rewirebio.iobenchmarks
Evaluation

PLM-CLA: Clathrin independent test: selected-embedding classifiers

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Evaluation results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

Protocol: Clathrin independent test: selected-embedding classifiers (clathrin protein classification) · Dataset: Clathrin independent test: selected-embedding classifiers

Sorted by Accuracy (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configurationAccuracyAUROCF1MCCRecallSpecificity
PLM-CLAEvaluation0.9610.9970.9490.9170.9420.973
All 6 result rows with coverage, uncertainty and sources
Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: PLM-CLAProtocol: Clathrin independent test: selected-embedding classifiers (clathrin protein classification)
Dataset: Clathrin independent test: selected-embedding classifiers
0.917 MCC
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

PLM-CLA: Clathrin independent test: selected-embedding classifiers

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Aggregation: Not reported

Advancing the accuracy of clathrin protein prediction through multi-source protein language models · Table 3, row PLM-CLA, column MCC; XML row14 column5
Configuration: PLM-CLAProtocol: Clathrin independent test: selected-embedding classifiers (clathrin protein classification)
Dataset: Clathrin independent test: selected-embedding classifiers
0.949 F1
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

PLM-CLA: Clathrin independent test: selected-embedding classifiers

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Aggregation: Not reported

Advancing the accuracy of clathrin protein prediction through multi-source protein language models · Table 3, row PLM-CLA, column F1; XML row14 column6
Configuration: PLM-CLAProtocol: Clathrin independent test: selected-embedding classifiers (clathrin protein classification)
Dataset: Clathrin independent test: selected-embedding classifiers
0.961 Accuracy
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

PLM-CLA: Clathrin independent test: selected-embedding classifiers

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Aggregation: Not reported

Advancing the accuracy of clathrin protein prediction through multi-source protein language models · Table 3, row PLM-CLA, column ACC; XML row14 column2
Configuration: PLM-CLAProtocol: Clathrin independent test: selected-embedding classifiers (clathrin protein classification)
Dataset: Clathrin independent test: selected-embedding classifiers
0.997 AUROC
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

PLM-CLA: Clathrin independent test: selected-embedding classifiers

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Aggregation: Not reported

Advancing the accuracy of clathrin protein prediction through multi-source protein language models · Table 3, row PLM-CLA, column AUC; XML row14 column7
Configuration: PLM-CLAProtocol: Clathrin independent test: selected-embedding classifiers (clathrin protein classification)
Dataset: Clathrin independent test: selected-embedding classifiers
0.973 Specificity
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

PLM-CLA: Clathrin independent test: selected-embedding classifiers

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Aggregation: Not reported

Advancing the accuracy of clathrin protein prediction through multi-source protein language models · Table 3, row PLM-CLA, column SP; XML row14 column4
Configuration: PLM-CLAProtocol: Clathrin independent test: selected-embedding classifiers (clathrin protein classification)
Dataset: Clathrin independent test: selected-embedding classifiers
0.942 Recall
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

PLM-CLA: Clathrin independent test: selected-embedding classifiers

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Aggregation: Not reported

Advancing the accuracy of clathrin protein prediction through multi-source protein language models · Table 3, row PLM-CLA, column SN; XML row14 column3

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.

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  • 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

Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.

Configuration
PLM-CLA
Protocol
Clathrin independent test: selected-embedding classifiers (clathrin protein classification)
Dataset
Clathrin independent test: selected-embedding classifiers
origin
Author-reported evaluation
configuration
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
protocol id
paper-protocol-bbffa94da73852557b
dataset version
Not reported
split
CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.
subset
Clathrin independent test: selected-embedding classifiers
population
Not reported
aggregation
Not reported
inputs
Not reported
adaptation
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
budget
Not reported
metric implementation
Not reported

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

Reproduction

Split
CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.
Adaptation
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
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.

19 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
Comparison: adaptation
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: aggregation
Not reported
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: budget
Not reported
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: dataset version
Not reported
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: inputs
Not reported
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: metric implementation
Not reported
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: population
Not reported
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: protocol id
paper-protocol-bbffa94da73852557b
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: split
CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: subset
Clathrin independent test: selected-embedding classifiers
Context-only references
Advancing the accuracy of clathrin protein prediction through multi-source protein language models

Original source ↗

Table 3: ACC, Clathrin independent test: selected-embedding classifiers

Version: journal full text in PMC
Retrieved: 2026-09-17T07:56:20.050842+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.subset

Source artifact SHA-256: 2edc86b25707c1b737d26117093ce8d856e79cc5d0b335f27c1c341f887f1c7e

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

How to read the evidence

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: paper-evaluation-8e43ee270e308f9c9b

areas
proteins-complexes
tasks
clathrin protein classification
origin
author_reported
protocol
Conventional classifiers and PLM-CLA compared using paper-selected features. CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.
version
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
comparison
protocol id: paper-protocol-bbffa94da73852557b; dataset version: Not reported; split: CLA-IND 0.6 independent test from Shoombuatong 2024 dataset; source Table 1 carries cohort counts.; subset: Clathrin independent test: selected-embedding classifiers; population: Not reported; aggregation: Not reported; inputs: Not reported; adaptation: Paper-specific evaluated pipeline; exact checkpoint not inferred from label; budget: Not reported; metric implementation: Not reported
source locator
Table 3: ACC, Clathrin independent test: selected-embedding classifiers
missing metadata
budget: reason: unreported; checkpoint revision: reason: unextracted; split manifest: reason: unextracted
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