Abstract
<jats:p>CVDs are heterogeneous, multifactorial disorders that remain the leading cause of global mor- tality from infancy to old age. It requires an early identification and treatment of risk factors to accelerate disease prevention and morbidity improvement. Advancements in transcriptomics tech- nologies gives large pool of heterogenous gene expression data. The technical heterogeneity of gene expression data reduces ability to compare multiple cross-platform datasets at once. To bridge gap, we systematically evaluate three data harmonization techniques: Shambhala-2, TDM, and UPC to align heterogeneous data into a shared expression space while preserving biological signals. Our pipeline integrates 25 independent datasets comprising 983 samples across 23 distinct CVDs phe- notypes from both RNA-seq and microarray platforms. The framework benchmarks 35 Machine learning (ML) and Deep learning (DL) classifiers, including Transformers and ResNets, across three data modalities such as RNA-seq, microarray hybridization and RNA-seq + microarray and multiple tissue types. To ensure clinical trustworthiness, we apply multiple Explainable artificial intelligence (XAI) methods, such as SHapley additive exPlanations (SHAP) and Integrated gradi- entss (IGs), and assess their reliability using quantitative metrics like Area over the perturbation curve (AOPC), Sensitivity, and Infidelity. Results indicate that Shambhala-2 provides superior harmonization by maximizing the biological signal-to-platform ratio. Evaluation of XAI methods reveals that Shapley-based approaches offer the highest stability for identifying influential genomic features in high-dimensional data. Functional enrichment and pathway analyses further confirmed the involvement of identified biomarkers in key cardiovascular processes, including inflammation, immune regulation, oxidative stress, and vascular remodeling. Collectively, this study provides a scalable and interpretable road-map that integrates XAI with cross-dataset biomarker discovery, supporting the transition toward precision cardiology.</jats:p>