14 papers · ranked by Valyu relevance
Matthias Volk, Borzoo Bonakdarpour, Joost-Pieter Katoen, Saba Aflaki
Randomization is a key concept in distributed computing to tackle impossibility results. This also holds for self-stabilization in anonymous networks where coin flips are often used to break symmetry. Although the use of randomization in self-stabilizing algorithms is rather common, it is unclear what the optimal coin…
Lesia Mochurad, Andrii Sydor, Oleh Ratinskiy
Introduction Streaming services are highly popular today. Millions of people watch live streams or videos and listen to music. Methods One of the most popular streaming platforms is Twitch, and data from this type of service can be a good example for applying the parallel DBSCAN algorithm proposed in this paper. Unlike…
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…
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt
The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and a major contributor to overall runtime due to the associated quadratic…
Guohao Dou
We propose an algorithm to simulate Markovian SIS epidemics with homogeneous rates and pairwise interactions on a fixed undirected graph, assuming a distributed memory model of parallel programming and limited bandwidth. We offer an implementation of the algorithm in the form of pseudocode in the Appendix. Also, we…
Zhen Shang, Jin-Kao Hao, Fei Ma, Daniele D’Agostino
Product development projects usually contain many interrelated activities with complex information dependences, which induce activity rework, project delay and cost overrun. To reduce negative impacts, scheduling interrelated activities in an appropriate sequence is an important issue for project managers. This study…
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.…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
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…
Zeyu Xia, Canqun Yang, Chenchen Peng, Yifei Guo + 3 more
'Tao Tang' 'Yingbo Cui'] Background The advent of Single Molecule Real-Time (SMRT) sequencing has overcome many limitations of second-generation sequencing, such as limited read lengths, PCR amplification biases. However, longer reads increase data volume exponentially and high error rates make many existing alignment…
Ragnar Groot Koerkamp, Igor Martayan
Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular…
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez + 2 more
Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation of longer sequences at a much lower price. Thus, long-read sequencing technologies have become increasingly popular in sequencing-based studies. However…