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Popular parametric models of speech sounds such as the sourcefilter model provide a fixed means of describing the variability inherent in speech waveform data. However, nonlinear dimensionality reduction techniques such as the intrinsic Fourier analysis method of Jansen and Niyogi provide a more flexible means of adaptively estimating such structure directly from data. Here we employ this approach to learn a low-dimensional manifold whose geometry is meant to reflect the structure implied by the human speech production system. We derive a novel algorithm to efficiently learn this manifold for the case of many training examples - the setting of both greatest practical interest and computational difficulty. We then demonstrate the utility of our method by way of a proof-of-concept phoneme identification system that operates effectively in the intrinsic Fourier domain.