rewirebio.iobenchmarks
Evidence claim

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

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

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Citation locations
6 values
  • 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
Context-only references
Amino-acid composition + fixed ridge: local execution report (20 September 2026)

Original source ↗

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
Retrieved: 2026-09-20T20:54:03Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: abd08d3f493428d06f43740c94e268575d755560e72120c73b294127acb395e6

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Citation locations
6 values
  • 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
Context-only references
Training-mean control: local execution report (20 September 2026)

Original source ↗

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
Retrieved: 2026-09-20T20:54:03Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: eb89260f6e138bb9ae2fdf3b882a87fdf8aeabd54a0ac6f17a73f5671c96b4d8

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Citation locations
6 values
  • 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
Context-only references
ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): execution and verification instructions

Original source ↗

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
Retrieved: 2026-09-22T21:18:22Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: 075be1919b8364a3ef1028f9204431d3caa7c3b4da586212d0ed6dd4b024c8da

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Citation locations
6 values
  • 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
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  • 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
Context-only references
Protein composition + fixed ridge probe: report

Original source ↗

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
Retrieved: 2026-09-22T21:18:22Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: 2071ac2487d56df4150109b944a42944ed12e1398d00899c054580f709921317

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Citation locations
6 values
  • 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
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    locator
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  • source id
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    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
Context-only references
ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report

Original source ↗

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
Retrieved: 2026-09-22T21:18:22Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: 29d7c0ae7f47d45861a769eb8813bf8c650c9a95b3a6821c524b216b0b907ef0

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Citation locations
6 values
  • 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
Context-only references
ESM-2 8M frozen residue-mean embeddings + fixed ridge (Rewire): report

Original source ↗

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
Retrieved: 2026-09-22T21:18:22Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: d6df9e916e77872112571b404265e918276974c79dcbe25721b3eca0eae4e51a

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Constraints
3 values
  • 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.
Context-only references
Amino-acid composition + fixed ridge: local execution report (20 September 2026)

Original source ↗

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
Retrieved: 2026-09-20T20:54:03Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.constraints

Source artifact SHA-256: abd08d3f493428d06f43740c94e268575d755560e72120c73b294127acb395e6

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Constraints
3 values
  • 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.
Context-only references
Training-mean control: local execution report (20 September 2026)

Original source ↗

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
Retrieved: 2026-09-20T20:54:03Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.constraints

Source artifact SHA-256: eb89260f6e138bb9ae2fdf3b882a87fdf8aeabd54a0ac6f17a73f5671c96b4d8

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Constraints
3 values
  • 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.
Context-only references
ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): execution and verification instructions

Original source ↗

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
Retrieved: 2026-09-22T21:18:22Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.constraints

Source artifact SHA-256: 075be1919b8364a3ef1028f9204431d3caa7c3b4da586212d0ed6dd4b024c8da

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Constraints
3 values
  • 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.
Context-only references
Protein composition + fixed ridge probe: report

Original source ↗

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
Retrieved: 2026-09-22T21:18:22Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.constraints

Source artifact SHA-256: 2071ac2487d56df4150109b944a42944ed12e1398d00899c054580f709921317

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

How to read the evidence

Sources and history

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

6 source records and release historyDownload this release (gzip)
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
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