Many reported discovery systems build discrete models of hidden structure, properties, or processes in the diverse fields of biology, chemistry, and physics. We show that the search spaces underlying many well-known systems are remarkably similar when re-interpreted as search in matrix spaces. A small number of matrix types are used to represent the input data and output models. Most of the constraints can be represented as matrix constraints; most notably, conservation laws and their analogues can be represented as matrix equations. Typically, one or more matrix dimensions grow as these systems consider more complex models after simpler models fail, and we introduce a notation to express this. The novel framework of matrix-space search serves to unify previous systems and suggests how at least two of them can be integrated. Our analysis constitutes an advance toward a generalized account of model-building in science.