Protocol

GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3)

GUANinE v1.1 task cadd-snv: Proxy deleteriousness of hg38 SNVs (CADD-style proxy labels; Nazaretyan et al. 2025).

Overview

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

23 recorded evaluations, 23 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

23 evaluations · 23 results. Different protocols are not a single leaderboard.

Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) · Dataset: GUANinE cadd-snv test set

Sorted by Spearman (GUANinE v1.1 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	Spearman (GUANinE v1.1 test set)
GPN-MSA (zero-shot, GUANinE v1.1)Evaluation	29.1 (best in column)
phyloP-30way (zero-shot, GUANinE v1.1)Evaluation	28.7
GPN-MSA (Position) (zero-shot, GUANinE v1.1)Evaluation	26.6
NTv2-500m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	26.5
NTv2-250m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	25.4
Evo2_1B_base (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	24.5
NTv2-100m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	23.9
PhyloGPN (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	23.6
phyloP-100way (zero-shot, GUANinE v1.1)Evaluation	23.3
NTv3-100m-pre (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	22.9
NTv3-100m-post (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	22.1
Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	21
Sei (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	19.9
CADD v1.7 (Position) (zero-shot, GUANinE v1.1)Evaluation	19.7
NTv3-8m-pre (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	19.5
CADD v1.7 (zero-shot, GUANinE v1.1)Evaluation	18.1
ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	17.3
Enformer (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	17.1
ChromBPNet-ATAC-F3 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	16.8
PhyloGPN (zero-shot, GUANinE v1.1)Evaluation	9.8
deltaSVM GM12878 DHS (zero-shot, GUANinE v1.1)Evaluation	7.61
GC-content (zero-shot, GUANinE v1.1)Evaluation	1.47
Naïve VEP 115 Conseq. (1% eval (evaluated with 1% of the training set), GUANinE v1.1)Evaluation	0.16

All 23 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: Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	21 Spearman (GUANinE v1.1 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 Borzoi on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'Borzoi', column 'cadd-snv' (ρ)
Configuration: CADD v1.7 (Position) (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	19.7 Spearman (GUANinE v1.1 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 CADD v1.7 (Position) on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'CADD v1.7 (Position)', column 'cadd-snv' (ρ)
Configuration: CADD v1.7 (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	18.1 Spearman (GUANinE v1.1 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 CADD v1.7 on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'CADD v1.7', column 'cadd-snv' (ρ)
Configuration: ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	17.3 Spearman (GUANinE v1.1 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 ChromBPNet-ATAC-F0 on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'ChromBPNet-ATAC-F0', column 'cadd-snv' (ρ)
Configuration: ChromBPNet-ATAC-F3 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	16.8 Spearman (GUANinE v1.1 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 ChromBPNet-ATAC-F3 on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'ChromBPNet-ATAC-F3', column 'cadd-snv' (ρ)
Configuration: deltaSVM GM12878 DHS (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	7.61 Spearman (GUANinE v1.1 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 deltaSVM GM12878 DHS on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'deltaSVM GM12878 DHS', column 'cadd-snv' (ρ)
Configuration: Enformer (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	17.1 Spearman (GUANinE v1.1 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 Enformer on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'Enformer', column 'cadd-snv' (ρ)
Configuration: Evo2_1B_base (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	24.5 Spearman (GUANinE v1.1 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_1B_base on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'Evo2_1B_base', column 'cadd-snv' (ρ)
Configuration: GC-content (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	1.47 Spearman (GUANinE v1.1 test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GC-content on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'GC-content', column 'cadd-snv' (ρ)
Configuration: GPN-MSA (Position) (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	26.6 Spearman (GUANinE v1.1 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 GPN-MSA (Position) on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'GPN-MSA (Position)', column 'cadd-snv' (ρ)
Configuration: GPN-MSA (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	29.1 Spearman (GUANinE v1.1 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 GPN-MSA on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'GPN-MSA', column 'cadd-snv' (ρ)
Configuration: Naïve VEP 115 Conseq. (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	0.16 Spearman (GUANinE v1.1 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 Naïve VEP 115 Conseq. on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'Naïve VEP 115 Conseq.', column 'cadd-snv' (ρ)
Configuration: NTv2-100m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	23.9 Spearman (GUANinE v1.1 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 NTv2-100m on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'NTv2-100m', column 'cadd-snv' (ρ)
Configuration: NTv2-250m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	25.4 Spearman (GUANinE v1.1 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 NTv2-250m on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'NTv2-250m', column 'cadd-snv' (ρ)
Configuration: NTv2-500m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	26.5 Spearman (GUANinE v1.1 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 NTv2-500m on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'NTv2-500m', column 'cadd-snv' (ρ)
Configuration: NTv3-100m-post (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	22.1 Spearman (GUANinE v1.1 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 NTv3-100m-post on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'NTv3-100m-post', column 'cadd-snv' (ρ)
Configuration: NTv3-100m-pre (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	22.9 Spearman (GUANinE v1.1 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 NTv3-100m-pre on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'NTv3-100m-pre', column 'cadd-snv' (ρ)
Configuration: NTv3-8m-pre (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	19.5 Spearman (GUANinE v1.1 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 NTv3-8m-pre on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'NTv3-8m-pre', column 'cadd-snv' (ρ)
Configuration: PhyloGPN (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	23.6 Spearman (GUANinE v1.1 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 PhyloGPN on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'PhyloGPN' with Eval. 'X', column 'cadd-snv' (ρ)
Configuration: PhyloGPN (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	9.8 Spearman (GUANinE v1.1 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 PhyloGPN on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'PhyloGPN' with Eval. 'blank', column 'cadd-snv' (ρ)
Configuration: phyloP-100way (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	23.3 Spearman (GUANinE v1.1 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 phyloP-100way on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'phyloP-100way', column 'cadd-snv' (ρ)
Configuration: phyloP-30way (zero-shot, GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	28.7 Spearman (GUANinE v1.1 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 phyloP-30way on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'phyloP-30way', column 'cadd-snv' (ρ)
Configuration: Sei (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	Protocol: GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3) Dataset: GUANinE cadd-snv test set	19.9 Spearman (GUANinE v1.1 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 Sei on GUANinE cadd-snv lit-genomics-20261011-guanine-protocol-cadd-snv Aggregation: Not reported GUANinE v1.1 reveals complementarity of supervised and genomic language models · Table 3, row 'Sei', column 'cadd-snv' (ρ)

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GUANinE v1.1 reveals complementarity of supervised and genomic language models · Original source · Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-guanine-protocol-cadd-snv

areas: dna-genomes
contexts: research
protocol: GUANinE v1.1 cadd-snv test set; score is the printed column 'ρ'
version: GUANinE v1.1
metric: spearman-correlation
metric direction: higher
unit: unitless
unit detail: Printed as Spearman rho multiplied by 100
limitations: The benchmark authors evaluated the models; GUANinE v1.1 is by the developers of hgT5 and the T5 baseline.; Previously reported performances are marked in blue in the published table; the colour is not in the XML artifact, so prior and new cells are not distinguished here.; Many rows are '1% eval': models were evaluated with 1% of the training set (Table 2 footnote).; ρ against a Boolean label is a rank correlation with a binary target; the source does not define it further; not comparable with AUROC or AUPRC on similar ClinVar tasks.
source locator: Table 3 column 'cadd-snv'

Related records

part of: GUANinE v1.1
uses data: GUANinE cadd-snv test set
assessment: Borzoi on GUANinE cadd-snv
assessment: CADD v1.7 (Position) on GUANinE cadd-snv
assessment: CADD v1.7 on GUANinE cadd-snv
assessment: ChromBPNet-ATAC-F0 on GUANinE cadd-snv
assessment: ChromBPNet-ATAC-F3 on GUANinE cadd-snv
assessment: deltaSVM GM12878 DHS on GUANinE cadd-snv
assessment: Enformer on GUANinE cadd-snv
assessment: Evo2_1B_base on GUANinE cadd-snv
assessment: GC-content on GUANinE cadd-snv
assessment: GPN-MSA (Position) on GUANinE cadd-snv
assessment: GPN-MSA on GUANinE cadd-snv
assessment: Naïve VEP 115 Conseq. on GUANinE cadd-snv
assessment: NTv2-100m on GUANinE cadd-snv
assessment: NTv2-250m on GUANinE cadd-snv
assessment: NTv2-500m on GUANinE cadd-snv
assessment: NTv3-100m-post on GUANinE cadd-snv
assessment: NTv3-100m-pre on GUANinE cadd-snv
assessment: NTv3-8m-pre on GUANinE cadd-snv
assessment: PhyloGPN on GUANinE cadd-snv
assessment: PhyloGPN on GUANinE cadd-snv
assessment: phyloP-100way on GUANinE cadd-snv
assessment: phyloP-30way on GUANinE cadd-snv
assessment: Sei on GUANinE cadd-snv

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