VERDICT: Agreement Beats Pixel-Space Verification in Real-Document OCSR

Abstract:Optical Chemical Structure Recognition (OCSR) converts 2D molecular depictions in the published literature into SMILES, and is increasingly important for constructing large-scale chemical training datasets. Automation at that scale requires identifying unreliable predictions in the absence of ground truth. Three families of label-free signals were compared on $263$ ACS journal depictions with verified ground truth: model confidence, re-rendering similarity, and agreement among recognizers. Pixel-space re-rendering performed little better than chance (AUROC $0.547$, $95\%$ CI $[0.465,0.629]$), and an oracle-tuned threshold on it reduced correct labels per image from $0.745$ to $0.205$. Agreement among four architecturally distinct recognizers instead reached an AUROC of $0.916$ ($[0.880,0.952]$). The two-of-four rule accepted $81.7\%$ of images at $88.8\%$ precision, the three-of-four rule $52.1\%$ at $98.5\%$. The same pattern held on CLEF-IP, UOB, and USPTO. This distinction is obscured on synthetic benchmarks, where re-rendered predictions naturally resemble their inputs. A substance filter removed $2{,}193$ false agreements on wildcards and R-group fragments, after which the three-of-four rule rejected all $68$ generic depictions. VERDICT was then applied to PMC Open Access, producing $6{,}146$ structure labels for $4{,}833$ molecules; chemist adjudication of $400$ released labels in two independent samples yielded precisions of $0.995$ for the three-of-four tier and $0.958$ for the two-of-four tier. VERDICT therefore enables validated labels for multimodal molecular databases linking structure images, machine-readable representations, and source-publication information. In SES AI's Molecular Universe platform, VERDICT further serves as an image-based interface for searching and retrieving molecular records.

Computer Vision and Pattern Recognition (cs.CV); Information Retrieval (cs.IR); Machine Learning (cs.LG)

arXiv:2608.22183 [cs.CV]

(or arXiv:2608.22183v1 [cs.CV] for this version)

https://doi.org/10.48550/arXiv.2608.22183 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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