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In this paper, we develop an efficient fuzzy wavelet packet (WP) based feature extraction method for the classification of high-dimensional biomedical data such as magnetic resonance spectra. The key design phases involve: 1) a WP transformation mapping the original signals to many WP feature spaces and finding optimal WP decomposition for signal classification; 2) feature extraction based on the optimal WP decomposition; and 3) signal classification realized by a linear classifier. In contrast to the standard method of feature extraction used in WPs, guided by the criteria of signal compression or signal energy, our method is used to extract discriminatory features from the WP coefficients of the optimal decomposition. The extraction algorithm constructs fuzzy sets of features (via fuzzy clustering) to assess their discriminatory effectiveness. This paper includes a number of numerical experiments using magnetic resonance spectra. Classification results are compared with those obtained from common feature extraction methods in the WP domain.