Honey Botanical Origin Authentication Using HS-SPME-GC-MS Volatile Profiling and Advanced Machine Learning Models (Random Forest, XGBoost, and Neural Network)

Abstract

This study develops a comprehensive workflow integrating Headspace Solid-Phase Microextraction Gas Chromatography–Mass Spectrometry (HS-SPME-GC-MS) with advanced supervised machine learning to authenticate the botanical origin of honeys from five distinct floral sources—coriander, orange blossom, astragalus, rosemary, and chehelgiah. While HS-SPME-GC-MS combined with traditional chemometrics (e.g., PCA, LDA, OPLS-DA) is well-established for honey discrimination, the application and direct comparison of Random Forest (RF), eXtreme Gradient Boosting (XGBoost), and Neural Network (NN) models represent a significant advancement in multiclass prediction accuracy and model robustness. A total of 57 honey samples were analyzed to generate detailed volatile organic compound (VOC) profiles. Key chemotaxonomic markers were identified: anethole in coriander and chehelgiah, thymoquinone in astragalus, p-menth-8-en-1-ol in orange blossom, and dill ester (3,6-dimethyl-2,3,3a,4,5,7a-hexahydrobenzofuran) in rosemary. Principal component analysis (PCA) revealed clear separation across botanical classes (PC1: 49.8%; PC2: 22.6%). Three classification models—RF, XGBoost, and NN—were trained on standardized, stratified data. The NN model achieved the highest accuracy (90.32%), followed by XGBoost (86.69%) and RF (83.47%), with superior per-class F1-scores and near-perfect specificity (>0.95). Confusion matrices confirmed minimal misclassification, particularly in the NN model. This work establishes HS-SPME-GC-MS coupled with deep learning as a rapid, sensitive, and reliable tool for multiclass honey botanical authentication, offering strong potential for real-time quality control, fraud detection, and premium market certification.