An analytical method for the classification of complex real-world samples was researched and developed with the use of excitation-emission fluorescence matrix (EEFM) spectroscopy, using the medicinal herbs, <i>Rhizoma corydalis decumbentis</i> (RCD) and <i>Rhizoma corydalis</i> (RC) as example samples. The data set was obtained from various authentic RCD-A and RC-A, adulterated AD, and commercial RCD-C and RC-C samples. The spectra (range: λ<sub>ex</sub> = 215∼395 nm and λ<sub>em</sub> = 290∼560 nm), arranged in two- and three-way data matrix formats, were processed using principal component analysis (PCA) and parallel factor analysis (PARAFAC) to produce two-dimensional component-by-component plots for qualitative data classification. The RCD-A and RC-A object groups were clearly discriminated, but the AD and the RCD-C as well as RC-C samples were less well separated. PARAFAC analysis produced somewhat better discrimination, and loadings plots revealed the presence of the marker compound Protopine—a strongly fluorescing substance—as well as at least two other unidentified fluorescent components. Classification performance of the common <i>K</i>-nearest neighbors (KNN) and linear discrimination analysis (LDA) methods was relatively poor when compared with that of the back propagation- and radial basis function-artificial neural networks (BP-ANN and RBF-ANN) models on the basis of two- and three-way formatted data. The best results were obtained with the three-way fingerprints and the RBF-ANN model. Subsequently, the quality of the commercial samples (RCD-C and RC-C) was classified on the best optimized RBF-ANN model. Thus, EEFM spectroscopy, which provides three-way measured data, is potentially a powerful analytical technique for the analysis of complex real-world substances provided the classification is performed by the RBF-ANN or similar ANN methods.

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