, FlashAttention fails…
Lazy search trees (Sandlund & Wild FOCS 2020, Sandlund & Zhang SODA 2022) are sorted dictionaries whose update and query performance smoothly interpolates between that of efficient priority queues and binary search trees - automatically,…
We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…
We present a simple algorithm for computing the document array given a string collection and its suffix array as input. Our algorithm runs in linear time using constant additional space for strings from constant alphabets.
In 1979 Stockman introduced the SSS* minimax search algorithm that domi- nates Alpha-Beta in the number of leaf nodes expanded. Further investigation of the algorithm showed that it had three serious drawbacks, which prevented its use by…
GPU-based concurrent data structures (CDSs) achieve high throughput for read-only queries, but efficient support for dynamic updates on fully GPU-resident data remains challenging. Ordered CDSs (e.g., B-trees and LSM-trees) maintain an…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
In this paper, we propose a learning-based supervised discrete hashing method. Binary hashing is widely used for large-scale image retrieval as well as video and document searches because the compact representation of binary code is…
Data series indexes are necessary for managing and analyzing the increasing amounts of data series collections that are nowadays available. These indexes support both exact and approximate similarity search, with approximate search…
We attempt to determine the best order and search algorithm to store $n$ comparable data items in an array, $A$, of length $n$ so that we can, for any query value, $x$, quickly find the smallest value in $A$ that is greater than or equal to…
Sorting and binary searching a dense array can be considered the simplest and most space efficient form of indexing. This holds especially on GPUs as they exhibit exceptional sorting performance. However, the popular opinion is that such a…
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…
Graph similarity search has received considerable attention in many applications, such as bioinformatics, data mining, pattern recognition, and social networks. Existing methods for this problem have limited scalability because of the huge…
The longest common prefix (LCP) array is a versatile auxiliary data structure in indexed string matching. It can be used to speed up searching using the suffix array (SA) and provides an implicit representation of the topology of an…
We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using…