Graph-based modeling apparatus and techniques are disclosed. Based on a model including model nodes that represent components of a modeled system, operational dependencies between model nodes, and model edges that interconnect the nodes and represent relationships between the components in the modeled system, subset computations are performed to compute subsets of the model nodes that can impact operational dependencies between other model nodes. When the model changes, a determination is made as to whether an incremental subset computation should be performed for one or more particular operational dependencies between model nodes in the changed model, and if so, an incremental subset computation is performed. Otherwise, a full subset computation or no subset computation might be performed. In this manner, model changes are considered on a case-by-case basis to determine an extent, if any, to which subsets should be re-computed.