Explainable AI-Driven Raman Spectroscopy for Rapid Bacterial Identification

Raman spectroscopy is a rapid, label-free, and non-destructive technique for probing molecular structures, making it a powerful tool for clinical pathogen identification. However, interpreting its complex spectral data remains challenging. In this study, we evaluate and compare a suite of machine learning models—including Support Vector Machines (SVM), XGBoost, LightGBM, Random Forests, k-nearest Neighbors (k-NN), Convolutional Neural Networks (CNNs), and fully connected Neural Networks—with and without Principal Component Analysis (PCA) for dimensionality reduction. Using Raman spectral data from 30 clinically important bacterial and fungal species that collectively account for over 90% of human infections in hospital settings, we conducted rigorous hyperparameter tuning and assessed model performance based on accuracy, precision, recall, and F1-score. The SVM with an RBF kernel combined with PCA emerged as the top-performing model, achieving the highest accuracy (0.9454) and F1-score (0.9454). Ensemble methods such as LightGBM and XGBoost also demonstrated strong performance, while CNNs provided competitive results among deep learning approaches. Importantly, interpretability was achieved via SHAP (Shapley Additive exPlanations), which identified class-specific Raman wavenumber regions critical to prediction. These interpretable insights, combined with strong classification performance, underscore the potential of explainable AI-driven Raman analysis to accelerate clinical microbiology diagnostics, optimize antimicrobial therapy, and improve patient outcomes.