PSO-FeatureFusion: a general framework for fusing heterogeneous features via particle swarm optimization.

Motivation: Integrating heterogeneous biological data is a central challenge in bioinformatics, especially when modeling complex relationships among entities such as drugs, diseases, and molecular features. Existing methods often rely on static or separate feature extraction processes, which may fail to capture interactions across diverse feature types and reduce predictive accuracy. Results: To address these limitations, we propose PSO-FeatureFusion, a unified framework that combines particle swarm optimization with neural networks to jointly integrate and optimize features from multiple biological entities. By modeling pairwise feature interactions and learning their optimal contributions, the framework captures individual feature signals and their interdependencies in a task-agnostic and modular manner. We applied PSO-FeatureFusion to two bioinformatics tasks-drug-drug interaction and drug-disease association prediction-using multiple benchmark datasets. Across both tasks, the framework achieved strong performance across evaluation metrics, often outperforming or matching state-of-the-art baselines, including deep learning and graph-based models. The method also demonstrated robustness with limited hyperparameter tuning and flexibility across datasets with varying feature structures. PSO-FeatureFusion provides a scalable and practical solution for researchers working with high-dimensional biological data. Its adaptability and interpretability make it well-suited for applications in drug discovery, disease prediction, and other bioinformatics domains. Availability and implementation: The source code and datasets are available at https://github.com/raziyehmasumshah/PSO-FeatureFusion.