EvoFuzzy: Evolutionary Fuzzy Approach for Ensembling Reconstructed Genetic Networks
Hasini Nakulugamuwa Gamage, Jaskaran Kaur Gill, Madhu Chetty, Suryani Lim, Jennifer Hallinan · BioMedInformatics · 2025
Background: Reconstructing gene regulatory networks (GRNs) from gene expression data remains a major challenge in systems biology due to the inherent complexity of biological systems and the limitations of existing reconstruction methods, which often yield high false-positive rates. This study aims to develop a robust and adaptive approach to enhance the accuracy of inferred GRNs by integrating multiple modelling paradigms. Methods: We introduce EvoFuzzy, a novel algorithm that integrates evolutionary computation and fuzzy logic to aggregate GRNs reconstructed using Boolean, regression, and fuzzy modelling techniques. The algorithm initializes an equal number of individuals from each modelling method to form a diverse population, which evolves through fuzzy trigonometric differential evolution. Gene expression values are predicted using a fuzzy logic-based predictor with confidence levels, and a fitness function is applied to identify the optimal consensus network. Results: The proposed method was evaluated using simulated benchmark datasets and a real-world SOS gene repair dataset. Experimental results demonstrated that EvoFuzzy consistently outperformed existing state-of-the-art GRN reconstruction methods in terms of accuracy and robustness. Conclusions: The fuzzy trigonometric differential evolution approach plays a pivotal role in refining and aggregating multiple network outputs into a single, optimal consensus network, making EvoFuzzy a powerful and reliable framework for reconstructing biologically meaningful gene regulatory networks.