Debate, Not Voting: Agentic Arbitration over Weak Optical Chemical Structure Recognition Models

Abstract

Optical chemical structure recognition (OCSR) turns a picture of a molecule into a machine-readable string, and it stands between decades of printed chemistry and any computational use. On real documents individual models remain unreliable. Over a 1000-molecule sample of MolParser, three readers score $46.0\%$, $43.4\%$ and $42.4\%$ exact match, yet at least one of them is right on $60.8\%$ of molecules. That gap is an ensembling problem, but not one voting can solve, because the readers seldom agree and seldom err together. We place the readers inside a multi-agent scaffold. Four language-model agents with cheminformatics tools argue about a candidate structure, write findings to an append-only knowledge base, and are held to render-and-compare gates that admit a correction only when it is demonstrably better. The debate reaches $61.9\%$, beating the best single reader by $15.9$ points and plurality voting by $9.2$ points ($p<10^{-9}$ for both, robust to correction for all $27$ tests we report), and is indistinguishable from the any-reader-right ceiling. That aggregate hides two opposing effects. On the $661$ molecules with no stereochemistry the debate is $3.9$ points above the ceiling ($p=0.004$), constructing structures no reader proposed, while on the $339$ stereochemical ones it falls below. We then swap the arbitrating model. A stronger arbitrator adds $2.2$ points (nominal $p=0.039$; neither this nor the $+3.9$ survives Bonferroni correction over all $27$ tests, so both are suggestive), and its mechanism is visible: it opens a correction on $423$ of $1000$ molecules against $120$, and an interaction test indicates it depends less on the readers (nominal $p=0.018$, not correction-robust). We conclude that the useful unit of progress is the arbitration policy rather than the reader, and that OCSR accuracy is better read against the union oracle than against the best single model.