Stochastic dynamical systems are ubiquitous in physics, biology, and engineering, where both deterministic drifts and random fluctuations govern system behavior. Learning these dynamics from data is particularly challenging in high-dimensional settings with complex, correlated, or state-dependent noise. We introduce a noise-aware system identification framework that jointly recovers the deterministic drift and full noise structure directly from the trajectory data, without requiring prior assumptions on the noise model. Our method accommodates a broad class of stochastic dynamics, including colored and multiplicative noise, that scales efficiently to high-dimensional systems, and accurately reconstructs the underlying dynamics. Numerical experiments on diverse systems validate the approach and highlight its potential for data-driven modeling in complex stochastic environments.
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