rewire.itbenchmarks
Evaluation

Borzoi (paper Table 3): RNA-seq track prediction at 32 bp

Align predicted and experimental values on the same 32-bp tracks and test intervals.

Research readiness

These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

Release 2026-09-29-06401fd5b220 · 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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • metric replay: verification is missing

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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • metric replay: verification is missing
  • annotations: verification is missing
  • dependence: verification is missing

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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • recipe pinned: verification is missing
  • resource estimate: verification is missing

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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • independent validation: verification is missing
  • overlap checked: verification is missing

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.

Read reviewed discrepancy investigations

Evaluation results

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

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Borzoi (paper Table 3)Protocol: RNA-seq track prediction at 32 bp (AlphaGenome paper)
Dataset subset: RNA-seq track prediction at 32 bp: evaluated data subset
0.747 pearsonr
correlation · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

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

Borzoi (paper Table 3): RNA-seq track prediction at 32 bp

Align predicted and experimental values on the same 32-bp tracks and test intervals.

Aggregation: Pearson correlation; group summaries derive from individual track correlations.

AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J12

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Evaluation procedure

Align predicted and experimental values on the same 32-bp tracks and test intervals.

Configuration
Borzoi (paper Table 3)
Protocol
RNA-seq track prediction at 32 bp (AlphaGenome paper)
Dataset subset
RNA-seq track prediction at 32 bp: evaluated data subset
origin
Author-reported evaluation
configuration
Borzoi (paper Table 3)
protocol id
alphagenome-2026-t3-protocol-6
dataset version
Not reported
split
Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1.
population
Original Borzoi TFRecords, retaining their scaling and 32-bp target bins.
inputs
Not reported
adaptation
Borzoi (paper Table 3)
metric implementation
Not reported
aggregation
Pearson correlation; group summaries derive from individual track correlations.
budget
Not reported

Metadata review: needs review. Unreported conditions prevent automatic comparisons.

Reproduction

Split
Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1.
Adaptation
Borzoi (paper Table 3)
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.

63 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statementOriginal source and locationReview and provenance
attributes.comparison.adaptation
Borzoi (paper Table 3)
Context-only references
alphagenome: Journal full-text XML

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.009088+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

attributes.comparison.adaptation
Borzoi (paper Table 3)
Context-only references
AlphaGenome Nature 2026 supplementary methods

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplement to Nature version of record, 28 January 2026; content hash pinned
Retrieved: 2026-09-17T06:37:01.778972+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0

Hash scope: SHA-256 of exact publisher PDF bytes

Format: original_pdf

Inspected artifact

attributes.comparison.adaptation
Borzoi (paper Table 3)
Context-only references
AlphaGenome Nature 2026 supplementary comparison tables

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Nature version of record, 28 January 2026
Retrieved: 2026-09-17T06:31:06.887921+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154

Hash scope: SHA-256 of exact retrieved original artifact bytes

Format: xlsx

Inspected artifact

attributes.comparison.aggregation
Pearson correlation; group summaries derive from individual track correlations.
Context-only references
alphagenome: Journal full-text XML

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.009088+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

attributes.comparison.aggregation
Pearson correlation; group summaries derive from individual track correlations.
Context-only references
AlphaGenome Nature 2026 supplementary methods

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplement to Nature version of record, 28 January 2026; content hash pinned
Retrieved: 2026-09-17T06:37:01.778972+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0

Hash scope: SHA-256 of exact publisher PDF bytes

Format: original_pdf

Inspected artifact

attributes.comparison.aggregation
Pearson correlation; group summaries derive from individual track correlations.
Context-only references
AlphaGenome Nature 2026 supplementary comparison tables

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Nature version of record, 28 January 2026
Retrieved: 2026-09-17T06:31:06.887921+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154

Hash scope: SHA-256 of exact retrieved original artifact bytes

Format: xlsx

Inspected artifact

attributes.comparison.budget
Not reported
Context-only references
alphagenome: Journal full-text XML

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.009088+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

attributes.comparison.budget
Not reported
Context-only references
AlphaGenome Nature 2026 supplementary methods

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplement to Nature version of record, 28 January 2026; content hash pinned
Retrieved: 2026-09-17T06:37:01.778972+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0

Hash scope: SHA-256 of exact publisher PDF bytes

Format: original_pdf

Inspected artifact

attributes.comparison.budget
Not reported
Context-only references
AlphaGenome Nature 2026 supplementary comparison tables

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Nature version of record, 28 January 2026
Retrieved: 2026-09-17T06:31:06.887921+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154

Hash scope: SHA-256 of exact retrieved original artifact bytes

Format: xlsx

Inspected artifact

attributes.comparison.dataset_version
Not reported
Context-only references
alphagenome: Journal full-text XML

Original source ↗

No field-specific location recorded

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.009088+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Sources and history

View linked audit checks and correction history

Release 2026-09-29-06401fd5b220 · Record review: needs review

3 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: alphagenome-2026-evaluation-ec0e5d0bbab1412a

areas
dna-genomes
origin
author_reported
protocol
Align predicted and experimental values on the same 32-bp tracks and test intervals.
version
Borzoi (paper Table 3)
source evaluation index
6
source table
3
comparison
protocol id: alphagenome-2026-t3-protocol-6; dataset version: Not reported; split: Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1.; population: Original Borzoi TFRecords, retaining their scaling and 32-bp target bins.; inputs: Not reported; adaptation: Borzoi (paper Table 3); metric implementation: Not reported; aggregation: Pearson correlation; group summaries derive from individual track correlations.; budget: Not reported
context
allowed inputs: Reference DNA and the dedicated Borzoi-matched AlphaGenome output head; compare published Borzoi fold-1 predictions.; limitations: This is a fine-tuned comparison head, not the generic distilled variant model. Scaling and resolution differ from the separate base-resolution RNA endpoint.
missing metadata
dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
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