rewirebio.iobenchmarks
Dataset

ProteinGym substitutions

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
Pipeline: ESM2 OFS pseudo-perplexityTask: protein variant fitness prediction
Dataset: ProteinGym substitutions
0.403 Spearman
unitless · unknown

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

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

ESM2 OFS pseudo-perplexity: protein variant fitness prediction

authors’ zero-shot ESM2 OFS pseudo-perplexity evaluation; aggregate mean across ProteinGym substitution assays

Aggregation: Not reported

Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Published PDF page 6 (033014-6), Table I, ESM2: OFS PP row, Aggregate mean column

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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 2026-11-02-a7f03c9e55a5 · 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.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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.

3 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Split
aggregate across assays
Context-only references
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation

Original source ↗

No field-specific location recorded

Version: PRX Life 2025 journal article
Retrieved: 2026-09-16T10:45:41.099916+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: 085ef646f11b8e5335c4b3d86b15fb6c7bf5edf4a80a8b622753ac69d9991a67

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

Inspected artifact

Description
No value recorded
Context-only references
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation

Original source ↗

No field-specific location recorded

Version: PRX Life 2025 journal article
Retrieved: 2026-09-16T10:45:41.099916+00:00

missing or unspecified

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: 085ef646f11b8e5335c4b3d86b15fb6c7bf5edf4a80a8b622753ac69d9991a67

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

Inspected artifact

Name
ProteinGym substitutions
Context-only references
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation

Original source ↗

No field-specific location recorded

Version: PRX Life 2025 journal article
Retrieved: 2026-09-16T10:45:41.099916+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: 085ef646f11b8e5335c4b3d86b15fb6c7bf5edf4a80a8b622753ac69d9991a67

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

Inspected artifact

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: needs review

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: reported-dataset-9c186c8f4ed3f4

areas
proteins-complexes
split
aggregate across assays
missing metadata
accession: reason: unextracted; version: reason: unextracted
entity classification
review date: 2026-09-17; rationale: This record identifies a biological data collection or source-labelled evaluation cohort. Keep its dataset identity; split, assay, taxonomic level, candidate restrictions and comparison context remain attributes rather than automatically becoming new entity kinds.; source ids: esm2-ofs-fitness-2025; source locator: ProteinGym evaluation section and Table I; PDF text lines 346–369 and Table I caption; ambiguities: None recorded
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