Equivariant Neural Primal-Dual Assignment for Maximum Common Edge Subgraphs

Maximum common edge subgraph (MCES) matching finds a partial vertex correspondence between two labeled graphs that preserves as many labeled edges as possible. Molecular similarity search requires matching many graph pairs, making the cost of repeated queries important. The strongest baseline attains accurate MCES solutions but trains a separate network for each pair. We introduce Equivariant Neural Primal–Dual Assignment (ENPDA), which learns a shared matching policy and applies it to new pairs without further training, answering queries roughly three orders of magnitude faster than the strongest baseline and recovering its training cost after only a few dozen queries. The policy recomputes exact objective marginals for candidate matches and learns corrections and step sizes that update their scores. Target prices respond to competition when several source vertices favor the same target. Four update rounds and a Hungarian projection produce a partial one-to-one matching. We prove per-pair guarantees that hold for any network parameters. In exact arithmetic, reordering either graph reorders the continuous assignment and price states accordingly, the projected matching is one-to-one, and repaired prices give a valid MCES upper bound. Subtracting the preserved-edge count bounds the optimality gap; combined with structural and exact incident-assignment caps, these certificates prove global optimality for 60 of 291 native test pairs. On three molecular benchmarks with no graphs shared across training, validation, and test, ENPDA improves over an analytic counterpart with the same update and projection budget by 7.4–8.6 accuracy points; after one second of additional refinement search, 2.5–3 points of the gain remain. Transferred without fine-tuning to edge-deletion tasks built from social and protein graphs, the policy gains 9.1–17.6 points over the analytic counterpart. When output matchings must keep aromatic rings intact, ENPDA recovers more reference bonds than the baselines on all three datasets.