rewirebio.iobenchmarks
Evidence claim

Relevance of EVEE Evo 2 embedding extraction compute (Pearce et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics"

Use case
Select an execution workflow for large-scale diagnostic genomics
Assessed by
EVEE Evo 2 embedding extraction compute (Pearce et al. 2026)
Relevance
Proxy evidence
Endpoint
Approximate total H100 GPU-hours to extract Evo 2 7B layer-27 embeddings (reference and variant, both strands, 65 kb windows) for 4,252,870 ClinVar variants

Proxy. The only linked figure for running a genomic foundation model over human variants at the scale of a whole variant database, which bears on the accelerator budget for scoring variants with such a model. It is a one-off research embedding harvest rather than a diagnostic workflow, and gives one approximate total with no GPU count, batch size, wall-clock time or per-sample figure.

1 reviewed evaluation

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.

18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Citation locations
1 values
  • source id
    gfm-guide-20261014-source-evee-v4
    locator
    Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Comparison group
evee2026-evo2-embedding-extraction
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison_group

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Comparison title
Evo 2 7B embedding extraction for all ClinVar variants (Pearce et al. 2026)
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison_title

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Constraints
4 values
  • Inspect every linked evaluation's source locator before citing a result.
  • Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources.
  • Read the value as approximate; it is printed as '∼20,000 H100-hours'.
  • Do not divide it into a per-variant or per-sample cost without saying the division is yours; the source prints no per-variant timing, and the workload covers both strands and both alleles.
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.constraints

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Endpoint
Approximate total H100 GPU-hours to extract Evo 2 7B layer-27 embeddings (reference and variant, both strands, 65 kb windows) for 4,252,870 ClinVar variants
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.endpoint

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Claimed field
links:assessed_by:gfm-guide-20261014-protocol-evee-embedding-extraction-compute
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.field

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Headline metric
accelerator-time
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.headline_metric

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Limitations
5 values
  • Developer-reported: EVEE's authors built the extraction pipeline, and three of them co-authored Evo 2 (claim gfm-guide-20261014-claim-evee-developer-overlap).
  • Stated once in Methods (the 'Dataset' paragraph after 'Harvesting'); GPU count, batch size, wall-clock time and software versions are not given.
  • The workload stores per-position embeddings (bf16, about 34 TB), which a diagnostic scoring pipeline would not need; the figure therefore includes work beyond scoring.
  • Preprint (bioRxiv v4), not peer reviewed.
  • The source carries an evidence concern about the NTv3 column of Figures 1b and 1c. It does not touch this figure, but an active judgement needs clean protocol sources, so this judgement stays withheld after review until that concern is resolved.
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.limitations

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Pinned records
5 values
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    fields
    • status
    • links
    • attributes.origin
    • attributes.comparison
    sha256
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  • record id
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    fields
    • status
    • name
    • description
    • facets
    • source_ids
    • links
    • attributes
    sha256
    c5c5c758a9673043af191956af05d68bfe66247b928364969f52684a897c9294
  • record id
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    fields
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    • attributes.printed_value
    • attributes.numeric_value
    sha256
    87e35eacbfca259a686cae9b9fa7b3829ee9358124ea5b57f1d002c6fa0dd6eb
  • record id
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    fields
    • status
    • attributes.artifact_sha256
    sha256
    7fa901d074087100fbb320434beaf2f77ce2000077cd20e456c03c9285263dd7
  • record id
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    fields
    • status
    • name
    • description
    • facets
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    • attributes.decision
    • attributes.inputs
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    • attributes.exclusions
    • attributes.setting
    • attributes.clinical_scope
    • attributes.intended_users
    sha256
    1c2a12431556cc6581f5aab019cf91576d2393387b88a8a2bea35ea2a3ee4a70
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.pins

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

Rationale
Proxy. The only linked figure for running a genomic foundation model over human variants at the scale of a whole variant database, which bears on the accelerator budget for scoring variants with such a model. It is a one-off research embedding harvest rather than a diagnostic workflow, and gives one approximate total with no GPU count, batch size, wall-clock time or per-sample figure.
Context-only references
Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4

Original source ↗

gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)

Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
Retrieved: 2026-10-14T12:02:25Z

not individually reviewed

No individual claim review recorded

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.rationale

Source artifact SHA-256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8

Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present.

Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: use-case-mapping-gfm-guide-20261014-evee-embedding-extraction

field
links:assessed_by:gfm-guide-20261014-protocol-evee-embedding-extraction-compute
value
gfm-guide-20261014-protocol-evee-embedding-extraction-compute
relevance
proxy
endpoint
Approximate total H100 GPU-hours to extract Evo 2 7B layer-27 embeddings (reference and variant, both strands, 65 kb windows) for 4,252,870 ClinVar variants
rationale
Proxy. The only linked figure for running a genomic foundation model over human variants at the scale of a whole variant database, which bears on the accelerator budget for scoring variants with such a model. It is a one-off research embedding harvest rather than a diagnostic workflow, and gives one approximate total with no GPU count, batch size, wall-clock time or per-sample figure.
constraints
Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources.; Read the value as approximate; it is printed as '∼20,000 H100-hours'.; Do not divide it into a per-variant or per-sample cost without saying the division is yours; the source prints no per-variant timing, and the workload covers both strands and both alleles.
limitations
Developer-reported: EVEE's authors built the extraction pipeline, and three of them co-authored Evo 2 (claim gfm-guide-20261014-claim-evee-developer-overlap).; Stated once in Methods (the 'Dataset' paragraph after 'Harvesting'); GPU count, batch size, wall-clock time and software versions are not given.; The workload stores per-position embeddings (bf16, about 34 TB), which a diagnostic scoring pipeline would not need; the figure therefore includes work beyond scoring.; Preprint (bioRxiv v4), not peer reviewed.; The source carries an evidence concern about the NTv3 column of Figures 1b and 1c. It does not touch this figure, but an active judgement needs clean protocol sources, so this judgement stays withheld after review until that concern is resolved.
revision
1
reason
Add relevance judgements for the execution and compute protocols of the genomic foundation model guide sources batch (data/omics/gfm-guide-sources-20261014, issue #162), independently reviewed in PR #169.
citation locators
source id: gfm-guide-20261014-source-evee-v4; locator: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)
source locator
gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)
comparison group
evee2026-evo2-embedding-extraction
comparison title
Evo 2 7B embedding extraction for all ClinVar variants (Pearce et al. 2026)
headline metric
accelerator-time
reviewed evaluations
gfm-guide-20261014-eval-evee-embedding-extraction-compute
review
method: independent-cell-check; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent review-169, independent of the agent that drafted these judgements for issue #162; no human review claimed; reviewed at: 2026-10-14T19:00:00Z; note: Independent relevance review: grade, endpoint, rationale, constraints, limitations and locators checked against the use case and the source text; every value of the listed evaluations checked against the source. No execution, reproduction, qualified human scientific review or clinical validation. See docs/reviews/use-cases/diagnostic-genomics-model-execution-judgements-2026-10-14.md. Checked in a fresh copy of the bioRxiv v4 PDF; bioRxiv stamps each download, so its hash differs from the pinned bytes (hash_scope on the source). Stays withheld while the source carries its evidence concern.
pins
record id: gfm-guide-20261014-eval-evee-embedding-extraction-compute; fields: status; links; attributes.origin; attributes.comparison; sha256: 53403c68ad5bea53431fee3eb1b4e81b5cff414530d292e710041a63abd5422a; record id: gfm-guide-20261014-protocol-evee-embedding-extraction-compute; fields: status; name; description; facets; source_ids; links; attributes; sha256: c5c5c758a9673043af191956af05d68bfe66247b928364969f52684a897c9294; record id: gfm-guide-20261014-result-evee-embedding-extraction-h100-hours; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 87e35eacbfca259a686cae9b9fa7b3829ee9358124ea5b57f1d002c6fa0dd6eb; record id: gfm-guide-20261014-source-evee-v4; fields: status; attributes.artifact_sha256; sha256: 7fa901d074087100fbb320434beaf2f77ce2000077cd20e456c03c9285263dd7; record id: use-case-diagnostic-genomics-model-execution; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 1c2a12431556cc6581f5aab019cf91576d2393387b88a8a2bea35ea2a3ee4a70
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