Constructing a PPI Network Based on Deep Transfer Learning for Protein Complex Detection

Xin Yuan, Hangyu Deng, Jinglu Hu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


In the detection of protein complexes, the completeness of a protein–protein interaction (PPI) network is crucial. Complete PPI networks, however, are not available for most species because experimentally identified PPIs are usually very limited. This paper proposes a deep learning based PPI predictor to construct a complete PPI network, from which protein complexes are detected using a spectral clustering method. For this purpose, the unknown PPIs are estimated by using a deep PPI predictor consisting of a semi-supervised SVM classifier and a deep feature extractor of the convolutional neural network (CNN). Meanwhile, the similarities of gene ontology (GO) annotations contribute to protein interactions, and the differences of subcellular localizations contribute to negative interactions. Considering that, we pretrain the deep CNN feature extractor in a class of deep GO annotation and subcellular localization predictors using datasets from the type species, then transfer it to the PPI prediction model for fine-tuning. In this way, we have a deep PPI detector enhanced with transfer learning of GO annotation and subcellular localization prediction. Experimental results on benchmark datasets show that the proposed method outperforms the state-of-the-art methods.

Original languageEnglish
Pages (from-to)436-444
Number of pages9
JournalIEEJ Transactions on Electrical and Electronic Engineering
Issue number3
Publication statusPublished - 2022 Mar

ASJC Scopus subject areas

  • Electrical and Electronic Engineering


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