The exponential computational cost of describing strongly correlated electrons can be mitigated by adopting a reduced-density matrix (RDM)-based description of the electronic structure. While variational two-electron RDM (v2RDM) methods can enable large-scale calculations on such systems, the quality of the solution is limited by the fact that only a subset of known necessary N-representability constraints can be applied to the 2RDM in practical calculations. Here, we demonstrate that violations of partial three-particle (T1 and T2) N-representability conditions, which can be evaluated with knowledge of only the 2RDM, can serve as physics-based features in a machine-learning (ML) protocol for improving energies from v2RDM calculations that consider only two-particle (PQG) conditions. Proof-of-principle calculations demonstrate that the model yields substantially improved energies relative to reference values from configuration-interaction-based calculations.