A method determines from an input noisy signal sequences of hidden variables including at least one sequence of hidden variables representing an excitation component of the clean speech signal, at least one sequence of hidden variables representing a filter component of the clean speech signal, and at least one sequence of hidden variables representing the noise signal. The sequences of hidden variables include hidden variables determined as a non-negative linear combination of non-negative basis functions. The determination uses the model of the clean speech signal that includes a non-negative source-filter dynamical system (NSFDS) constraining the hidden variables representing the excitation and the filter components to be statistically dependent over time. The method generates an output signal using a product of corresponding hidden variables representing the excitation and the filter components.