rewire.itbenchmarks
Evaluation

AlphaGenome distilled all-fold student: European-ancestry LCL caQTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

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: AlphaGenome distilled all-fold studentProtocol: European-ancestry LCL caQTL effect-size prediction (AlphaGenome paper)
Dataset subset: European-ancestry LCL caQTL effect-size prediction: evaluated data subset
0.59 pearsonr
correlation · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

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

AlphaGenome distilled all-fold student: European-ancestry LCL caQTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.

AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M27; 'Suppl Table 4 Variant performan'!M28

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

Evaluation procedure

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Configuration
AlphaGenome distilled all-fold student
Protocol
European-ancestry LCL caQTL effect-size prediction (AlphaGenome paper)
Dataset subset
European-ancestry LCL caQTL effect-size prediction: evaluated data subset
origin
Author-reported evaluation
configuration
AlphaGenome distilled all-fold student
protocol id
alphagenome-2026-t4-protocol-21
dataset version
Not reported
split
Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds.
population
European-ancestry LCL caQTL data reused from the ChromBPNet evaluation; retain this ancestry/cell-type/trait identity.
inputs
Not reported
adaptation
AlphaGenome distilled all-fold student
metric implementation
Not reported
aggregation
Pearson correlation against reported effect sizes of the causal/significant QTL set.
budget
Not reported

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

Reproduction

Split
Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds.
Adaptation
AlphaGenome distilled all-fold student
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
AlphaGenome distilled all-fold student
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
AlphaGenome distilled all-fold student
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
AlphaGenome distilled all-fold student
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 against reported effect sizes of the causal/significant QTL set.
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 against reported effect sizes of the causal/significant QTL set.
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 against reported effect sizes of the causal/significant QTL set.
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-50f0972d99499cf7

areas
dna-genomes
origin
author_reported
protocol
Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.
version
AlphaGenome distilled all-fold student
source evaluation index
21
source table
4
comparison
protocol id: alphagenome-2026-t4-protocol-21; dataset version: Not reported; split: Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds.; population: European-ancestry LCL caQTL data reused from the ChromBPNet evaluation; retain this ancestry/cell-type/trait identity.; inputs: Not reported; adaptation: AlphaGenome distilled all-fold student; metric implementation: Not reported; aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.; budget: Not reported
context
allowed inputs: REF/ALT sequence and local predicted assay-signal changes. AlphaGenome DNase GM12878; Borzoi averages its two DNase GM12878 tracks.; limitations: Proxy tracks differ across models and are part of the evaluation configuration. ChromBPNet is specialized by cell type; AlphaGenome/Borzoi are evaluated without task-label training. The inspected paper delegates detailed QTL preprocessing to ChromBPNet and does not enumerate final row-level sample counts.
missing metadata
dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records

Suggest a correction