rewire.itbenchmarks
Evaluation

structure-informed pLM: protein variant-effect classification

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: structure-informed pLMTask: protein variant-effect classification
Dataset: variant-effects benchmark
0.803 AUROC
fraction · unknown

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

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

structure-informed pLM: protein variant-effect classification

combined amino-acid, secondary structure, solvent accessibility and contact-map scoring

Aggregation: Not reported

Structure-Informed Protein Language Models are Robust Predictors for Variant Effects · PMC12068927 HTML, Table4, AA+SS+RSA+CM row, AUROC column

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

Evaluation procedure

combined amino-acid, secondary structure, solvent accessibility and contact-map scoring

Configuration
structure-informed pLM
Task
protein variant-effect classification
Dataset
variant-effects benchmark
origin
Author-reported evaluation
configuration
not stated in table
protocol id
Not reported
dataset version
Not reported
split
paper evaluation
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
paper evaluation
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

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.

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
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.aggregation
Not reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.budget
Not reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.dataset_version
Not reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.inputs
Not reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.metric_implementation
Not reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.population
Not reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.protocol_id
Not reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.comparison.split
paper evaluation
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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

Inspected artifact

attributes.origin
author_reported
Context-only references
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects

Original source ↗

No field-specific location recorded

Version: Human Genetics 2025 journal article (online 2024)
Retrieved: 2026-09-16T10:45:41.099916+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.origin

Source artifact SHA-256: 76082e1cd992d2c09c38f86d05aba575cc76c5022b53a297123b713bb1ce9267

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-b2-structure-informed-plm-2025

areas
proteins-complexes
tasks
protein variant-effect classification
origin
author_reported
protocol
combined amino-acid, secondary structure, solvent accessibility and contact-map scoring
version
not stated in table
comparison
protocol id: Not reported; dataset version: Not reported; split: paper evaluation; population: Not reported; inputs: Not reported; adaptation: Not reported; metric implementation: Not reported; aggregation: Not reported; budget: Not reported
missing metadata
dataset version: not_reported_in_legacy_extract
Related records

Suggest a correction