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We present an empirical strategy to determine the Hamiltonian dynamics of a two-qubit system using only initialization and measurement in a single fixed basis. Signal parameters are estimated from measurement data using Bayesian methods from which the underlying Hamiltonian is reconstructed, up to three unobservable phase factors. We extend the method to achieve full control Hamiltonian tomography for controllable systems via a multi-step approach. The technique is demonstrated and evaluated by analyzing data from simulated experiments including projection noise.

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