Relevance of Nucleotide Transformer IA3 fine-tuning run time (Dalla-Torre et al. 2025 Methods 'Hardware') to "Select an execution workflow for large-scale diagnostic genomics"
- Use case
- Select an execution workflow for large-scale diagnostic genomics
- Assessed by
- Nucleotide Transformer IA3 fine-tuning run time (Dalla-Torre et al. 2025 Methods 'Hardware')
- Relevance
- Proxy evidence
- Endpoint
- Mean wall time of one IA3 fine-tuning run on one node of eight A100 GPUs, Nucleotide Transformer 500M- and 2.5B-parameter models
Proxy. Developer-reported time to adapt Nucleotide Transformer models of two sizes with parameter-efficient fine-tuning on a stated node, which informs the adaptation cost of a model before it enters a workflow. It is not a per-sample execution measurement, the runs and tasks averaged over are not stated, and the article's Discussion gives a conflicting figure.
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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations1 values
| Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group nt2025-ia3-finetune Context-only references | Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title Nucleotide Transformer IA3 fine-tuning time on one 8 × A100 node (Dalla-Torre et al. 2025) Context-only references | Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Mean wall time of one IA3 fine-tuning run on one node of eight A100 GPUs, Nucleotide Transformer 500M- and 2.5B-parameter models Context-only references | Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field links:assessed_by:gfm-guide-20261014-protocol-nt-ia3-finetune-runtime Context-only references | Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Headline metric runtime Context-only references | Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations4 values
| Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records7 values
| Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale Proxy. Developer-reported time to adapt Nucleotide Transformer models of two sizes with parameter-efficient fine-tuning on a stated node, which informs the adaptation cost of a model before it enters a workflow. It is not a per-sample execution measurement, the runs and tasks averaged over are not stated, and the article's Discussion gives a conflicting figure. Context-only references | Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3 Version: Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. 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
1 source record and release history
- Nucleotide Transformer: building and evaluating robust foundation models for human genomics (Nature Methods) · Original source · Nature Methods 22, 287-297 (published online 2024-11-28); PMC11810778 full-text XML
Technical metadata and extraction receipts
Stable ID: use-case-mapping-gfm-guide-20261014-nt-ia3-finetune
- field
- links:assessed_by:gfm-guide-20261014-protocol-nt-ia3-finetune-runtime
- value
- gfm-guide-20261014-protocol-nt-ia3-finetune-runtime
- relevance
- proxy
- endpoint
- Mean wall time of one IA3 fine-tuning run on one node of eight A100 GPUs, Nucleotide Transformer 500M- and 2.5B-parameter models
- rationale
- Proxy. Developer-reported time to adapt Nucleotide Transformer models of two sizes with parameter-efficient fine-tuning on a stated node, which informs the adaptation cost of a model before it enters a workflow. It is not a per-sample execution measurement, the runs and tasks averaged over are not stated, and the article's Discussion gives a conflicting figure.
- constraints
- Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources.; Cite the Methods figures together with the Discussion's 'under 15 min on a single GPU' (claim gfm-guide-20261014-claim-nt-fine-tuning-single-gpu); neither is preferred.
- limitations
- Developer-reported by the authors of the Nucleotide Transformer.; Average over an unstated number of runs, tasks and 500M-parameter models (the Methods say 'the 500M-parameter models'); no spread is printed.; Weights replicated on eight GPUs with one sample per GPU, so the node time does not show what one GPU would take.; The source carries an evidence concern on the conflict between Methods 'Hardware' and the Discussion, so this judgement stays withheld after review until that concern is resolved.
- revision
- 1
- reason
- Add relevance judgements for the execution and compute protocols of the genomic foundation model guide sources batch (data/omics/gfm-guide-sources-20261014, issue #162), independently reviewed in PR #169.
- citation locators
- source id: gfm-guide-20261014-source-nt-nature-methods; locator: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3
- source locator
- gfm-guide-20261014-source-nt-nature-methods: Methods 'Data preparation > Hardware', paragraph 1; Discussion, paragraph 3
- comparison group
- nt2025-ia3-finetune
- comparison title
- Nucleotide Transformer IA3 fine-tuning time on one 8 × A100 node (Dalla-Torre et al. 2025)
- headline metric
- runtime
- reviewed evaluations
- gfm-guide-20261014-eval-nt-2-5b-ia3-fine-tuning-runtime; gfm-guide-20261014-eval-nt-500m-ia3-fine-tuning-runtime
- review
- method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent review-169, independent of the agent that drafted these judgements for issue #162; no human review claimed; reviewed at: 2026-10-14T19:00:00Z; note: Independent relevance review: grade, endpoint, rationale, constraints, limitations and locators checked against the use case and the source text; every value of the listed evaluations checked against the source. No execution, reproduction, qualified human scientific review or clinical validation. See docs/reviews/use-cases/diagnostic-genomics-model-execution-judgements-2026-10-14.md. Stays withheld while the source carries its evidence concern.
- pins
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