Variational Autoencoders for Generative Drug-Gene Interactions in Periodontal Bone Resorption

Introduction Periodontal bone resorption is a significant dental problem causing tooth loss and impaired oral function. It is influenced by factors such as bacterial plaque, genetic predisposition, smoking, systemic diseases, medications, hormonal changes, and poor oral hygiene. This condition disrupts bone remodeling, favoring resorptive processes. Variational autoencoders (VAEs) can learn the distribution of drug-gene interactions from existing data, identify potential drug targets, and predict therapeutic effects. This study investigates the generation of drug-gene interactions in periodontal bone resorption using VAEs. Methods A bone resorptive drugs dataset was retrieved from Probes and Drugs and analyzed using Cytoscape (https://cytoscape.org/) and CytoHubba (https://apps.cytoscape.org/apps/cytohubba), powerful tools for studying drug-gene interactions in bone resorption. The dataset was then prepared for matrix representation, with normalized input data. It was subsequently divided into training, validation, and testing sets. We then built an encoder-decoder network, defined a loss function, optimized parameters, and fine-tuned hyperparameters. Using VAEs, we generated new drug-gene interactions, assessed model performance, and visualized the latent space with reconstructed drug-gene interactions for further insights. Results The analysis revealed the top hub genes in drug-gene interactions, including Matrix Metalloproteinase (MMP) 14, MMP 9, HIF1A, STAT1, MAPT, CAS9, MMP2, CASP3, MMP1, and MAK1. The VAE's reconstruction accuracy was measured using mean squared error (MSE), with an average squared difference of 0.077. Additionally, the KL divergence value was 2.349, and the average reconstruction log-likelihood was -246. Conclusion The generative variational encoder model for drug-gene interactions in bone resorption demonstrates high accuracy and reliability in representing complex drug-gene relationships within this context.