Automated drug design for druggable target identification using integrated stacked autoencoder and hierarchically self-adaptive optimization

• Published in: Scientific reports Vol. 15; no. 1; pp. 32205 - 22
• Main Authors: Masoomkhah, Seyed Saeed, Rezaee, Khosro, Ansari, Mojtaba, Eslami, Hossein, Shirani, Shahin, Alizadeh, Mohammad Hossein
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.09.2025; Nature Publishing Group; Nature Portfolio
• Subjects: 631/154; 631/181; 631/378; 639/166; Accuracy; Algorithms; Artificial intelligence; Autoencoder; Automation; Classification; Computer applications; Convergence; Costs; Datasets; Deep Learning; Design; Drug Design; Drug development; Drug discovery; Drug Discovery - methods; Efficiency; Feature selection; Genetic algorithms; Humanities and Social Sciences; Humans; Informatics; Machine learning; multidisciplinary; Neural networks; Optimization techniques; Particle swarm optimization algorithm; Pharmaceuticals; Proteins; R&D; Regulatory approval; Research & development; Science; Science (multidisciplinary); Stacked autoencoder; Support Vector Machine; Support vector machines; Deep learning; Stacked autoencoder; Drug design; Machine learning; Particle swarm optimization algorithm
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-025-18091-x

Drug classification and target identification are crucial yet challenging steps in drug discovery. Existing methods often suffer from inefficiencies, overfitting, and limited scalability. Traditional approaches like support vector machines and XGBoost struggle to handle large, complex pharmaceutical datasets effectively. Deep learning models, while powerful, face challenges with interpretability, computational complexity, and generalization to unseen data. This study addresses these limitations by introducing a novel framework: optSAE + HSAPSO. This framework integrates a stacked autoencoder (SAE) for robust feature extraction with a hierarchically self-adaptive particle swarm optimization (HSAPSO) algorithm for adaptive parameter optimization. This combination delivers superior performance across various classification metrics. Experimental evaluations on datasets from DrugBank and Swiss-Prot demonstrate that optSAE + HSAPSO achieves a high accuracy of 95.52%. Notably, it exhibits significantly reduced computational complexity (0.010 s per sample) and exceptional stability (± 0.003). Compared to state-of-the-art methods, the framework offers higher accuracy, faster convergence, and greater resilience to variability. Furthermore, ROC and convergence analyses confirm its robustness and generalization capability, maintaining consistent performance across both validation and unseen datasets. By leveraging advanced optimization techniques, the framework efficiently handles large feature sets and diverse pharmaceutical data, making it a scalable and adaptable solution for real-world drug discovery applications. However, the method’s performance is dependent on the quality of the training data, and fine-tuning may be necessary for high-dimensional datasets. Despite these limitations, the optSAE + HSAPSO framework demonstrates transformative potential, significantly reducing computational overhead while improving classification accuracy and reliability. This work advances the field of pharmaceutical informatics by presenting a reliable and efficient framework for drug classification and target identification. These findings open promising avenues for future research, including extending the framework to other domains such as disease diagnostics or genetic data classification, ultimately accelerating the drug development process.