A Distributed Framework for Large-scale Protein-protein Interaction Data Analysis and Prediction Using MapReduce

doi:10.1109/JAS.2021.1004198

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	A Distributed Framework for Large-scale Protein-protein Interaction Data Analysis and Prediction Using MapReduce
	Lun Hu; Shicheng Yang; Xin Luo; Huaqiang Yuan; Khaled Sedraoui; MengChu Zhou
刊名	IEEE/CAA Journal of Automatica Sinica
	2022
卷号	9 期号:1 页码:160-172
关键词	Distributed computing large-scale prediction machine learning MapReduce protein-protein interaction (PPI)
ISSN号	2329-9266
DOI	10.1109/JAS.2021.1004198
英文摘要	Protein-protein interactions are of great significance for human to understand the functional mechanisms of proteins. With the rapid development of high-throughput genomic technologies, massive protein-protein interaction (PPI) data have been generated, making it very difficult to analyze them efficiently. To address this problem, this paper presents a distributed framework by reimplementing one of state-of-the-art algorithms, i.e., CoFex, using MapReduce. To do so, an in-depth analysis of its limitations is conducted from the perspectives of efficiency and memory consumption when applying it for large-scale PPI data analysis and prediction. Respective solutions are then devised to overcome these limitations. In particular, we adopt a novel tree-based data structure to reduce the heavy memory consumption caused by the huge sequence information of proteins. After that, its procedure is modified by following the MapReduce framework to take the prediction task distributively. A series of extensive experiments have been conducted to evaluate the performance of our framework in terms of both efficiency and accuracy. Experimental results well demonstrate that the proposed framework can considerably improve its computational efficiency by more than two orders of magnitude while retaining the same high accuracy.
内容类型	期刊论文
源URL	[http://ir.ia.ac.cn/handle/173211/45982]
专题	自动化研究所_学术期刊_IEEE/CAA Journal of Automatica Sinica
推荐引用方式 GB/T 7714	Lun Hu,Shicheng Yang,Xin Luo,et al. A Distributed Framework for Large-scale Protein-protein Interaction Data Analysis and Prediction Using MapReduce[J]. IEEE/CAA Journal of Automatica Sinica,2022,9(1):160-172.
APA	Lun Hu,Shicheng Yang,Xin Luo,Huaqiang Yuan,Khaled Sedraoui,&MengChu Zhou.(2022).A Distributed Framework for Large-scale Protein-protein Interaction Data Analysis and Prediction Using MapReduce.IEEE/CAA Journal of Automatica Sinica,9(1),160-172.
MLA	Lun Hu,et al."A Distributed Framework for Large-scale Protein-protein Interaction Data Analysis and Prediction Using MapReduce".IEEE/CAA Journal of Automatica Sinica 9.1(2022):160-172.