rewirebio.iobenchmarks
Evaluation

Provean: ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22)

Official ProteinGym summary row; transcribed, 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: Provean [ProteinGym 144fe22 clinical summary]Protocol: ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22)
Dataset subset: ProteinGym clinical indel benchmark at commit 144fe22
0.927 AUROC (ProteinGym clinical indels, zero-shot, Average_AUC over proteins)
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Evaluation origin not reported · Source checked
Methods, coverage and source

Provean: ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22)

ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22)

Aggregation: Not reported

ProteinGym clinical zero-shot indels AUC summary at commit 144fe22 · benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3, row 'Provean', column 'Average_AUC'

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

ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22)

Configuration
Provean [ProteinGym 144fe22 clinical summary]
Protocol
ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22)
Dataset subset
ProteinGym clinical indel benchmark at commit 144fe22
origin
Evaluation origin not reported
configuration
Not reported
protocol id
vep-lit-20261014-protocol-proteingym-clinical-zero-shot-indels-auc-144fe22
dataset version
144fe22b07dfaeec2b366f2346203a9838a55b4c
split
Not reported
population
Not reported
inputs
ProteinGym label 'Provean', model type 'MSA'
adaptation
Zero-shot
metric implementation
Not reported
aggregation
Not reported
budget
Not reported

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

Reproduction

Split
Not reported
Adaptation
Zero-shot
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
Zero-shot
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: aggregation
Not reported
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

missing or unspecified

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: budget
Not reported
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

missing or unspecified

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: dataset version
144fe22b07dfaeec2b366f2346203a9838a55b4c
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: inputs
ProteinGym label 'Provean', model type 'MSA'
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: metric implementation
Not reported
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

missing or unspecified

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: population
Not reported
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

missing or unspecified

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: protocol id
vep-lit-20261014-protocol-proteingym-clinical-zero-shot-indels-auc-144fe22
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Comparison: split
Not reported
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

missing or unspecified

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

Inspected artifact

Input information
ProteinGym 'Model type' label: MSA
Context-only references
ProteinGym clinical zero-shot indels AUC summary at commit 144fe22

Original source ↗

benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-10-14T13:39:33Z

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.input_information

Source artifact SHA-256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836

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

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: vep-lit-20261014-eval-pg-czi-proteingym-clinical-provean

areas
proteins-complexes; dna-genomes
contexts
clinical_research
origin
unreported
protocol
ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22)
input information
ProteinGym 'Model type' label: MSA
comparison
protocol id: vep-lit-20261014-protocol-proteingym-clinical-zero-shot-indels-auc-144fe22; dataset version: 144fe22b07dfaeec2b366f2346203a9838a55b4c; split: Not reported; population: Not reported; inputs: ProteinGym label 'Provean', model type 'MSA'; adaptation: Zero-shot; metric implementation: Not reported; aggregation: Not reported; budget: Not reported
source locator
benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv line 3
missing metadata
aggregation: reason: unextracted; note: Clinical scoring script not read; budget: reason: unreported; metric implementation: reason: unextracted; note: Clinical scoring script not read; split: reason: inapplicable
review
reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T15:30:00Z; artifact sha256: 98a532c0e2c3d4720b73b7c05cf0dcf0419438c326761aaae3b788799f5aa836; retrieval url: https://raw.githubusercontent.com/OATML-Markslab/ProteinGym/144fe22b07dfaeec2b366f2346203a9838a55b4c/benchmarks/clinical_zero_shot/indels/AUC/Summary_performance_clinical_indels_AUC.csv; method: source-hash-verification; deterministic-table-parse; scope-review; method note: Links, origin and comparison fields checked against the source and the linked protocol; results checked by review/check_values.py.; note: Origin set to unreported in review: ProteinGym computed the metric with its own scripts, but the summary file does not say who generated each model's scores (the README says new baselines are added with scores supplied by the requester, and others are scored by the maintainers), and most models are not by the ProteinGym authors. author_reported would wrongly mark most rows as developer-reported; paper_compilation would wrongly mark them as copied from earlier papers.
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