The presentation reviews a benchmark study evaluating deep learning models for diagnosing viral infections using single-cell RNA sequencing (scRNA-seq) data. The study compared multiple models—including PCA, SAVER, scVI, scGPT, and contrastiveVI—on a large dataset of over 200,000 immune cells from patients with COVID-19, influenza, and dengue. Key challenges addressed were batch effects and reliable classification across diverse experimental conditions. Results showed that contrastiveVI outperformed others in classification accuracy, while scGPT contributed to effective batch harmonization. Evaluation metrics included ARI, NMI, k-nearest neighbor accuracy, and S-score, with UMAP used for visual confirmation. The findings demonstrate the importance of model choice, preprocessing, and batch control in applying scRNA-seq analysis for infection diagnosis.