PPISB : A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

16 Scopus Citations
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Author(s)

  • Xiaojuan Wang
  • Yue Yang
  • Yizhou He
  • Jun Zhang
  • Lun Hu

Related Research Unit(s)

Detail(s)

Original languageEnglish
Pages (from-to)1606-1612
Journal / PublicationIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume20
Issue number2
Online published8 Aug 2022
Publication statusPublished - Mar 2023

Abstract

Protein-protein interactions (PPIs) play an essential role for most of biological processes in cells. Many computational algorithms have thus been proposed to predict PPIs. However, most of them heavily rest on the biological information of proteins while ignoring the latent structural features of proteins presented in a PPI network. In this paper, we propose an efficient network-based prediction algorithm, namely PPISB, based on a mixed membership stochastic blockmodel. By simulating the generative process of a PPI network, PPISB is able to capture the latent community structures. The inference procedure adopted by PPISB further optimizes the membership distributions of proteins over different complexes. After that, a distance measure is designed to compute the similarity between two proteins in terms of their likelihoods of being in the same complex, thus verifying whether they interact with each other or not. To evaluate the performance of PPISB, a series of extensive experiments have been conducted with five PPI networks collected from different species and the results demonstrate that PPISB has a promising performance when applied to predict PPIs in terms of several evaluation metrics. Hence, we reason that PPISB is preferred over state-of-the-art network-based prediction algorithms especially for predicting potential PPIs. © 2022 IEEE.

Research Area(s)

  • Bioinformatics, Biology, Feature extraction, Genomics, Machine learning, PPI network, prediction, Prediction algorithms, protein-protein interaction, Proteins, stochastic blockmodel, Task analysis

Citation Format(s)

PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel. / Wang, Xiaojuan; Yang, Wen; Yang, Yue et al.
In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 20, No. 2, 03.2023, p. 1606-1612.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review