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© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

High-throughput microarrays contain a huge number of genes. Determining the relationships between all these genes is a time-consuming computation. In this paper, the authors provide a parallel algorithm for finding the Pearson’s correlation coefficient between genes measured in the Affymetrix microarrays. The main idea in the proposed algorithm, ForkJoinPcc, mimics the well-known parallel programming model: the fork–join model. The parallel MATLAB APIs have been employed and evaluated on shared or distributed multiprocessing systems. Two performance metrics—the processing and communication times—have been used to assess the performance of the ForkJoinPcc. The experimental results reveal that the ForkJoinPcc algorithm achieves a substantial speedup on the cluster platform of 62× compared with a 3.8× speedup on the multicore platform.

Details

Title
ForkJoinPcc Algorithm for Computing the Pcc Matrix in Gene Co-Expression Networks
Author
Amel Ali Alhussan 1   VIAFID ORCID Logo  ; Hussah Nasser AlEisa 1 ; Atteia, Ghada 2   VIAFID ORCID Logo  ; Solouma, Nahed H 3 ; Rania Ahmed Abdel Azeem Abul Seoud 4   VIAFID ORCID Logo  ; Ayoub, Ola S 5 ; Ghoneim, Vidan F 6 ; Nagwan Abdel Samee 2   VIAFID ORCID Logo 

 Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; [email protected] 
 Department of Information Technology, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; [email protected] (G.A.); [email protected] (N.A.S.) 
 Biomedical Engineering Department, King Faisal University, P.O. Box 9149, Alahsa 13980, Saudi Arabia; [email protected] 
 Department of Electronics and Communication Engineering, Faculty of Engineering, Fayoum University, Fayoum 63511, Egypt; [email protected] 
 Biomedical Engineering Department, Cairo University, Giza 12511, Egypt; [email protected] 
 Biomedical Engineering Department, Helwan University, Helwan 11731, Egypt; [email protected] 
First page
1174
Publication year
2022
Publication date
2022
Publisher
MDPI AG
e-ISSN
20799292
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2652969968
Copyright
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.