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As quantum devices become more complex and the requirements on these devices become more demanding, it is crucial to be able to verify the performance of such devices in a scalable and reliable fashion. A cornerstone task in this challenge is quantifying how close an experimentally prepared quantum state is to the desired one. Here we present a method to construct an estimator for the quantum state fidelity that is compatible with any measurement protocol. Our method provides a confidence interval on this estimator that is guaranteed to be nearly minimax optimal for the specified measurement protocol. For a well-chosen measurement scheme, our method is competitive in the number of measurement outcomes required for estimation. We demonstrate our method using simulations and experimental data from a trapped-ion quantum computer and compare the results to state-of-the-art techniques. Our …