13 papers · ranked by Valyu relevance
A. V. Baranov, E. A. Kiselev, B. M. Shabanov, A. A. Sorokin + 1 more
'P. N. Telegin'] Abstract—Performance of supercomputer depends on the quality of resource manager, one of its functions is assignment of jobs to the nodes of clusters or MPP computers. Parts of parallel programs interact with each other with different intensity, and mapping of program to supercomputer nodes influence…
Valerie Engelmayer, Dobrik Georgiev, Petar Veličković
Neural algorithmic reasoners are parallel processors. Teaching them sequential algorithms contradicts this nature, rendering a significant share of their computations redundant. Parallel algorithms however may exploit their full computational power, therefore requiring fewer layers to be executed. This drastically…
Donald S. Ene, V.I.E Anireh
- Evaluating how well a whole system or set of subsystems performs is one of the primary objectives of performance testing. We can tell via performance assessment if the architecture implementation meets the design objectives. Performance evaluations of several parallel algorithms are compared in this study. Both…
Jesper Larsson Träff
These lecture notes are designed to accompany an imaginary, virtual, undergraduate, one or two semester course on fundamentals of Parallel Computing as well as to serve as background and reference for graduate courses on High-Performance Computing, parallel algorithms and shared-memory multiprocessor programming. They…
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…
Michael T. Goodrich, Vinesh Sridhar
Embedded systems and Internet of Things (IoT) applications motivate in-place parallel algorithms, which avoid allocating additional shared memory past the input. Work by Gu, Obeya, and Shun [APOCS '21] defines a family of PIP (parallel in-place) models and parallel algorithms that eschew auxiliary memory at high…
Rajendra Purohit, K. R. Chowdhary, Sunıl Dutt Purohıt
—Arrival of multicore systems has enforced a new scenario in computing, the parallel and distributed algorithms are fast replacing the older sequential algorithms, with many challenges of these techniques. The distributed algorithms provide distributed processing using distributed file systems and processing units…
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…
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…
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…