Drug-Drug Interaction Prediction Based on Probability Transfer Multi-modal Feature Representation Learning

Yu Wei, Lei Wang, Chang Qin Yu, Shuo Yang, Meng Meng Wei, Zhu Hong You

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

In drug discovery and combination therapy, drug-drug interactions can lead to adverse reactions, affecting not only disease treatment but also risking the market withdrawal of new drugs. Traditional experiments in vitro and in vivo are labor-intensive and time-consuming for identifying potential DDIs. Although existing computational methods offer new perspectives for DDIs identification, they still have limitations. This paper innovatively uses the probability transfer matrix combined with Stacked Denoising Autoencoder to propose a model named MultiPT-DDI to calculate the correlation of edge nodes in the adjacency matrix, which effectively learns the multi-level representation of nodes and mitigates the probabilistic bias of the edge nodes in the sparse matrices and the noise of the original data. Specifically, the method first samples multiple bipartite graph networks using random surfing thus obtaining multiple probabilistic transfer matrices. Subsequently, multiple denoising autoencoder modules are employed for layer-wise unsupervised pre-training of the network. Finally, we infer the relationships between drug pairs using the Random Forest algorithm. The experiment obtains the AUC score of 0.9433 and the AUPR score of 0.9372 in the 5-fold cross-validation, significantly outperforming existing models. In the case studies, 26 of the top 30 drug pairs with the highest scores were validated. The empirical evidence indicates that MultiPT-DDI is an effective complementary model for predicting potential DDIs, providing a reliable reference for traditional experimental methods.

Original languageEnglish
Title of host publicationProceedings - 2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024
EditorsMario Cannataro, Huiru Zheng, Lin Gao, Jianlin Cheng, Joao Luis de Miranda, Ester Zumpano, Xiaohua Hu, Young-Rae Cho, Taesung Park
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1238-1243
Number of pages6
ISBN (Electronic)9798350386226
DOIs
StatePublished - 2024
Event2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024 - Lisbon, Portugal
Duration: 3 Dec 20246 Dec 2024

Publication series

NameProceedings - 2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

Conference

Conference2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024
Country/TerritoryPortugal
CityLisbon
Period3/12/246/12/24

Keywords

  • bipartite graph networks
  • drug-drug interaction
  • multi-level representation
  • probability transfer matrix

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