arXiv:2610.16559v1 Announce Type: new Abstract: We present a scalable method for identifying nonlinear dynamics from partial measurements, supporting physics-based, neural-network, and gray-box models. We use the Prediction Error Method (PEM) coupled with state estimation performed by a Moving Horizon Estimation (MHE) scheme, which can account directly for general nonlinear dynamics. This results in a bi-level optimization problem that scales poorly with increasing model parameters. To improve computational efficiency, we derive a reformulation that avoids explicit parameter-wide sensitivity matrices and exploits the temporal structure of the underlying optimization problem. Numerical comparisons show up to a $215\times$ speedup in hypergradient evaluation. Racing-vehicle simulations demonstrate accurate prediction and physical-parameter recovery in tire-force identification. Real-world data show that the gray-box model improves prediction accuracy with a neural residual while retaining physical interpretability.