rewirebio.iobenchmarks
Evaluation

Evo-generated IS605-like designs, in vitro activity (Nguyen et al. 2024)

Published result transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Evo fine-tuned on IS200/IS605 elements (Nguyen et al. 2024)Protocol: In vitro activity of Evo-generated mobile-element designs (Nguyen et al. 2024)
Dataset: Evo-generated IS200-like and IS605-like designs selected for in vitro testing (Nguyen et al. 2024)
3 Count (generated designs active in vitro, out of 24 tested; IS605-like family)
count · higher

Uncertainty: Not applicable: A single count of a binary assay outcome; no spread printed

Coverage: 24/24 designs scored (All 24 selected designs of the family were tested; the number of generations the 24 were selected from is not printed.)

Author-reported evaluation · Source checked
Methods, coverage and source

Evo-generated IS605-like designs, in vitro activity (Nguyen et al. 2024)

gfm-guides-20261014-evo-generation-protocol-in-vitro-activity

Aggregation: Not reported

Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024) · Results, section 'Generative design of transposon systems', sentence beginning 'We observed that 11 out of 24': '3 out of 24 Evo-generated IS605-like elements'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

In vitro activity of Evo-generated mobile-element designs (Nguyen et al. 2024)

Configuration
Evo fine-tuned on IS200/IS605 elements (Nguyen et al. 2024)
Protocol
In vitro activity of Evo-generated mobile-element designs (Nguyen et al. 2024)
Dataset
Evo-generated IS200-like and IS605-like designs selected for in vitro testing (Nguyen et al. 2024)
origin
Author-reported evaluation
configuration
Primary source as retrieved 2026-10-14
protocol id
gfm-guides-20261014-evo-generation-protocol-in-vitro-activity
dataset version
As published, Science 386, eado9336 (2024)
split
No split
population
24 generated IS605-like designs selected for testing
inputs
Sequences generated by the fine-tuned model with the family prompt token
adaptation
Fine-tuned on mobile-element loci, then prompted
metric implementation
Not reported
aggregation
Not reported
budget
Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split
No split
Adaptation
Fine-tuned on mobile-element loci, then prompted
Scoring implementation
Not reported

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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
Comparison: adaptation
Fine-tuned on mobile-element loci, then prompted
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: aggregation
Not reported
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: budget
Not reported
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: dataset version
As published, Science 386, eado9336 (2024)
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: inputs
Sequences generated by the fine-tuned model with the family prompt token
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: metric implementation
Not reported
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: population
24 generated IS605-like designs selected for testing
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: protocol id
gfm-guides-20261014-evo-generation-protocol-in-vitro-activity
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Comparison: split
No split
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

Inspected artifact

Origin
author_reported
Context-only references
Sequence modeling and design from molecular to genome scale with Evo (Nguyen et al., Science 2024)

Original source ↗

Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')

Version: Science 386, eado9336 (15 November 2024); PubMed Central author manuscript PMC12057570, PMC version 1, JATS full text
Retrieved: 2026-10-14T12:12:36Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.origin

Source artifact SHA-256: 6bf1e0563c2870088e9c6c46361052fd0e9418c3122ee29aa4a2373794e65caa

Hash scope: SHA-256 of the retrieved efetch JATS XML bytes

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: gfm-guides-20261014-evo-generation-eval-evo-finetuned-is605

areas
dna-genomes
contexts
research
origin
author_reported
protocol
gfm-guides-20261014-evo-generation-protocol-in-vitro-activity
version
Primary source as retrieved 2026-10-14
comparison
protocol id: gfm-guides-20261014-evo-generation-protocol-in-vitro-activity; dataset version: As published, Science 386, eado9336 (2024); split: No split; population: 24 generated IS605-like designs selected for testing; inputs: Sequences generated by the fine-tuned model with the family prompt token; adaptation: Fine-tuned on mobile-element loci, then prompted; metric implementation: Not reported; aggregation: Not reported; budget: Not reported
source locator
Results, section 'Generative design of transposon systems' (sentence beginning 'We observed that 11 out of 24')
missing metadata
comparison.aggregation: reason: unreported; comparison.budget: reason: unreported; comparison.metric implementation: reason: unreported
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