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Evaluation

ESM-2: Zero-shot variant effect prediction

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

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Missing or unresolved evidence

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  • 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.

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Verified: Not verified

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Validate independently

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Verified: Not verified

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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: ESM-2Task: Zero-shot variant effect prediction
Dataset: ProteinShake VEP datasets
0.489 Mean |Spearman rho|
unitless · unknown

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

ESM-2: Zero-shot variant effect prediction

Zero-shot VEP; paper averages absolute Spearman correlations.

Aggregation: Not reported

Endowing protein language models with structural knowledge · Table 2, ESM-2 row, Zero-shot VEP Mean |ρ| column

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

Evaluation procedure

Zero-shot VEP; paper averages absolute Spearman correlations.

Configuration
ESM-2
Task
Zero-shot variant effect prediction
Dataset
ProteinShake VEP datasets
origin
Independent external evaluation
configuration
Not reported
protocol id
Not reported
dataset version
Not reported
split
Not reported
population
Not reported
inputs
Not reported
adaptation
Not reported
metric implementation
Not reported
aggregation
Not reported
budget
Not reported

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

Reproduction

Split
Not reported
Adaptation
Not reported
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

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

17 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
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.aggregation
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.budget
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.dataset_version
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.inputs
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.metric_implementation
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.population
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.protocol_id
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.comparison.split
Not reported
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

attributes.origin
independent_paper
Context-only references
Endowing protein language models with structural knowledge

Original source ↗

No field-specific location recorded

Version: PMC12603367.1
Retrieved: 2026-09-16T10:41:16.527633+00:00

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.origin

Source artifact SHA-256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3

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

Inspected artifact

Sources and history

View linked audit checks and correction history

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

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

Stable ID: evaluation-lit-024

areas
proteins-complexes
tasks
Zero-shot variant effect prediction
origin
independent_paper
protocol
Zero-shot VEP; paper averages absolute Spearman correlations.
version
Not reported
comparison
protocol id: Not reported; dataset version: Not reported; split: Not reported; population: Not reported; inputs: Not reported; adaptation: Not reported; metric implementation: Not reported; aggregation: Not reported; budget: Not reported
missing metadata
model version: not_reported_in_legacy_extract; dataset version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
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