A method and system for adaptive auto-encoders is disclosed. An input audio training signal may be transformed into a sequence of feature vectors, each bearing quantitative measures of acoustic properties of the input audio training signal. An auto-encoder may process the feature vectors to generate an encoded form of the quantitative measures, and a recovered form of the quantitative measures based on an inverse operation by the auto-encoder on the encoded form of the quantitative measures. A duplicate copy of the sequence of feature vectors may be normalized to form a normalized signal in which supra-phonetic acoustic properties are reduced in comparison with phonetic acoustic properties of the input audio training signal. The auto-encoder may then be trained to compensate for supra-phonetic features by reducing the magnitude of an error signal corresponding to a difference between the normalized signal and the recovered form of the quantitative measures.