Dual framework for rainfall prediction: a multi-seed machine and deep learning evaluation across Pakistan's climatic regimes.

Accurate prediction of rainfall events is vital for agriculture, hydrology, flood preparedness, and climate-adaptive strategies in regions of Pakistan susceptible to monsoons and droughts. Increasing climate variability highlights the need for reliable data-driven forecasting systems capable of precisely representing nonlinear atmospheric dynamics across different forecast intervals. This study introduces an extensive hybrid machine learning-deep learning (ML-DL) framework designed to classify daily rainfall events (rain vs. no rain) and predict several horizons (RainDay0-RainDay5) by utilizing 130,230 daily meteorological data collected from 10 geographically diverse cities in Pakistan between 1990 and 2025. Machine learning models, such as Extra Trees classifier, Histogram Gradient Boosting, Ridge Classifier, and Gaussian Naïve Bayes, underwent evaluation using leakage-free TimeSeriesSplit validation with SMOTE applied only to training folds using various seeds.To improve the quality of sequence representation, Variational Mode Decomposition (VMD) was utilized to extract band-limited intrinsic mode functions from meteorological signals, while Particle Swarm Optimization (PSO) was employed for adaptive hyperparameter tuning and genetic algorithms were used. Experimental findings indicate that ensemble ML models delivered robust baseline classification results across various cities, while VMD-augmented deep learning frameworks enhanced robustness and temporal learning consistency throughout different forecast horizons. Specifically, VMD-LSTM demonstrated robust performance in Hyderabad (Acc = 0.862, F1 = 0.871, AUC = 0.941), whereas VMD-GRU exhibited dependable discrimination ability in Jamshoro (AUC = 0.918), Quetta (AUC = 0.867), and Thatta (AUC = 0.896).The enhanced VMD-PSO-GRU (VPG) framework demonstrated superior rainfall classification performance across various cities, particularly excelling in Hyderabad (AUC = 0.912), Jamshoro (Acc = 0.882), and Thatta (Acc = 0.878). In multi-horizon forecasting, a proposed multi-head VMD-GRU-Attention model, improved by hybrid PSO-GA, provided the most reliable results across forecast lead times RainDay0-RainDay5. In short-term forecasting, the system achieved an Accuracy of 0.872 (RainDay0) in Hyderabad, while maintaining steady medium-term performance at RainDay3 (approximately 0.819 for Hyderabad; about 0.808 for Thatta) and long-term predictions near 0.80 at RainDay5 across Gharo, Thatta, and Mirpur Khas, showcasing resilience despite increasing forecast uncertainty. The proposed hybrid framework demonstrates improved stability in temporal learning, robustness against noise, and capacity to generalize across areas, validating its effectiveness for operational rainfall early-warning systems in various climatic settings of Pakistan.