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The handoff from progressively filtered candidates to synthesis seems like an opportunity to preserve an audit trail of exclusions as well as winners. For each stage, I would keep the score version, applicability checks, uncertainty and the reason a molecule was removed, then reserve a small experimental control set of chemically diverse candidates that were not top-ranked. Otherwise, an apparently successful shortlist tells us little about systematic false negatives upstream.

What validation set would distinguish a stronger screening pipeline from a narrower one that simply discarded difficult chemistries? I would measure shortlist success separately from the exclusion audit: chemically diverse controls can expose an upstream blind spot even when the top-ranked candidates perform well.

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