Configuration

Evo2 (linear probing, GFMBench-API)

Configuration of Evo 2: 1B parameters; NVIDIA BioNeMo implementation; linear probing; frozen weights, linear classification head.

9 evaluations · 36 results

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Evaluations and results

9 evaluations · 36 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (test set) (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	Accuracy (test set)	AUPRC (test set)	AUROC (test set)	MCC (test set)
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API Var Bench Non Coding Pathogenicity, supervised, Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.898 (best in column)	0.415	0.659	0.204
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API GUE Promoter All, supervised, GUE Promoter All test set (GFMBench-API)	0.754	0.778 (best in column)	0.815 (best in column)	0.51 (best in column)
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect Causal eQTL, supervised, LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.615	0.641	0.662	0.23
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API Var Bench Expression, supervised, Var Bench Expression test set (GFMBench-API)	0.595	0.589	0.628	0.197
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API GUE Transcription Factor, supervised, GUE Transcription Factor test set (GFMBench-API)	0.585	0.602	0.63	0.176
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API Var Bench Coding Pathogenicity, supervised, Var Bench Coding Pathogenicity test set (GFMBench-API)	0.58	0.568	0.658	0.0941
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API GUE Splice Site, supervised, GUE Splice Site test set (GFMBench-API)	0.565	0.46	0.657	0.0384
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API Var Bench meQTL, supervised, Var Bench meQTL test set (GFMBench-API)	0.539	0.485	0.567	−0.0031
Evo2 (linear probing, GFMBench-API)Evaluation	GFMBench-API Var Bench Common Vs Rare, supervised, Var Bench Common Vs Rare test set (GFMBench-API)	0.515	0.518	0.524	0.039

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.754 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Promoter All', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.778 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Promoter All', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.815 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Promoter All', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.51 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Promoter All', row 'Evo2', column 'MCC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.565 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Splice Site', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.46 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Splice Site', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.657 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Splice Site', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.0384 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Splice Site', row 'Evo2', column 'MCC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.585 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Transcription Factor', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.602 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Transcription Factor', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.63 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Transcription Factor', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.176 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'GUE Transcription Factor', row 'Evo2', column 'MCC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.615 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'LRB Variant Effect Causal eQTL', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.641 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'LRB Variant Effect Causal eQTL', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.662 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'LRB Variant Effect Causal eQTL', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.23 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'LRB Variant Effect Causal eQTL', row 'Evo2', column 'MCC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.58 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.568 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.658 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.0941 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'MCC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.515 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Common Vs Rare', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.518 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Common Vs Rare', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.524 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Common Vs Rare', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.039 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Common Vs Rare', row 'Evo2', column 'MCC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API)	0.595 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Expression', row 'Evo2', column 'Accuracy'

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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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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-gfmbench-config-evo2-linear-probing

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: Evo2
foundation model eligible: true
parameters: 1B parameters; NVIDIA BioNeMo implementation; linear probing; frozen weights, linear classification head
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: Evo2 as evaluated in GFMBench-API, linear probing.

Related records

configuration of: Evo 2
system: Evo2 on GFMBench-API GUE Promoter All (supervised)
system: Evo2 on GFMBench-API GUE Splice Site (supervised)
system: Evo2 on GFMBench-API GUE Transcription Factor (supervised)
system: Evo2 on GFMBench-API LRB Variant Effect Causal eQTL (supervised)
system: Evo2 on GFMBench-API Var Bench Coding Pathogenicity (supervised)
system: Evo2 on GFMBench-API Var Bench Common Vs Rare (supervised)
system: Evo2 on GFMBench-API Var Bench Expression (supervised)
system: Evo2 on GFMBench-API Var Bench meQTL (supervised)
system: Evo2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)

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