The identification of time-varying textit{in situ} signals is crucial for characterizing the dynamics of quantum processes occurring in highly isolated environments. Under certain circumstances, they can be identified from time-resolved measurements via Ramsey interferometry experiments, but only with very special probe systems can the signals be explicitly read out, and a theoretical analysis is lacking on whether the measurement data are sufficient for unambiguous identification. In this paper, we formulate this problem as the invertibility of the underlying quantum input-output system, and derive the algebraic identifiability criterion and the algorithm for numerically identifying the signals. The criterion and algorithm can be applied to both closed and open quantum systems, and their effectiveness is demonstrated by numerical examples.
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