ESM3 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
PFMBench evaluation of ESM3 on ProteinGym zero-shot variant effect prediction, scored with Spearman.
Methods and reproduction
PFMBench evaluation of ESM3 on ProteinGym zero-shot variant effect prediction, scored with Spearman.
- task
- PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
- configuration
- ESM3
- dataset subset
- ProteinGym (PFMBench split)
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- Spearman
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.
Evaluation procedure
Scored zero-shot, with no fine-tuning, as reported in PFMBench Table 4.
- Configuration
- ESM3
- Task
- PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
- Dataset subset
- ProteinGym (PFMBench split)
- origin
- Author-reported evaluation
- configuration
- Not reported
- protocol id
- pfmbench-task-proteingym-zs
- metric implementation
- Spearman
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-134cd1815de8 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM3 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Configuration: ESM3Task: PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect predictionDataset subset: ProteinGym (PFMBench split) Scored zero-shot, with no fine-tuning, as reported in PFMBench Table 4. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.41401 spearman Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Source checking is not 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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.metric_implementation Spearman Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.protocol_id pfmbench-task-proteingym-zs Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.origin author_reported Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.protocol Scored zero-shot, with no fine-tuning, as reported in PFMBench Table 4. Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.source_locator Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| description PFMBench evaluation of ESM3 on ProteinGym zero-shot variant effect prediction, scored with Spearman. Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: benchmark pfmbench-task-proteingym-zs Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: dataset pfmbench-dataset-proteingym Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: model pfmbench-method-esm3 Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name ESM3 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Context-only references | pfmbench primary benchmark evidence Table 4, row(ESM3 [ 18 ]), column(ProteinGym) Version: 2506.14796v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- pfmbench primary benchmark evidence · Original source · 2506.14796v1
Technical metadata and extraction receipts
Stable ID: pfmbench-evaluation-esm3-proteingym-zs
- areas
- proteins-complexes
- tasks
- ProteinGym zero-shot variant effect prediction
- origin
- author_reported
- protocol
- Scored zero-shot, with no fine-tuning, as reported in PFMBench Table 4.
- comparison
- protocol id: pfmbench-task-proteingym-zs; metric implementation: Spearman
- missing metadata
- checkpoint revision: unreported; seeds: unreported; budget: unreported; split manifest: unextracted
- source locator
- Table 4, row(ESM3 [ 18 ]), column(ProteinGym)
Related records
- benchmark: PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
- model: ESM3
- dataset: ProteinGym (PFMBench split)
- evaluation: ESM3 · PFMBench PROTEINGYM-ZS · Spearman