Accurately predicting protein subcellular localization is essential for understanding biological function and informing medical research. To address the limitations of traditional laboratory techniques, this study introduces two deep learning frameworks-ML-FGAT and ML-GRat-for multi-label protein subcellular localization (ML-PSL). ML-FGAT integrates seven diverse feature encoding schemes-DC, PsePSSM, CTD, GO, CT, DDE, and EBGW [5]-followed by Differential Evolution (DE)-based feature fusion and entropy-guided selection. To enhance representation quality, a self-attention-based feature recalibration (SAFR) module is introduced to emphasize biologically relevant features. A Feature-Generative Adversarial Network (F-GAN) then balances class distributions, and classification is performed using a Graph Attention Network (GAT). ML-FGAT achieved OAA scores ranging from 93.5% to 98.8% across five test datasets. ML-GRat uses DE for feature weighting and Canonical Correlation Analysis (CCA) for dimensionality reduction, followed by SAFR and a hybrid GAT-ResNet classifier. This model achieved OAA scores between 94.0% and 98.9% on six independent datasets, including SARS-CoV-2 and human proteins [6]. The proposed models demonstrate robust generalization, high predictive performance, and improved interpretability for ML-PSL tasks in computational biology.