Although many efficient heuristics have been developed to solve binary
optimization problems, these typically produce correlated solutions for
degenerate problems. Most notably, transverse-field quantum annealing - the
heuristic employed in current commercially-available quantum annealing machines
- has been shown to often be exponentially biased when sampling the solution
space. Here we present an approach to sample ground-state (or low-energy)
configurations for binary optimization problems. The method samples degenerate
states with almost equal probability and is based on a combination of parallel
tempering Monte Carlo with isoenergetic cluster moves. We illustrate the
approach using two-dimensional Ising spin glasses, as well as spin glasses on
the D-Wave Systems Inc. quantum annealer chimera topology. In addition, a
simple heuristic to approximate the number of solutions of a degenerate problem
is introduced.