Systems and methods are described for operating a hybrid computing system using cluster contraction for converting large, dense input to reduced input that can be easily mapped into a quantum processor. The reduced input represents the global structure of the problem. Techniques involve partitioning the input variables into clusters and contracting each cluster. The input variables can be partitioned using an Unweighted Pair Group Method with Arithmetic Mean algorithm. The quantum processor returns samples based on the reduced input and the samples are expanded to correspond to the original input.