rewirebio.iobenchmarks
Evaluation

MUPro on Mega-scale dataset (Chu et al. 2024)

Published stability-change predictor comparison; transcribed, not reproduced.

Research readiness

These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

Release 2026-10-10-7fcc3e48a123 · 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

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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: MUPro (Chu et al. 2024)Protocol: Mega-scale dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1)
Dataset: Mega-scale dataset: multiple, cDNA display proteolysis
0.31 spearman-correlation
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

MUPro on Mega-scale dataset (Chu et al. 2024)

protein-stability-20261009-protocol-chu2024-mega-scale

Aggregation: Not reported

Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset · Table 1, row 'Mega-scale dataset', column 'MUPro' (supervised group)

Source checking is not independent reproduction. Release 2026-10-10-7fcc3e48a123.

Evaluation procedure

protein-stability-20261009-protocol-chu2024-mega-scale

Configuration
MUPro (Chu et al. 2024)
Protocol
Mega-scale dataset stability ranking, Spearman correlation (Chu et al. 2024 Table 1)
Dataset
Mega-scale dataset: multiple, cDNA display proteolysis
origin
Independent external evaluation
configuration
Primary source as retrieved 2026-10-09
protocol id
protein-stability-20261009-protocol-chu2024-mega-scale
dataset version
Not reported
split
Test-set-only domains
population
100,794 (test set) sequences
inputs
Protein sequence and the variant
adaptation
Not reported
metric implementation
Spearman correlation
aggregation
Pooled over variants, or mean over domains for the mega-scale set
budget
Not reported

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

Reproduction

Split
Test-set-only domains
Adaptation
Not reported
Scoring implementation
Spearman correlation

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.

19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-7fcc3e48a123
Property and statementOriginal source and locationReview and provenance
attributes.comparison.adaptation
Not reported
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.aggregation
Pooled over variants, or mean over domains for the mega-scale set
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.budget
Not reported
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.dataset_version
Not reported
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.inputs
Protein sequence and the variant
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.metric_implementation
Spearman correlation
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.population
100,794 (test set) sequences
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.protocol_id
protein-stability-20261009-protocol-chu2024-mega-scale
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.comparison.split
Test-set-only domains
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

attributes.limitations
1 values
  • Run as a comparator by the ESM therm developers (Chu et al. 2024), not by this tool's developers.
Context-only references
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Original source ↗

Table 1, row 'Mega-scale dataset', column 'MUPro'

Version: PLOS Computational Biology 20(7):e1012248, published 2024-07-22; PMC11293664 full-text XML
Retrieved: 2026-10-09T21:01:08Z

not individually reviewed

No individual claim review recorded

independent paper

Audit details

Field: attributes.limitations

Source artifact SHA-256: bb9830cbd6bab1b3e0ddbb52edb2a9afd4b06e427dbfeb19e6a07f843ebd914f

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

Inspected artifact

Sources and history

Release 2026-10-10-7fcc3e48a123 · Record review: source checked

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

Stable ID: protein-stability-20261009-eval-chu2024-mupro-mega-scale

areas
proteins-complexes
contexts
research
origin
independent_paper
protocol
protein-stability-20261009-protocol-chu2024-mega-scale
version
Primary source as retrieved 2026-10-09
comparison
protocol id: protein-stability-20261009-protocol-chu2024-mega-scale; dataset version: Not reported; split: Test-set-only domains; population: 100,794 (test set) sequences; inputs: Protein sequence and the variant; adaptation: Not reported; metric implementation: Spearman correlation; aggregation: Pooled over variants, or mean over domains for the mega-scale set; budget: Not reported
source locator
Table 1, row 'Mega-scale dataset', column 'MUPro'
missing metadata
comparison.dataset version: reason: unreported
limitations
Run as a comparator by the ESM therm developers (Chu et al. 2024), not by this tool's developers.
Related records

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