Configuration

NTv3 (zero-shot, GFMBench-API)

NTv3, a configuration of Nucleotide Transformer v3: Nucleotide Transformer v3, about 8M parameters; Hugging Face checkpoint; zero-shot.

18 evaluations · 72 results

Overview

An explanatory profile has not yet been reviewed for this record.

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

Evaluations and results

18 evaluations · 72 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) (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	Protocol and dataset	AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings)	AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings)	AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings)	AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings)	AUPRC (zero-shot; cosine similarity of embeddings at the SNV position)	AUPRC (zero-shot; masked log-likelihood ratio)	AUROC (zero-shot; cosine similarity of embeddings at the SNV position)	AUROC (zero-shot; masked log-likelihood ratio)
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API ClinVar Indel Pathogenicity, zs-embedding, ClinVar Indel Pathogenicity test set (GFMBench-API)	0.944 (best in column)	0.946 (best in column)	0.642	0.647	Not reported	Not reported	Not reported	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Songlab ClinVar, zs-embedding, Songlab ClinVar test set (GFMBench-API)	0.552	0.559	0.508	0.516	0.593 (best in column)	Not reported	0.555	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API VEP-eval, zs-embedding, VEP-eval test set (GFMBench-API)	0.472	0.479	0.684	0.691	0.383	Not reported	0.585	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API BRCA1, zs-embedding, BRCA1 test set (GFMBench-API)	0.246	0.25	0.557	0.562	0.303	Not reported	0.624	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Disease, zs-embedding, Bend Variant Effects Disease test set (GFMBench-API)	0.147	0.152	0.713 (best in column)	0.72 (best in column)	0.275	Not reported	0.768 (best in column)	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Complex, zs-embedding, TraitGym Complex test set (GFMBench-API)	0.103	0.106	0.507	0.518	0.102	Not reported	0.5	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Mendelian, zs-embedding, TraitGym Mendelian test set (GFMBench-API)	0.103	0.107	0.537	0.553	0.0933	Not reported	0.481	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API LOL-EVE, zs-embedding, LOL-EVE test set (GFMBench-API)	0.0867	0.0903	0.495	0.503	Not reported	Not reported	Not reported	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Expression, zs-embedding, Bend Variant Effects Expression test set (GFMBench-API)	0.0789	0.0818	0.514	0.532	0.064	Not reported	0.447	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect OMIM, zs-embedding, LRB Variant Effect OMIM test set (GFMBench-API)	0.0018	0.0019	0.48	0.5	0.0018	Not reported	0.474	Not reported
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Disease, zs-mlm-llr, Bend Variant Effects Disease test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.158	Not reported	0.665
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Expression, zs-mlm-llr, Bend Variant Effects Expression test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0682	Not reported	0.487
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API BRCA1, zs-mlm-llr, BRCA1 test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.221	Not reported	0.493
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect OMIM, zs-mlm-llr, LRB Variant Effect OMIM test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0017	Not reported	0.463
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Songlab ClinVar, zs-mlm-llr, Songlab ClinVar test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.583 (best in column)	Not reported	0.55
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Complex, zs-mlm-llr, TraitGym Complex test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0941	Not reported	0.49
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Mendelian, zs-mlm-llr, TraitGym Mendelian test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0957	Not reported	0.509
NTv3 (zero-shot, GFMBench-API)Evaluation	GFMBench-API VEP-eval, zs-mlm-llr, VEP-eval test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.573	Not reported	0.712 (best in column)

All 72 result rows with coverage, uncertainty and sources

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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: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.147 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'NTv3', column 'Cos AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.713 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'NTv3', column 'Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.152 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'NTv3', column 'L2 AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.72 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'NTv3', column 'L2 AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.275 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'NTv3', column 'SNV Cos AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.768 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'NTv3', column 'SNV Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-mlm-llr Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.158 AUPRC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Disease', row 'NTv3', column 'Msk LLR PRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-mlm-llr Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.665 AUROC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Disease (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Disease', row 'NTv3', column 'Msk LLR ROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0789 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'NTv3', column 'Cos AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.514 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'NTv3', column 'Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0818 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'NTv3', column 'L2 AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.532 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'NTv3', column 'L2 AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.064 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'NTv3', column 'SNV Cos AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.447 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'NTv3', column 'SNV Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-mlm-llr Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0682 AUPRC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Expression', row 'NTv3', column 'Msk LLR PRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-mlm-llr Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.487 AUROC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API Bend Variant Effects Expression (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Expression', row 'NTv3', column 'Msk LLR ROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.246 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'NTv3', column 'Cos AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.557 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'NTv3', column 'Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.25 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'NTv3', column 'L2 AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.562 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'NTv3', column 'L2 AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.303 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'NTv3', column 'SNV Cos AUPRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.624 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'NTv3', column 'SNV Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.221 AUPRC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'NTv3', column 'Msk LLR PRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.493 AUROC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'NTv3', column 'Msk LLR ROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API ClinVar Indel Pathogenicity, zs-embedding Dataset: ClinVar Indel Pathogenicity test set (GFMBench-API)	0.944 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API ClinVar Indel Pathogenicity (zs-embedding) lit-genomics-20261011-gfmbench-protocol-clinvar-indel-pathogenicity-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'ClinVar Indel Pathogenicity', row 'NTv3', column 'Cos AUPRC'

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GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Original source · bioRxiv preprint version 2, posted 2026-08-11

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Stable ID: lit-genomics-20261011-gfmbench-config-ntv3-zero-shot

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: NTv3
foundation model eligible: true
parameters: Nucleotide Transformer v3, about 8M parameters; Hugging Face checkpoint; zero-shot
access reuse: Public checkpoint (Hugging Face; Evo2 via NVIDIA BioNeMo)
source locator: Benchmark Results sections A and B
missing metadata: version: reason: unreported; note: Checkpoint revision not printed; parameter count only
provenance note: NTv3 as evaluated in GFMBench-API, zero-shot.

Related records

configuration of: Nucleotide Transformer v3
system: NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding)
system: NTv3 on GFMBench-API Bend Variant Effects Disease (zs-mlm-llr)
system: NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding)
system: NTv3 on GFMBench-API Bend Variant Effects Expression (zs-mlm-llr)
system: NTv3 on GFMBench-API BRCA1 (zs-embedding)
system: NTv3 on GFMBench-API BRCA1 (zs-mlm-llr)
system: NTv3 on GFMBench-API ClinVar Indel Pathogenicity (zs-embedding)
system: NTv3 on GFMBench-API LOL-EVE (zs-embedding)
system: NTv3 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
system: NTv3 on GFMBench-API LRB Variant Effect OMIM (zs-mlm-llr)
system: NTv3 on GFMBench-API Songlab ClinVar (zs-embedding)
system: NTv3 on GFMBench-API Songlab ClinVar (zs-mlm-llr)
system: NTv3 on GFMBench-API TraitGym Complex (zs-embedding)
system: NTv3 on GFMBench-API TraitGym Complex (zs-mlm-llr)
system: NTv3 on GFMBench-API TraitGym Mendelian (zs-embedding)
system: NTv3 on GFMBench-API TraitGym Mendelian (zs-mlm-llr)
system: NTv3 on GFMBench-API VEP-eval (zs-embedding)
system: NTv3 on GFMBench-API VEP-eval (zs-mlm-llr)

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