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DNABERT-2 (pathogenic/common SNP classification)

DNABERT-2 (pathogenic/common SNP classification): Alternate-minus-reference frozen representation; Supervised random forest fitted separately for this task.

2 evaluations · 5 results

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Evaluations and results

2 evaluations · 5 results. Different protocols are not a single leaderboard.

Protocol: Feng pathogenic-versus-common SNP classification · Dataset: Feng pathogenic/common SNP short-window dataset

Sorted by AUROC (task: pathogenic vs common snp; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUROC (task: pathogenic vs common snp; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged)	AUROC (task: pathogenic vs common snp; outer test group 2 only (chromosomes 2, 5, 11, 14, 17, 20, 22, X), not averaged)	AUROC (task: pathogenic vs common snp; outer test group 3 only (chromosomes 1, 4, 7, 8, 10, 13, 15), not averaged)	AUROC (task: pathogenic vs common snp)	Cohen's d (task: pathogenic vs common snp)
DNABERT-2 (pathogenic/common SNP classification)Evaluation	0.547	0.532	0.535	Not reported	Not reported
DNABERT-2 (pathogenic/common SNP classification)Evaluation	Not reported	Not reported	Not reported	0.538	0.134

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DNABERT-2 (pathogenic/common SNP classification)	Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset	0.538 AUROC (task: pathogenic vs common snp) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, DNABERT-2 row, AUC column (deterministic XML extraction)
Configuration: DNABERT-2 (pathogenic/common SNP classification)	Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset	0.134 Cohen's d (task: pathogenic vs common snp) unitless · unknown Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, DNABERT-2 row, Cohen's d column (deterministic XML extraction). Signed effect size; the source does not state a universal desirable sign/direction, so direction is recorded as unknown rather than assumed higher-is-better.
Configuration: DNABERT-2 (pathogenic/common SNP classification)	Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset	0.547 AUROC (task: pathogenic vs common snp; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 Pathogenic variants vs common per-test-group evaluation Table 5 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'Pathogenic variants vs common', row 'DNABERT-2', column 'Test Group 1 AUC' (cell B5). Test group 1 is chromosomes 3, 6, 9, 12, 16, 18, 19, 21 (Methods, 'Variant effect quantification benchmark').
Configuration: DNABERT-2 (pathogenic/common SNP classification)	Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset	0.532 AUROC (task: pathogenic vs common snp; outer test group 2 only (chromosomes 2, 5, 11, 14, 17, 20, 22, X), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 Pathogenic variants vs common per-test-group evaluation Table 5 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'Pathogenic variants vs common', row 'DNABERT-2', column 'Test Group 2 AUC' (cell C5). Test group 2 is chromosomes 2, 5, 11, 14, 17, 20, 22, X (Methods, 'Variant effect quantification benchmark').
Configuration: DNABERT-2 (pathogenic/common SNP classification)	Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset	0.535 AUROC (task: pathogenic vs common snp; outer test group 3 only (chromosomes 1, 4, 7, 8, 10, 13, 15), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 Pathogenic variants vs common per-test-group evaluation Table 5 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'Pathogenic variants vs common', row 'DNABERT-2', column 'Test Group 3 AUC' (cell D5). Test group 3 is chromosomes 1, 4, 7, 8, 10, 13, 15 (Methods, 'Variant effect quantification benchmark').

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

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Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1

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Technical metadata and extraction receipts

Stable ID: amp-feng-20261007-config-variant-dnabert-2

method types: foundation_model
foundation model eligible: true
head: Supervised random forest fitted separately for this task
missing metadata: actual input bp: reason: unextracted; head revision: reason: unextracted; output aggregation bp: reason: unextracted; version: reason: unreported; note: Printed model name and input representation only; immutable checkpoint/head revision is unreported in the inspected primary text.
reported name: DNABERT-2
representation: Alternate-minus-reference frozen representation
task: pathogenic/common SNP classification
provenance note: DNABERT-2 (pathogenic/common SNP classification); Feng et al. 2025 source-reported, task-scoped configuration.

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