Evidence summary: Assess rhodopsin wavelength prediction across sequence backgrounds

Stable ID: use-case-summary-rhodopsin-wavelength-transfer

field

summary

value

RhoMax, which adds structural binding-pocket inputs, had the lowest wavelength error on each of its own wild-type holdout splits. In separate Rewire runs on the FLIP2 split, two amino-acid composition probes outranked two frozen ESM-2 probes, and both ESM-2 probes fell below a constant control. Averaged over four RhoMax splits, mean absolute error was 10.45 nm for RhoMax, 13.46 nm for RhoMax plus retinal and 14.90 nm for the BLASSO comparator, with standard deviations of 10.9 to 11.7 nm; per-split RhoMax error ran from 7.28 to 16.68 nm. In electronvolts the three methods are closer, and on split 3 all three print the same mean absolute error of 0.045 eV. On the FLIP2 Rhomax by_wild_type split of 184 held-out sequences, Rewire's runs gave a Spearman correlation of 0.418 for a 40-feature amino-acid composition probe and 0.418 for a 22-feature one, against -0.146 for a frozen ESM-2 8M probe and -0.222 for a 35M probe; NDCG was 0.955, 0.955, 0.896 and 0.907 against 0.921 for a training-mean control, whose Spearman is undefined. The two split definitions are different and their scores must not be pooled. The RhoMax values are reported by its authors with no independent reproduction, and the Rewire runs are single runs with no seed variability, with the 35M checkpoint chosen after the 8M outcome was known.

source locator

uc20260930-source-rhomax-2024: per-split and mean rows of the wild-type holdout table, nm and eV columns; rewire-local-20260920 and rewire-local-20260921 run outputs: metrics.spearman and metrics.ndcg

review

method: independent-cell-check; ai-assisted-source-review; method note: Rebuilt the use case's active judgements with deriveUseCaseInputs and compared every number with the printed_value of the stored result it comes from, including its rounding, tool, dataset and split. Checked each comparative statement against every active evaluation on the protocol, not only the cited rows. Checked origin, publication status, truth-set and cohort limits against the evaluation, protocol, dataset and source records, that each cited source is source_checked with no evidence_concerns, and that nothing is recommended.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the author of the summary; the reviewer corrected the text; no human review claimed; reviewed at: 2026-10-10T07:00:00Z; note: Drafted for issue #87 and corrected in this review. Added the omitted 22-feature composition probe, which is the fifth active evaluation on the protocol, and its two sources. Qualified the opening to the nm columns and recorded that all three methods print 0.045 eV on split 3. Removed "the splits differ more than the methods do", which is interpretation that split 4 does not support. Every number traced to a stored source_checked result. Descriptive summary only; no execution, human scientific review or clinical validation. See data/omics/qa-data-fixes-20261010/review.md.

pins

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• subject: Assess rhodopsin wavelength prediction across sequence backgrounds