Related papers: Dismantling DivSufSort
We show how to modify the linear-time construction algorithm for suffix arrays based on induced sorting (Nong et al., DCC'09) such that it computes the array of longest common prefixes (LCP-array) as well. Practical tests show that this…
We present first algorithmic ideas for a practical and lightweight adaption of the DCX suffix array construction algorithm [Sanders et al., 2003] to the distributed-memory setting. Our approach relies on a bucketing technique which enables…
The suffix array is arguably one of the most important data structures in sequence analysis and consequently there is a multitude of suffix sorting algorithms. However, to this date the GSACA algorithm introduced in 2015 is the only known…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a…
The suffix tree is a very important data structure in string processing, but it suffers from a huge space consumption. In large-scale applications, compressed suffix trees (CSTs) are therefore used instead. A CST consists of three…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique which we call accelerated sampling. It runs in optimal O(n/p) local computation and communication, and requires a near…
Suffix sort plays a critical role in various computational algorithms including genomics as well as in frequently used day to day software applications. The sorting algorithm becomes tricky when we have lot of repeated characters in the…
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…
Motivated by the development of computer theory, the sorting algorithm is emerging in an endless stream. Inspired by decrease and conquer method, we propose a brand new sorting algorithmUltimately Heapsort. The algorithm consists of two…
The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
Sorting algorithms are the deciding factor for the performance of common operations such as removal of duplicates or database sort-merge joins. This work focuses on 32-bit integer keys, optionally paired with a 32-bit value. We present a…
We present a novel technique for constructing differentiable order-type operations, including soft ranking, soft top-k selection, and soft permutations. Our approach leverages an efficient closed-form formula for the inverse of the function…
This paper introduces a novel and efficient partitioning technique for quicksort, specifically designed for real-world data with duplicate elements (50-year-old problem). The method is referred to as "equal quicksort" or "eqsort". Based on…
Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…
Sorting is one of the oldest computing problems and is still very important in the age of big data. Various algorithms and implementation techniques have been proposed. In this study, we focus on comparison based, internal sorting…
Much of the copious literature on the subject of sorting has concentrated on minimizing the number of comparisons and/or exchanges/copies. However, a more appropriate yardstick for the performance of sorting algorithms is based on the total…
When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main…