Evaluation

VEST4 on CGC missense, oncogenes (gain of function) (Lee 2026)

Published comparison of variant effect predictors; transcribed, not reproduced.

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Evaluation results

1 evaluation · 2 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: VEST4 rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.713 average-precision unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source VEST4 on CGC missense, oncogenes (gain of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-oncogene Aggregation: Not reported An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'VEST4', group 'oncogene', column 'AUPRC'
Configuration: VEST4 rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.84 auroc unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source VEST4 on CGC missense, oncogenes (gain of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-oncogene Aggregation: Not reported An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'VEST4', group 'oncogene', column 'AUROC'

Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.

Evaluation procedure

somatic-oncogenicity-20261009-protocol-lee2026-oncogene

Configuration: VEST4 rank score, dbNSFP 5.3.1a (Lee 2026)
Protocol: CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv)
Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: somatic-oncogenicity-20261009-protocol-lee2026-oncogene
dataset version: Not reported
split: Whole labelled set
population: 5365 variants, 1430 positive
inputs: dbNSFP rank score
adaptation: Not reported
metric implementation: scikit-learn roc_auc_score and average_precision_score on dbNSFP 5.3.1a rank scores; tools with fewer than 50 scored variants or one class are skipped (src/evaluation/part_b.py, b1_tool_performance, at commit 40b7770f)
aggregation: Pooled over variants
budget: Not reported

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

Reproduction

Split: Whole labelled set
Adaptation: Not reported
Scoring implementation: scikit-learn roc_auc_score and average_precision_score on dbNSFP 5.3.1a rank scores; tools with fewer than 50 scored variants or one class are skipped (src/evaluation/part_b.py, b1_tool_performance, at commit 40b7770f)

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Evidence

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Evidence table

Inspect claims, sources and review details

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40 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Not reported Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
attributes.comparison.adaptation Not reported Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Pooled over variants Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
attributes.comparison.aggregation Pooled over variants Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
attributes.comparison.budget Not reported Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version Not reported Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
attributes.comparison.dataset_version Not reported Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs dbNSFP rank score Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
attributes.comparison.inputs dbNSFP rank score Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ tool_performance.tsv row ('VEST4', 'oncogene') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

2 source records and release history

An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers · Original source · bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page
OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) · Original source · commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11)

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Technical metadata and extraction receipts

Stable ID: somatic-oncogenicity-20261009-eval-lee2026-vest4-oncogene

areas: dna-genomes
contexts: clinical_research
origin: independent_paper
protocol: somatic-oncogenicity-20261009-protocol-lee2026-oncogene
version: Primary source as retrieved 2026-10-09
comparison: protocol id: somatic-oncogenicity-20261009-protocol-lee2026-oncogene; dataset version: Not reported; split: Whole labelled set; population: 5365 variants, 1430 positive; inputs: dbNSFP rank score; adaptation: Not reported; metric implementation: scikit-learn roc_auc_score and average_precision_score on dbNSFP 5.3.1a rank scores; tools with fewer than 50 scored variants or one class are skipped (src/evaluation/part_b.py, b1_tool_performance, at commit 40b7770f); aggregation: Pooled over variants; budget: Not reported
source locator: tool_performance.tsv row ('VEST4', 'oncogene')
missing metadata: comparison.dataset version: reason: unreported
denominator: 5365
positive count: 1430

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