Optimization or sampling of arbitrary pairwise Ising models, in a quantum annealing protocol of constrained interaction topology, can be enabled by a minor-embedding procedure. The logical problem of interest is transformed to a physical (device programmable) problem, where one binary variable is represented by a logical qubit consisting of multiple physical qubits. In this paper we discuss tuning of this transformation for the cases of clique, biclique, and cubic lattice problems on the D-Wave 2000Q quantum computer. We demonstrate parameter tuning protocols in spin glasses and channel communication problems, focusing on anneal duration, chain strength, and mapping from the result on physical qubits back to the logical space. Inhomogeneities in effective coupling strength arising from minor-embedding are shown to be mitigated by an efficient reweighting of programmed couplings, accounting for logical qubit topology.
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