AUTHOR=Zhou Senyu , Luo Jian , Tang Mei , Li Chaojun , Li Yang , He Wenhua 

TITLE=Predicting protein–protein interactions in microbes associated with cardiovascular diseases using deep denoising autoencoders and evolutionary information

JOURNAL=Frontiers in Pharmacology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2025.1565860

DOI=10.3389/fphar.2025.1565860

ISSN=1663-9812

ABSTRACT=IntroductionProtein–protein interactions (PPIs) are critical for understanding the molecular mechanisms underlying various biological processes, particularly in microbes associated with cardiovascular disease. Traditional experimental methods for detecting PPIs are often time-consuming and costly, leading to an urgent need for reliable computational approaches.MethodsIn this study, we present a novel model, the deep denoising autoencoder for protein–protein interaction (DAEPPI), which leverages the denoising autoencoder and the CatBoost algorithm to predict PPIs from the evolutionary information of protein sequences.ResultsOur extensive experiments demonstrate the effectiveness of the DAEPPI model, achieving average prediction accuracies of 97.85% and 98.49% on yeast and human datasets, respectively. Comparative analyses with existing effective methods further validate the robustness and reliability of our model in predicting PPIs.DiscussionAdditionally, we explore the application of DAEPPI in the context of cardiovascular disease, showcasing its potential to uncover significant interactions that could contribute to the understanding of disease mechanisms. Our findings indicate that DAEPPI is a powerful tool for advancing research in proteomics and could play a pivotal role in the identification of novel therapeutic targets in cardiovascular disease.