Relevance of FLIP2 Rhomax by_wild_type to "Assess rhodopsin wavelength prediction across sequence backgrounds"
- Use case
- Assess rhodopsin wavelength prediction across sequence backgrounds
- Assessed by
- FLIP2 Rhomax by_wild_type
- Relevance
- Proxy evidence
- Endpoint
- Spearman rank association and full-ranking NDCG for absorption-wavelength predictions on 184 held-out Rhomax sequences.
The archived background split directly tests one transfer setting; choosing constructs in a new experiment requires validation beyond those 184 rows.
5 reviewed evaluations
- Amino-acid composition + fixed ridge on FLIP2 Rhomax by_wild_type
- Training-mean control on FLIP2 Rhomax by_wild_type
- Protein composition + fixed ridge probe on FLIP2 Rhomax by_wild_type
- ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type
- ESM-2 8M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type
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.
90 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations6 values
| Amino-acid composition + fixed ridge: local execution report (20 September 2026) rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations6 values
| Training-mean control: local execution report (20 September 2026) rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations6 values
| ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): execution and verification instructions rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations6 values
| Protein composition + fixed ridge probe: report rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations6 values
| ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations6 values
| ESM-2 8M frozen residue-mean embeddings + fixed ridge (Rewire): report rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| Amino-acid composition + fixed ridge: local execution report (20 September 2026) rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| Training-mean control: local execution report (20 September 2026) rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): execution and verification instructions rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| Protein composition + fixed ridge probe: report rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
6 source records and release history
- ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): execution and verification instructions · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
- ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
- ESM-2 8M frozen residue-mean embeddings + fixed ridge (Rewire): report · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
- Protein composition + fixed ridge probe: report · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
- Training-mean control: local execution report (20 September 2026) · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
- Amino-acid composition + fixed ridge: local execution report (20 September 2026) · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
Technical metadata and extraction receipts
Stable ID: use-case-mapping-rhodopsin-wavelength-rhomax-fixed-probes
- field
- links:assessed_by:rewire-protocol-flip2-rhomax-by-wild-type-v1
- value
- rewire-protocol-flip2-rhomax-by-wild-type-v1
- relevance
- proxy
- endpoint
- Spearman rank association and full-ranking NDCG for absorption-wavelength predictions on 184 held-out Rhomax sequences.
- rationale
- The archived background split directly tests one transfer setting; choosing constructs in a new experiment requires validation beyond those 184 rows.
- constraints
- The same frozen Rhomax by_wild_type assignments cover 584 training, 116 validation and 184 test records. Validation labels do not select these fixed settings.; Two exact ESM-2 checkpoints use frozen final-layer residue means, no MSA or templates, and a train-only alpha-10 ridge probe with train-only target scaling. They are not zero-shot likelihood scorers.; The 40-feature and 22-feature composition controls are distinct configurations. Training mean is the existing constant-control evaluation; repeated control checks do not add replications.
- limitations
- A spectral-tuning endpoint is not opsin activation efficiency, expression, photostability, cellular function, general protein fitness or clinical usefulness.; Spearman and full-ranking NDCG do not establish wavelength calibration, top-k precision or a prospective experimental hit rate. Constant predictions have undefined Spearman; their NDCG is a control value, not strong predictive evidence.; No intervals or seed-variability estimates. The 35M checkpoint was chosen after seeing the 8M outcome; the source describes an exploratory follow-up, not a preregistered family-scale comparison.; ESM-2 pretraining overlap is unresolved. A frozen linear probe result does not establish the value of alternative pooling, fine-tuning or every model-family configuration.; Recorded timing covers sections of execution and is not a hardware-normalised deployment-cost comparison. Human domain review and external replication are not established.
- revision
- 1
- reason
- Initial applicability review: primary sources and separate automated cross-review support this exact protocol, its complete selected comparator group and the stated limits.
- citation locators
- source id: rewire-local-20260921-instructions-esm2-35m; locator: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; source id: rewire-local-20260921-source-esm2-35m; locator: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; source id: rewire-local-20260921-source-esm2-8m; locator: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; source id: rewire-local-20260921-source-composition22; locator: /metrics; /model_configuration; /protocol_configuration; source id: rewire-local-20260920-source-flip2-train-mean; locator: /metrics; /coverage; /model_configuration; source id: rewire-local-20260920-source-flip2-composition; locator: /metrics; /coverage; /model_configuration; /provenance
- source locator
- rewire-local-20260921-instructions-esm2-35m: Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect; rewire-local-20260921-source-esm2-35m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-esm2-8m: /metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance; rewire-local-20260921-source-composition22: /metrics; /model_configuration; /protocol_configuration; rewire-local-20260920-source-flip2-train-mean: /metrics; /coverage; /model_configuration; rewire-local-20260920-source-flip2-composition: /metrics; /coverage; /model_configuration; /provenance
- review
- method: automated-source-review; reviewer: codex; reviewer note: Codex research curation; reviewed at: 2026-09-28T12:11:40.845Z; note: Primary-source curation and separate automated cross-review checked exact evidence identities, comparator coverage, endpoint relevance and transfer limits. No new execution, human scientific review, independent replication or clinical validation.
- reviewed evaluations
- rewire-local-20260920-evaluation-flip2-composition; rewire-local-20260920-evaluation-flip2-train-mean; rewire-local-20260921-evaluation-composition22; rewire-local-20260921-evaluation-esm2-35m; rewire-local-20260921-evaluation-esm2-8m
- pins
- record id: rewire-local-20260920-evaluation-flip2-composition; fields: status; links; attributes.origin; attributes.comparison; sha256: 69f3c6f33b79d08e96cba9f333aa3fc7fc9ae989926fd9dcf231c7519028805a; record id: rewire-local-20260920-evaluation-flip2-train-mean; fields: status; links; attributes.origin; attributes.comparison; sha256: 97c418f42a1db544f7b200c3addda19d2f20a90a9517a281c2f1ad1f3d1b6ec0; record id: rewire-local-20260920-instructions-flip2; fields: status; attributes.artifact_sha256; sha256: f1cbbaffcaf7feff9112529102ed83a539cbda0681ec50fbc18a6894b56a5a68; record id: rewire-local-20260920-result-flip2-composition-ndcg; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 1a8005d6311878feea760fbfedd8daa4e75ba139c0f1ba8739be273461745889; record id: rewire-local-20260920-result-flip2-composition-spearman; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 301858467669d79cc3907f6558dd78f19f4dc7d211fe1c600a3bf6e8c243c9f3; record id: rewire-local-20260920-result-flip2-train-mean-ndcg; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 7ffb5fba7489652585a76c57f29677b7e1f013d02666ddaf5b10a747435673a7; record id: rewire-local-20260920-result-flip2-train-mean-spearman; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 2696e081937f1e35354a6d96cbea4c38ad17758fc535e5f8f21462c1b45515f1; record id: rewire-local-20260920-source-flip2-composition; fields: status; attributes.artifact_sha256; sha256: 4b19e1f6792aefc36d9ca1b31c3dd85f070384bbb72fd5117e5eea381d4f9cea; record id: rewire-local-20260920-source-flip2-train-mean; fields: status; attributes.artifact_sha256; sha256: c67dcec4b004b3672a29152a3bba1fe55ccffc0a85406ad59e0715bed9486d9e; record id: rewire-local-20260921-evaluation-composition22; fields: status; links; attributes.origin; attributes.comparison; sha256: 1783d0e5a073d800fb75dd15abac4f88bbc032a5a387fca3c1f0a484bed96eb3; record id: rewire-local-20260921-evaluation-esm2-35m; fields: status; links; attributes.origin; attributes.comparison; sha256: adbfc5c63a99cc46e6f61b9e9ef5decc1964b3db32466725e6d514fbb099f0ec; record id: rewire-local-20260921-evaluation-esm2-8m; fields: status; links; attributes.origin; attributes.comparison; sha256: a4dcd29c889aec24fbfc4ab89aeb430554fc378cc09ff148a9a78b3c3d5e7b19; record id: rewire-local-20260921-instructions-esm2-35m; fields: status; attributes.artifact_sha256; sha256: f9160ad804f21e44a80ce496127087f4ee9d591ae5fe79ed5ca8373eb4ec4330; record id: rewire-local-20260921-result-composition22-ndcg; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 9a164f218735e131d45fbb5637b68600723ab673b5d747d3aa94f6aa6e7e0a31; record id: rewire-local-20260921-result-composition22-spearman; fields: status; 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attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 33a9cb5a2f266778eb9903fdfcb71f8ec20fe6362108cebbf7edf935b927969e; record id: rewire-local-20260921-source-composition22; fields: status; attributes.artifact_sha256; sha256: c066babf9fa7fb985667c99466327e40157a1bbb6252ded47ae4ae22249f0c04; record id: rewire-local-20260921-source-esm2-35m; fields: status; attributes.artifact_sha256; sha256: e715d7dacec2bd37f2ea07d152e19aa8a950dadeff051e04d99458bf2a24675e; record id: rewire-local-20260921-source-esm2-8m; fields: status; attributes.artifact_sha256; sha256: 0d6c32bcbfcbafa1219ebf59760af8e3198074d6facc91f9498583c1de468a9e; record id: rewire-protocol-flip2-rhomax-by-wild-type-v1; fields: status; name; description; facets; source_ids; links; attributes; sha256: 345d04abc55eca61752c0bf8d4a81e3421b00de2e6e641bc7d08443ef424fc25; record id: use-case-rhodopsin-wavelength-transfer; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 2ccfaab7f48773a1dee5c217ad305428bd0197e48efc5dea75c956ec59be5756