SindyAutoEncoder, a novel hybrid model combining Sparse Identification of Nonlinear Dynamical systems (SINDy) with an autoencoder architecture to extract interpretable latent dynamics from time-series data. The model leverages the autoencoder’s capacity for nonlinear encoding and decoding, while enforcing sparse, low-order dynamics in the latent space using SINDy. Applied to synthetic and real-world biomedical signals, SindyAutoEncoder demonstrates superior performance in capturing underlying system dynamics with compact, interpretable equations, showing promise for applications in physiological modeling and neuroscience.