A circuit design is compiled for hardware-accelerated functional verification by removing internal gates of a uniform operator tree (e.g., an assertion tree) while retaining node information, and partitioning the circuit to optimize connectivity without being constrained by the uniform operator tree. After partitioning, sub-trees are constructed for the partitions, and aggregated to form a master tree. The sub-trees can have leaf nodes at varying depths based on ranks of the leaf nodes, and the master tree can similarly provide inputs from the sub-trees at varying depths based on simulation depths for the sub-trees. The resynthesized master tree is structurally distinct from the original uniform operator tree but, since the inputs are commutative (e.g., OR gates), the functional equivalence of the model is preserved.