Evidence claim

Evidence summary: Set baselines for UTR translation experiments

Summary of Set baselines for UTR translation experiments

Only two sequence-only controls have been measured on the target split, both in Rewire's own runs, so there is no model comparison on it yet. On the 15,003 held-out records of the mRNABench designed-reporter test split, the composition ridge control reached a mean squared error of 1.914 against 2.366 for the training-mean control, and a Pearson correlation of 0.437; the training-mean control has no defined correlation, because its prediction is constant. The published FramePool panels are the only model comparison recorded here: neural models (FramePool and Optimus) reached Pearson 0.743 to 0.966 on the two random-sequence panels and 0.700 to 0.894 on the two human panels, while k-mer random forests, which were evaluated on the random panels only, reached 0.616 to 0.877. Those values are reported in the FramePool study on its own library, one split per panel with no uncertainty interval, and they are not measured on the designed-reporter split, so they are not baselines for it. Both Rewire controls are single runs on one split with no seed variability, and their automated audit checks the run itself, not a published score.

Plain-language summary of what the reviewed evidence shows. Draft until reviewed.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

49 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Claimed field summary Context-only references	Sequence composition + RidgeCV: automated execution audit Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `9f50fa70c15eeb38d2266015f766ac800dad4b2cc5e32202fb91d52b6f6670df` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Training-mean control: automated execution audit Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `9aad168bcc131d8beb9fe152fe8550078ae03452128e339171761b8ac5911984` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Sequence composition + RidgeCV: local execution report (20 September 2026) Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `8b68dfe5725bf5d8c108265039e3787f4b3b55986eab8a430082c4d446a4f960` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Training-mean control: local execution report (20 September 2026) Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `c036d9fa75b6ba4d5c65d31cd575ee2bfc357beec3ca7e6c80f07e3128a04e71` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	FramePool 2021 primary article Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2021 journal article XML; PMC8136849.1 Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `689af3ecab7b5a928eacc5a76d965960708cbb253fc7cdeae463b16d30ffd2e3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	FramePool Supplementary Table S1 Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2021 published S1 XLSX Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `4ed99aebadc607b43fca67bc2c6336cf4f167cc4b9cdd57b0abfcad0d2a06562` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	FramePool Supplementary Table S4 Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2021 published S4 XLSX Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `38659a19f65ad0b64186d5bed88977c7d730f08ebdd38e323c908bea14cbbd89` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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+ RidgeCV: local execution report (20 September 2026) Original source ↗ rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `8b68dfe5725bf5d8c108265039e3787f4b3b55986eab8a430082c4d446a4f960` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Sequence composition + RidgeCV: automated execution audit · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
Training-mean control: automated execution audit · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
Sequence composition + RidgeCV: local execution report (20 September 2026) · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
Training-mean control: local execution report (20 September 2026) · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
FramePool 2021 primary article · Original source · 2021 journal article XML; PMC8136849.1
FramePool Supplementary Table S1 · Original source · 2021 published S1 XLSX
FramePool Supplementary Table S4 · Original source · 2021 published S4 XLSX

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Stable ID: use-case-summary-utr-translation-baselines

field: summary
value: Only two sequence-only controls have been measured on the target split, both in Rewire's own runs, so there is no model comparison on it yet. On the 15,003 held-out records of the mRNABench designed-reporter test split, the composition ridge control reached a mean squared error of 1.914 against 2.366 for the training-mean control, and a Pearson correlation of 0.437; the training-mean control has no defined correlation, because its prediction is constant. The published FramePool panels are the only model comparison recorded here: neural models (FramePool and Optimus) reached Pearson 0.743 to 0.966 on the two random-sequence panels and 0.700 to 0.894 on the two human panels, while k-mer random forests, which were evaluated on the random panels only, reached 0.616 to 0.877. Those values are reported in the FramePool study on its own library, one split per panel with no uncertainty interval, and they are not measured on the designed-reporter split, so they are not baselines for it. Both Rewire controls are single runs on one split with no seed variability, and their automated audit checks the run itself, not a published score.
source locator: rewire-local-20260920 run outputs: metrics.mse and metrics.pearson for the composition and training-mean controls; uc20260930-source-framepool-s1: S1 Table rows Random 50nt, Random 25-100nt, Human 50nt and Human 25-100nt; uc20260930-source-framepool-s4: S4 Table columns B and C
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 that both controls are Rewire runs and that their audit checks the run rather than a published score, and named the neural models. 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.
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