Systems and methods allow formulation of embeddings of problems via targeted hardware (e.g., particular quantum processor). In a first stage, sets of connected subgraphs are successively generated, each set including a respective subgraph for each decision variable in the problem graph, adjacent decisions variables in the problem graph mapped to respective vertices in the hardware graph, the respective vertices which are connected by at least one respective edge in the hardware graph. In a second stage, the connected subgraphs are refined such that no vertex represents more than a single decision variable.