rewirebio.iobenchmarks
Evaluation

PGLM on PFMBench EC: Enzyme Commission

PFMBench evaluation of PGLM on Enzyme Commission, scored with F1 score.

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: PGLMTask: PFMBench EC: Enzyme Commission
Dataset subset: Enzyme Commission (PFMBench split)
0.747 F1 max (multi-label; TorchDrug-style F1_score_max)
fraction · higher

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

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

PGLM on PFMBench EC: Enzyme Commission

Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.

Aggregation: Not reported

pfmbench primary benchmark evidence · Table 3, row(PGLM [ 5 ]), column(EC)

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.

Evaluation procedure

Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.

Configuration
PGLM
Task
PFMBench EC: Enzyme Commission
Dataset subset
Enzyme Commission (PFMBench split)
origin
Author-reported evaluation
configuration
Not reported
protocol id
pfmbench-task-ec
metric implementation
F1 score

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

Reproduction

Split
Not reported
Adaptation
Not reported
Scoring implementation
F1 score

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.

10 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: metric implementation
F1 score
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: protocol id
pfmbench-task-ec
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Origin
author_reported
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.origin

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Protocol
Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.protocol

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Source location
Table 3, row(PGLM [ 5 ]), column(EC)
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Description
PFMBench evaluation of PGLM on Enzyme Commission, scored with F1 score.
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: description

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: assessment
pfmbench-task-ec
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: links:assessment:pfmbench-task-ec

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: data
pfmbench-dataset-enzyme-commission
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: links:data:pfmbench-dataset-enzyme-commission

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: system
pfmbench-method-pglm
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: links:system:pfmbench-method-pglm

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Name
PGLM on PFMBench EC: Enzyme Commission
Context-only references
pfmbench primary benchmark evidence

Original source ↗

Table 3, row(PGLM [ 5 ]), column(EC)

Version: 2506.14796v1
Retrieved: 2026-09-16T21:06:29.716004+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: name

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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

Stable ID: pfmbench-evaluation-pglm-ec

areas
proteins-complexes
tasks
Enzyme Commission
origin
author_reported
protocol
Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.
comparison
protocol id: pfmbench-task-ec; metric implementation: F1 score
missing metadata
budget: reason: unreported; checkpoint revision: reason: unreported; seeds: reason: unreported; split manifest: reason: unextracted
source locator
Table 3, row(PGLM [ 5 ]), column(EC)
Related records

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