We propose a novel data-driven linear inverse model, called Colored-LIM, to extract the linear dynamics and diffusion matrix that define a linear stochastic process driven by an Ornstein-Uhlenbeck colored-noise. The Colored-LIM is a new variant of the classical linear inverse model (LIM) which relies on the white noise assumption. Similar to LIM, the Colored-LIM approximates the linear dynamics from a finite realization of a stochastic process and then solves the diffusion matrix based on, for instance, a generalized fluctuation-dissipation relation, which can be done by solving a system of linear equations. The main difficulty is that in practice, the colored-noise process can be hardly observed while it is correlated to the stochastic process of interest. Nevertheless, we show that the local behavior of the correlation function of the observable encodes the dynamics of the stochastic process and the diffusive behavior of the colored-noise. In this article, we review the classical LIM and develop Colored-LIM with a mathematical background and rigorous derivations. In the numerical experiments, we examine the performance of both LIM and Colored-LIM. Finally, we discuss some false attempts to build a linear inverse model for colored-noise driven processes, and investigate the potential misuse and its consequence of LIM in the appendices.

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