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We analyze the quantum process tomography (QPT) in the presence of decoherence, focusing on distinguishing local and non-local decoherence mechanisms for a two-partite system from experimental QPT data. In particular, we consider the gate realized with superconducting phase qubits and calculate the QPT matrix in the presence of several local and non-local decoherence processes. We determine specific patterns of these decoherence processes, which can be used for a fast identification of the main decoherence mechanisms from an experimental -matrix.

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