Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12)
Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) · Peer-reviewed
What this source contributed
Records in this release that cite this source. A record can cite several sources.
Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Models, benchmarks and other records
Models (1)
Methods (1)
Configurations (23)
- BPNet (large), trained from scratch (NT benchmark)
- BPNet (original), trained from scratch (NT benchmark)
- BPNet (X-large), trained from scratch (NT benchmark)
- DNABERT-1, fine-tuning (NT benchmark)
- DNABERT-2, parameter-efficient fine-tuning (NT benchmark)
- Enformer, parameter-efficient fine-tuning (NT benchmark)
- HyenaDNA-1KB, parameter-efficient fine-tuning (NT benchmark)
- HyenaDNA-32KB, parameter-efficient fine-tuning (NT benchmark)
- NT 2.5B Randomly Initialized, trained from scratch (NT benchmark)
- NT 500M Randomly Initialized, trained from scratch (NT benchmark)
- NT-1000G (2.5B), parameter-efficient fine-tuning (NT benchmark)
- NT-1000G (2.5B), probing (NT benchmark)
- NT-1000G (500M), parameter-efficient fine-tuning (NT benchmark)
- NT-1000G (500M), probing (NT benchmark)
- NT-HumanRef (500M), parameter-efficient fine-tuning (NT benchmark)
- NT-HumanRef (500M), probing (NT benchmark)
- NT-Multispecies (2.5B), parameter-efficient fine-tuning (NT benchmark)
- NT-Multispecies (2.5B), probing (NT benchmark)
- NT-Multispecies-v2 (50M), parameter-efficient fine-tuning (NT benchmark)
- NT-Multispecies-v2 (100M), parameter-efficient fine-tuning (NT benchmark)
- NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)
- NT-Multispecies-v2 (500M), parameter-efficient fine-tuning (NT benchmark)
- Raw Probe, probing of raw sequence (NT benchmark)
Benchmarks (1)
Protocols (37)
- NT benchmark Enhancer types, fine-tuning (PEFT)
- NT benchmark Enhancer types, probing
- NT benchmark Enhancer, fine-tuning (PEFT)
- NT benchmark Enhancer, probing
- NT benchmark H2AFZ, fine-tuning (PEFT)
- NT benchmark H2AFZ, probing
- NT benchmark H3K4me1, fine-tuning (PEFT)
- NT benchmark H3K4me1, probing
- NT benchmark H3K4me2, fine-tuning (PEFT)
- NT benchmark H3K4me2, probing
- NT benchmark H3K4me3, fine-tuning (PEFT)
- NT benchmark H3K4me3, probing
- NT benchmark H3K9ac, fine-tuning (PEFT)
- NT benchmark H3K9ac, probing
- NT benchmark H3K9me3, fine-tuning (PEFT)
- NT benchmark H3K9me3, probing
- NT benchmark H3K27ac, fine-tuning (PEFT)
- NT benchmark H3K27ac, probing
- NT benchmark H3K27me3, fine-tuning (PEFT)
- NT benchmark H3K27me3, probing
- NT benchmark H3K36me3, fine-tuning (PEFT)
- NT benchmark H3K36me3, probing
- NT benchmark H4K20me1, fine-tuning (PEFT)
- NT benchmark H4K20me1, probing
- NT benchmark normalised summed performance (Supplementary Table 9)
Datasets (19)
- NT benchmark Enhancer
- NT benchmark Enhancer types
- NT benchmark H2AFZ
- NT benchmark H3K4me1
- NT benchmark H3K4me2
- NT benchmark H3K4me3
- NT benchmark H3K9ac
- NT benchmark H3K9me3
- NT benchmark H3K27ac
- NT benchmark H3K27me3
- NT benchmark H3K36me3
- NT benchmark H4K20me1
- NT benchmark Promoter all
- NT benchmark Promoter non-TATA
- NT benchmark Promoter TATA
- NT benchmark Splice acceptor
- NT benchmark Splice donor
- NT benchmark Splice site all
- NT benchmark, all 18 tasks
Evaluations (419)
- BPNet (large) (control) NT benchmark normalised summed performance
- BPNet (large) on NT benchmark Enhancer (probing)
- BPNet (large) on NT benchmark Enhancer types (probing)
- BPNet (large) on NT benchmark H2AFZ (probing)
- BPNet (large) on NT benchmark H3K4me1 (probing)
- BPNet (large) on NT benchmark H3K4me2 (probing)
- BPNet (large) on NT benchmark H3K4me3 (probing)
- BPNet (large) on NT benchmark H3K9ac (probing)
- BPNet (large) on NT benchmark H3K9me3 (probing)
- BPNet (large) on NT benchmark H3K27ac (probing)
- BPNet (large) on NT benchmark H3K27me3 (probing)
- BPNet (large) on NT benchmark H3K36me3 (probing)
- BPNet (large) on NT benchmark H4K20me1 (probing)
- BPNet (large) on NT benchmark Promoter all (probing)
- BPNet (large) on NT benchmark Promoter non-TATA (probing)
- BPNet (large) on NT benchmark Promoter TATA (probing)
- BPNet (large) on NT benchmark Splice acceptor (probing)
- BPNet (large) on NT benchmark Splice donor (probing)
- BPNet (large) on NT benchmark Splice site all (probing)
- BPNet (original) (control) NT benchmark normalised summed performance
- BPNet (original) on NT benchmark Enhancer (probing)
- BPNet (original) on NT benchmark Enhancer types (probing)
- BPNet (original) on NT benchmark H2AFZ (probing)
- BPNet (original) on NT benchmark H3K4me1 (probing)
- BPNet (original) on NT benchmark H3K4me2 (probing)
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
23 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 ef0f357a1289aad1910059d455579e242a9a82ab3e32ec38d8ea2584effc436e Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-024-02523-z/MediaObjects/41592_2024_2523_MOESM1_ESM.pdf Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1038/s41592-024-02523-z Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Licence CC-BY-NC-ND-4.0 Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations3 values
| Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Media type application/pdf Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-10-11T01:37:37Z Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Review: date 2026-10-11 Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Review: method note Artifact re-retrieved or unpacked and SHA-256 matched. Source metadata | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) No field-specific location recorded Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Primary source retrieved and hashed for the 2026-10-11 genomics literature pass.
Technical metadata and extraction receipts
Stable ID: lit-genomics-20261011-ntbench-source-dallatorre2025-si
- areas
- dna-genomes
- contexts
- research
- url
- https://doi.org/10.1038/s41592-024-02523-z
- artifact url
- https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-024-02523-z/MediaObjects/41592_2024_2523_MOESM1_ESM.pdf
- version
- Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages)
- retrieved at
- 2026-10-11T01:37:37Z
- artifact sha256
- ef0f357a1289aad1910059d455579e242a9a82ab3e32ec38d8ea2584effc436e
- doi
- 10.1038/s41592-024-02523-z
- publication status
- peer_reviewed
- licence
- CC-BY-NC-ND-4.0
- media type
- application/pdf
- limitations
- Developer paper: the authors are InstaDeep and NVIDIA employees and developed the Nucleotide Transformer models (Competing interests). NT rows are author_reported.; Main-text Figure 2 and Extended Data are not read; the supplementary tables print the same per-task medians with standard deviations.; Supplementary Table 9 lists a DNABERT-1 fine-tuning average that has no per-task row in Supplementary Table 7.
- review
- method: source-hash-verification; method note: Artifact re-retrieved or unpacked and SHA-256 matched.; reviewer: claude; reviewer note: Claude review agent reviewer-gen-2, independent of the extractor lit-genomics; no human review claimed; date: 2026-10-11