Predicting Large-scale Protein-protein Interactions by Extracting Coevolutionary Patterns with MapReduce Paradigm

Lun Hu, Bo Wei Zhao, Shicheng Yang, Xin Luo, Mengchu Zhou

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Protein-protein interactions are of great significance for us to understand the functional mechanisms of proteins. With the rapid development of high-throughput genomic technology, the amount of protein-protein interaction data has become so big that most of existing prediction algorithms are no longer applicable. To address this problem, we develop a distributed framework by reimplementing one of state-of-the-art algorithms, i.e., CoFex, by using MapReduce. In particular, we adopt a novel tree-based data structure to reduce the heavy memory consumption cased by the huge sequence information of proteins. After that, the procedure of CoFex is modified by following the paradigm of MapReduce such that the prediction task can be completed in a distributed manner, thus fulfilling the demanding requirements of large-scale protein-protein interaction prediction. A series of experiments have been conducted to evaluate the performance of the proposed distributed framework in terms of both efficiency and effectiveness. Experimental results demonstrate that the proposed framework can considerably improve the efficiency of CoFex by achieving more than two-orders-of-magnitude improvement in computational efficiency while retaining a comparable level of accuracy.

Original languageEnglish (US)
Title of host publication2021 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2021
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages939-944
Number of pages6
ISBN (Electronic)9781665442077
DOIs
StatePublished - 2021
Event2021 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2021 - Melbourne, Australia
Duration: Oct 17 2021Oct 20 2021

Publication series

NameConference Proceedings - IEEE International Conference on Systems, Man and Cybernetics

Conference

Conference2021 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2021
Country/TerritoryAustralia
CityMelbourne
Period10/17/2110/20/21

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Control and Systems Engineering
  • Human-Computer Interaction

Keywords

  • large-scale prediction
  • MapReduce
  • Protein-protein interaction
  • system biology

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