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Task

PFMBench EC: Enzyme Commission

Enzyme Commission. Scored with F1 score on Enzyme Commission. Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.

12 evaluations · 12 results

Overview

Enzyme Commission. Scored with F1 score on Enzyme Commission. Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

PFMBench EC: Enzyme Commission

f1 (fraction) · Higher values are better.

PFMBench EC: Enzyme Commission · Enzyme Commission (PFMBench split)

Evidence origin: Author-reported evaluation.

pfmbench primary benchmark evidence · Table 1, row(Enzyme Commission)
  • The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.
  • Table 3 scores come from adapter fine-tuning; the ProteinGym figure is zero-shot and is not comparable to them.
Comparison details and limitations

Every method PFMBench reports on Enzyme Commission, scored with F1 score on Enzyme Commission.

  • Author-reported numbers, source checked but not independently reproduced.

Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Showing 12 of 12 matching rows.

Tested configuration
00.250.50.751
Reported score
  1. ProstT50.768
  2. ProTrek0 .76408
  3. ProtT50.762
  4. DPLM0.755
  5. VenusPLM0.752
  6. SaProt0.751
  7. PGLM0.747
  8. ESM-20.736
  9. ProtST0.718
  10. ESM-C0.717
  11. ProtGPT20.697
  12. ESM30.648

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

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Benchmarks

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Recorded evaluations

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Run instructions

No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

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Strengths, limitations and unresolved questions

Evidence

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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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statementOriginal source and locationReview and provenance
Relationship: part of
discovery-benchmark-pfmbench
Individual claims		pfmbench primary benchmark evidence

Original source ↗

Table 1, row(Enzyme Commission)

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

source checked

automated source review · 2026-09-18

Audit details

Primary-source transcription with no human sign-off and no independent reproduction.

Field: links:part_of:discovery-benchmark-pfmbench

Claim: pfmbench-association-ec

Source artifact SHA-256: 59c7bbb888e8e91f33c1e2cabfde062c32381d6ca727d23b6655c977aabf97a2

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-09-29-06401fd5b220 · Record review: source checked

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: pfmbench-task-ec

areas
proteins-complexes
tasks
Enzyme Commission
metric
F1 score
metric direction
higher
dataset
Enzyme Commission
protocol
Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1.
source locator
Table 1, row(Enzyme Commission)
comparison panels
id: pfmbench-panel-ec; title: PFMBench EC: Enzyme Commission; protocol id: pfmbench-task-ec; dataset id: pfmbench-dataset-enzyme-commission; metric: f1; unit: fraction; direction: higher; result ids: pfmbench-result-esm-2-ec-f1; pfmbench-result-venusplm-ec-f1; pfmbench-result-esm-c-ec-f1; pfmbench-result-protgpt2-ec-f1; pfmbench-result-pglm-ec-f1; pfmbench-result-prott5-ec-f1; pfmbench-result-dplm-ec-f1; pfmbench-result-saprot-ec-f1; pfmbench-result-prostt5-ec-f1; pfmbench-result-protst-ec-f1; pfmbench-result-esm3-ec-f1; pfmbench-result-protrek-ec-f1; source ids: expansion-p3-pfmbench; source locator: Table 1, row(Enzyme Commission); context: Every method PFMBench reports on Enzyme Commission, scored with F1 score on Enzyme Commission.; caveats: Author-reported numbers, source checked but not independently reproduced.; The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.; Table 3 scores come from adapter fine-tuning; the ProteinGym figure is zero-shot and is not comparable to them.; review: method: automated_source_review; date: 2026-09-18
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