Configuration
Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)
Nucleotide Transformer 2.5B multi-species scoring a variant as the L2 distance between reference and alternative CLS-token embeddings of 6,000 bp sequences.
14 evaluations · 14 results2 open disagreements between studies involve its model
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
14 evaluations · 14 results. Different protocols are not a single leaderboard.
Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)
Sorted by AUROC (ClinVar pathogenic vs benign SNVs, 3' UTR) (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 | AUROC (ClinVar pathogenic vs benign SNVs, 3' UTR) | AUROC (ClinVar pathogenic vs benign SNVs, 5' UTR) | AUROC (ClinVar pathogenic vs benign SNVs, All variants) | AUROC (ClinVar pathogenic vs benign SNVs, Intron (Non-splice)) | AUROC (ClinVar pathogenic vs benign SNVs, Missense & 3'UTR) | AUROC (ClinVar pathogenic vs benign SNVs, Missense & Intron (Non-splice)) | AUROC (ClinVar pathogenic vs benign SNVs, Missense) | AUROC (ClinVar pathogenic vs benign SNVs, Noncoding) | AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) | AUROC (ClinVar pathogenic vs benign SNVs, Splice) | AUROC (ClinVar pathogenic vs benign SNVs, Start loss) | AUROC (ClinVar pathogenic vs benign SNVs, Stop gain) | AUROC (ClinVar pathogenic vs benign SNVs, Stop loss) | AUROC (ClinVar pathogenic vs benign SNVs, Synonymous) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: 3' UTR (Figure 1) | 0.564 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: All variants (Figure 1) | Not reported | Not reported | 0.793 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Intron (Non-splice) (Figure 1) | Not reported | Not reported | Not reported | 0.75 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Missense & Intron (Non-splice) (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | 0.664 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Missense & 3'UTR (Figure 1) | Not reported | Not reported | Not reported | Not reported | 0.546 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Missense (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.594 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Noncoding (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.851 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: RNA gene (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.371 | Not reported | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Splice (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.617 | Not reported | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Start loss (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.569 | Not reported | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Stop gain (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.618 | Not reported | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Stop loss (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.609 | Not reported |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Synonymous (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.77 |
| Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: 5' UTR (Figure 1) | Not reported | 0.567 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
All 14 result rows with coverage, uncertainty and sources
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How it works, versions and access
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Evidence
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Evidence table
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Original source · bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages)
Technical metadata and extraction receipts
Stable ID: lu-hetero-20261019-config-nt-2-5b-multispecies-l2
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- foundation_model
- reported name
- Nucleotide Transformer
- parameters
- InstaDeepAI/nucleotide-transformer-2.5b-multi-species; 6,000 bp context; last hidden layer CLS embeddings; L2 distance.
- source locator
- Methods 'Nucleotide Transformer' (page 14)
Related records
- configuration of: Nucleotide Transformer
- system: Nucleotide Transformer on ClinVar All variants SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Intron (Non-splice) SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Missense & Intron (Non-splice) SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Missense & 3'UTR SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Missense SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Noncoding SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Splice SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Start loss SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Stop gain SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Stop loss SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar Synonymous SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar 3' UTR SNVs (Lu et al. 2025 Figure 1)
- system: Nucleotide Transformer on ClinVar 5' UTR SNVs (Lu et al. 2025 Figure 1)