A technique for determination of character and intensity of interaction between the elements of complex systems based on reconstruction of model equations for phase dynamics is extended to the case of short and noisy time series. Corrections, which eliminate systematic errors of the estimates, and expressions for confidence intervals are derived. Analytic results are presented for a particular case of linear uncoupled systems, and their validity for a much wider range of situations is demonstrated with numerical examples. The technique should be useful for the analysis of nonstationary processes in real time, including the situations of significant noise and restrictions on the observation time.
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