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

## TL;DR

This paper introduces a new deep learning model for predicting protein interactions in microbes linked to heart disease, showing high accuracy and potential for discovering new treatments.

## Contribution

A novel deep denoising autoencoder model (DAEPPI) that combines evolutionary information and CatBoost for accurate PPI prediction.

## Key findings

- DAEPPI achieved 97.85% and 98.49% accuracy on yeast and human datasets, respectively.
- The model outperformed existing methods in predicting protein–protein interactions.
- DAEPPI revealed significant interactions relevant to cardiovascular disease mechanisms.

## Abstract

Protein–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.

In 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.

Our 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.

Additionally, 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.