result · source checked
0.489 Mean |Spearman rho|
ESM-2 · Mean |Spearman rho| · ProteinShake VEP datasets
- Tested model
- ESM-2
- Task or benchmark
- Zero-shot variant effect prediction
- Dataset
- ProteinShake VEP datasets
- Procedure
- Zero-shot VEP; paper averages absolute Spearman correlations.
- Evaluation
- ESM-2: Zero-shot variant effect prediction
- Evidence
- Independent external evaluation · source checkedEndowing protein language models with structural knowledge · Table 2, ESM-2 row, Zero-shot VEP Mean |ρ| column
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: needs review. Source checked does not mean independently reproduced.
Evaluation results
Release 2026-09-16-d74d282221a9 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM-2: Zero-shot variant effect prediction Zero-shot VEP; paper averages absolute Spearman correlations. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.489 Mean |Spearman rho| Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedEndowing protein language models with structural knowledge · Table 2, ESM-2 row, Zero-shot VEP Mean |ρ| column Source checking is not independent reproduction. |
Sources and history
Release 2026-09-16-d74d282221a9 · Record review: source checked
- Endowing protein language models with structural knowledge · Original source · PMC12603367.1
Technical metadata and extraction receipts
Stable ID: lit-024
- areas
- proteins-complexes
- tasks
- Zero-shot variant effect prediction
- printed value
- 0.489
- numeric value
- 0.489
- metric
- Mean |Spearman rho|
- metric direction
- unknown
- unit
- unitless
- uncertainty
- Not reported
- source locator
- Table 2, ESM-2 row, Zero-shot VEP Mean |ρ| column
- review
- method: independent_ai_table_review; reviewer: Codex omics research agent; independent source-table review, not human review; reviewed at: 2026-09-16T10:41:16.528656+00:00; notes: Zero-shot VEP is the last metric group; selected Mean absolute rho, not GO/EC/binding-site metrics. This verifies the central score at its source location, not every metadata field or an experimental reproduction.; evidence: {"table_xml_id": "btaf582-T2", "row_cells": ["ESM-2", "0.648", "0.858", "0.698", "0.431", "0.791", "0.489"], "selected_cell_zero_based": 6, "selected_cell_xml": "<td rowspan=\"1\" colspan=\"1\">0.489</td>", "caption": "Comparison of PST and ESM-2 on ProteinShake tasks and VEP datasets.a"}; artifact sha256: c21ad593de589a7188ca86a8b7ce617e301d48dd939ecc7da03efb22cbe8d7a3; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12603367/fullTextXML
- legacy id
- lit-024
- legacy row
- id: lit-024; paper id: pst-2025; domain id: proteins-complexes; task: Zero-shot variant effect prediction; model: ESM-2; model version: Not reported; dataset: ProteinShake VEP datasets; dataset version: Not reported; split: Not reported; metric: Mean |Spearman rho|; value: 0.489; unit: unitless; uncertainty: Not reported; protocol: Zero-shot VEP; paper averages absolute Spearman correlations.; source locator: Table 2, ESM-2 row, Zero-shot VEP Mean |ρ| column; source url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12603367/; evaluation origin: independent_paper; reviewed utc: 2026-09-15T23:25:00Z
- missing metadata
- model version: not_reported_in_legacy_extract; dataset version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract; uncertainty: not_reported_in_legacy_extract
Related records
- evaluation: ESM-2: Zero-shot variant effect prediction
- subject: Reported Mean |Spearman rho| for ESM-2