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19 papers · ranked by Valyu relevance

01
AarXiv2012
In-place associative integer sorting
A. Emre Cetin
A novel integer value-sorting technique is proposed replacing bucket sort, distribution counting sort and address calculation sort family of algorithms. It requires only constant amount of additional memory. The technique is inspired from one of the ordinal theories of "serial order in behavior" and explained by the…
85relevance
02
AarXiv2012
Sorting distinct integers using improved in-place associative sort
A. Emre Cetin
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. Afterwards, the technique was further improved and an in-place sorting algorithm is…
85relevance
03
AarXiv2012
Sorting distinct integer keys using in-place associative sort
A. Emre Cetin
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. The technique was explained by the analogy with the three main stages in the…
84relevance
04
AarXiv2013
The technique of in-place associative sorting
A. Emre Cetin
In the first place, a novel, yet straightforward in-place integer value-sorting algorithm is presented. It sorts in linear time using constant amount of additional memory for storing counters and indices beside the input array. The technique is inspired from the principal idea behind one of the ordinal theories of…
80relevance
05
AarXiv2012
Comparison of Bucket Sort and RADIX Sort
Panu Horsmalahti
Bucket sort and RADIX sort are two well-known integer sorting algorithms. This paper measures empirically what is the time usage and memory consumption for different kinds of input sequences. The algorithms are compared both from a theoretical standpoint but also on how well they do in six different use cases using…
79relevance
06
AarXiv2018
Sorting Real Numbers in $O(n\sqrt{\log n})$ Time and Linear Space
Yijie Han
Sorting is a fundamental problem in computer science and is used almost everywhere in programming. Currently sorting can be classified as comparison sorting and integer sorting. It is well known that comparison sorting has θ(n log n) time [4] (logarithms in this paper have base 2). Integer sorting, on the other hand…
74relevance
07
PPubMed3 Feb 2026
Performance evaluation of GPU-based parallel sorting algorithms Performance evaluation of GPU
Mohammed Alaa Ala’anzy, Nurdaulet Tolendi, Baizhan Baubek, Abdulmohsen Algarni + 1 more
Sorting can be approached in two main ways: sequentially and in parallel. In sequential sorting, data is processed in a single-threaded manner, which can be slow for large datasets. However, parallel sorting divides the task across multiple processing units, enabling faster results by processing data simultaneously.…
70relevance
08
PPubMed19 Nov 2021
A fast vectorized sorting implementation based on the ARM scalable vector extension (SVE)
Bérenger Bramas, Muhammad Aleem
The way developers implement their algorithms and how these implementations behave on modern CPUs are governed by the design and organization of these. The vectorization units (SIMD) are among the few CPUs’ parts that can and must be explicitly controlled. In the HPC community, the x86 CPUs and their vectorization…
70relevance
09
PPubMed12 Feb 2021
Correct and stable sorting for overflow streaming data with a limited storage size and a uniprocessor
Suluk Chaikhan, Suphakant Phimoltares, Chidchanok Lursinsap, Marcin Woźniak
'Marcin Woźniak'] Tremendous quantities of numeric data have been generated as streams in various cyber ecosystems. Sorting is one of the most fundamental operations to gain knowledge from data. However, due to size restrictions of data storage which includes storage inside and outside CPU with respect to the massive…
69relevance
10
PPubMed5 Apr 2022
Fast continuous streaming sort in big streaming data environment under fixed-size single storage Fast continuous streaming sort in big streaming data environment under fixed-size single storage
Suluk Chaikhan, Suphakant Phimoltares, Chidchanok Lursinsap, Mohamed Hammad
'Mohamed Hammad'] Big streaming data environment concerns a complicated scenario where data to be processed continuously flow into a processing unit and certainly cause a memory overflow problem. This obstructs the adaptation of deploying all existing classic sorting algorithms because the data to be sorted must be…
65relevance
11
BbioRxiv15 Jan 2016
The 2-approximation algorithm of sorting by prefix transposition revisited
Md. Shafiqul Islam, Md. Khaledur Rahman, M. Sohel Rahman
A transposition is an operation that exchanges two adjacent blocks in a permutation. A prefix transposition always moves a prefix of the permutation to another location. In this article, we use a data structure, called the permutation tree, to improve the running time of the best known approximation algorithm (with…
64relevance
12
PPubMed19 Apr 2023
Parallel Multi-Deque Partition Dual-Deque Merge sorting algorithm using OpenMP
Sirilak Ketchaya, Apisit Rattanatranurak
Quicksort is an important algorithm that uses the divide and conquer concept, and it can be run to solve any problem. The performance of the algorithm can be improved by implementing this algorithm in parallel. In this paper, the parallel sorting algorithm named the Multi-Deque Partition Dual-Deque Merge Sorting…
62relevance
13
BbioRxiv26 Jul 2024
A fast and simple approach to *k*-mer decomposition
Patrick Kunzmann
Alignment searches are fast heuristic methods to identify similar regions between two sequences. This group of algorithms is ubiquitously used in a myriad of software to find homologous sequences or to map sequence reads to genomes. Often the first step in alignment searches is k-mer decomposition: listing all…
61relevance
14
CchemRxiv1 Mar 2024
A simple software program for sorting biological sequences into unique groups.
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
58relevance
15
BbioRxiv25 Oct 2023
gtfsort: a tool to efficiently sort GTF files
Alejandro Gonzales-Irribarren
The General Transfer Format (GTF) is a widely used format for gene annotation data, integral to various downstream analyses. Efficient management and sorting of GTF data are relevant, as unsorted data can intere with computational efficiency and interpretability. Sorted GTF data, on the other hand, enable more…
58relevance
16
CchemRxiv2 Mar 2022
CrystalNets.jl: Identification and Classification of Crystal Topologies
Lionel Zoubritzky, François-Xavier Coudert
We present here an open-source Julia library for the topological identification of crystalline materials, with algorithmic and computational improvements over the previously available software in the field, resulting in a speed increase of one order of magnitude. This new algorithm and implementation can therefore be…
57relevance
17
BbioRxiv8 Jul 2020
Bedtk: Finding Interval Overlap with Implicit Interval Tree
Heng Li, Jiazhen Rong
We present bedtk, a new toolkit for manipulating genomic intervals in the BED format. It supports sorting, merging, intersection, subtraction and the calculation of the breadth of coverage. Bedtk employs implicit interval tree, a new data structure for fast interval overlap queries. It is several to tens of times…
56relevance
18
BbioRxiv4 Jun 2019
Prefix Block-Interchanges on Binary and Ternary Strings
Md. Khaledur Rahman, M. Sohel Rahman
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and in a prefix block-interchange, one block is always the prefix of that…
55relevance
19
BbioRxiv13 Jul 2024
Where the patterns are: repetition-aware compression for colored de Bruijn graphs^⋆^
Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro
We describe lossless compressed data structures for the colored de Bruijn graph (or, c-dBG). Given a collection of reference sequences, a c-dBG can be essentially regarded as a map from k-mers to their color sets. The color set of a k-mer is the set of all identifiers, or colors, of the references that contain the…
54relevance

Results for integer sorting

In-place associative integer sorting

Sorting distinct integers using improved in-place associative sort

Sorting distinct integer keys using in-place associative sort

The technique of in-place associative sorting

Comparison of Bucket Sort and RADIX Sort

Sorting Real Numbers in $O(n\sqrt{\log n})$ Time and Linear Space

Performance evaluation of GPU-based parallel sorting algorithms Performance evaluation of GPU

A fast vectorized sorting implementation based on the ARM scalable vector extension (SVE)

Correct and stable sorting for overflow streaming data with a limited storage size and a uniprocessor

Fast continuous streaming sort in big streaming data environment under fixed-size single storage Fast continuous streaming sort in big streaming data environment under fixed-size single storage

The 2-approximation algorithm of sorting by prefix transposition revisited

Parallel Multi-Deque Partition Dual-Deque Merge sorting algorithm using OpenMP

A fast and simple approach to k-mer decomposition

A simple software program for sorting biological sequences into unique groups.

gtfsort: a tool to efficiently sort GTF files

CrystalNets.jl: Identification and Classification of Crystal Topologies

Bedtk: Finding Interval Overlap with Implicit Interval Tree

Prefix Block-Interchanges on Binary and Ternary Strings

Where the patterns are: repetition-aware compression for colored de Bruijn graphs^⋆^

In-place associative integer sorting

Sorting distinct integers using improved in-place associative sort

Sorting distinct integer keys using in-place associative sort

The technique of in-place associative sorting

Comparison of Bucket Sort and RADIX Sort

Sorting Real Numbers in $O(n\sqrt{\log n})$ Time and Linear Space

Performance evaluation of GPU-based parallel sorting algorithms Performance evaluation of GPU

A fast vectorized sorting implementation based on the ARM scalable vector extension (SVE)

Correct and stable sorting for overflow streaming data with a limited storage size and a uniprocessor

Fast continuous streaming sort in big streaming data environment under fixed-size single storage Fast continuous streaming sort in big streaming data environment under fixed-size single storage

The 2-approximation algorithm of sorting by prefix transposition revisited

Parallel Multi-Deque Partition Dual-Deque Merge sorting algorithm using OpenMP

A fast and simple approach to k-mer decomposition

A simple software program for sorting biological sequences into unique groups.

gtfsort: a tool to efficiently sort GTF files

CrystalNets.jl: Identification and Classification of Crystal Topologies

Bedtk: Finding Interval Overlap with Implicit Interval Tree

Prefix Block-Interchanges on Binary and Ternary Strings

Where the patterns are: repetition-aware compression for colored de Bruijn graphs^⋆^

Results for integer sorting

In-place associative integer sorting

Sorting distinct integers using improved in-place associative sort

Sorting distinct integer keys using in-place associative sort

The technique of in-place associative sorting

Comparison of Bucket Sort and RADIX Sort

Sorting Real Numbers in $O(n\sqrt{\log n})$ Time and Linear Space

Performance evaluation of GPU-based parallel sorting algorithms Performance evaluation of GPU

A fast vectorized sorting implementation based on the ARM scalable vector extension (SVE)

Correct and stable sorting for overflow streaming data with a limited storage size and a uniprocessor

Fast continuous streaming sort in big streaming data environment under fixed-size single storage Fast continuous streaming sort in big streaming data environment under fixed-size single storage

The 2-approximation algorithm of sorting by prefix transposition revisited

Parallel Multi-Deque Partition Dual-Deque Merge sorting algorithm using OpenMP

A fast and simple approach to *k*-mer decomposition

A simple software program for sorting biological sequences into unique groups.

gtfsort: a tool to efficiently sort GTF files

CrystalNets.jl: Identification and Classification of Crystal Topologies

Bedtk: Finding Interval Overlap with Implicit Interval Tree

Prefix Block-Interchanges on Binary and Ternary Strings

Where the patterns are: repetition-aware compression for colored de Bruijn graphs^⋆^

In-place associative integer sorting

Sorting distinct integers using improved in-place associative sort

Sorting distinct integer keys using in-place associative sort

The technique of in-place associative sorting

Comparison of Bucket Sort and RADIX Sort

Sorting Real Numbers in $O(n\sqrt{\log n})$ Time and Linear Space

Performance evaluation of GPU-based parallel sorting algorithms Performance evaluation of GPU

A fast vectorized sorting implementation based on the ARM scalable vector extension (SVE)

Correct and stable sorting for overflow streaming data with a limited storage size and a uniprocessor

Fast continuous streaming sort in big streaming data environment under fixed-size single storage Fast continuous streaming sort in big streaming data environment under fixed-size single storage

The 2-approximation algorithm of sorting by prefix transposition revisited

Parallel Multi-Deque Partition Dual-Deque Merge sorting algorithm using OpenMP

A fast and simple approach to *k*-mer decomposition

A simple software program for sorting biological sequences into unique groups.

gtfsort: a tool to efficiently sort GTF files

CrystalNets.jl: Identification and Classification of Crystal Topologies

Bedtk: Finding Interval Overlap with Implicit Interval Tree

Prefix Block-Interchanges on Binary and Ternary Strings

Where the patterns are: repetition-aware compression for colored de Bruijn graphs^⋆^

A fast and simple approach to k-mer decomposition

A fast and simple approach to k-mer decomposition