Configuration

Nucleotide Transformer 2.5B pretraining (HyenaDNA Table A.2)

Evidence concern: excluded from comparisons

Table A.2 GPU-hours for the DNABERT and Nucleotide Transformer columns do not equal the GPUs × wall clock printed in the same table: 8 GPUs × 25 days is 4,800 GPU-hours against 12,000 printed, and 128 GPUs × 28 days is 86,016 GPU-hours against 215,000 printed, both about 2.5 times higher. The HyenaDNA columns agree (1 GPU × 80 min, about 1.3 GPU-hours). The Nucleotide Transformer article (Methods 'Hardware') also gives 128 A100 GPUs for 28 days. The table cites no source for these columns. Values are kept as printed and should not be compared until the discrepancy is resolved.HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution, arXiv v2 · Table A.2 (page 17), rows 'GPUs', 'Wall clock' and 'GPU-hrs', columns 'DNABERT' and 'Nucleotide Transformer'

Nucleotide Transformer with 2.5B parameters, in its pretraining run.

1 evaluation · 2 results

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1 evaluation · 2 results. Different protocols are not a single leaderboard.

Protocol: Pretraining GPUs and runtime for short-range models (HyenaDNA Table A.2) · Dataset: Pretraining corpora of the models in HyenaDNA Table A.2

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Tested configuration	Accelerator time (Pretraining, total)	Runtime (Pretraining, wall clock)
Nucleotide Transformer 2.5B pretraining (HyenaDNA Table A.2)Evaluation	215,000	28

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Nucleotide Transformer 2.5B pretraining (HyenaDNA Table A.2)	Protocol: Pretraining GPUs and runtime for short-range models (HyenaDNA Table A.2) Dataset: Pretraining corpora of the models in HyenaDNA Table A.2	215,000 Accelerator time (Pretraining, total) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Evidence concern: excluded from comparisons Table A.2 GPU-hours for the DNABERT and Nucleotide Transformer columns do not equal the GPUs × wall clock printed in the same table: 8 GPUs × 25 days is 4,800 GPU-hours against 12,000 printed, and 128 GPUs × 28 days is 86,016 GPU-hours against 215,000 printed, both about 2.5 times higher. The HyenaDNA columns agree (1 GPU × 80 min, about 1.3 GPU-hours). The Nucleotide Transformer article (Methods 'Hardware') also gives 128 A100 GPUs for 28 days. The table cites no source for these columns. Values are kept as printed and should not be compared until the discrepancy is resolved.HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution, arXiv v2 · Table A.2 (page 17), rows 'GPUs', 'Wall clock' and 'GPU-hrs', columns 'DNABERT' and 'Nucleotide Transformer' Methods, coverage and source Nucleotide Transformer 2.5B pretraining compute (HyenaDNA Table A.2) gfm-guide-20261014-protocol-hyenadna-pretraining-compute Aggregation: Not reported HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution, arXiv v2 · Table A.2 (page 17), row 'GPU-hrs', column 2 of 4 ('Nucleotide Transformer', 2.5B)
Configuration: Nucleotide Transformer 2.5B pretraining (HyenaDNA Table A.2)	Protocol: Pretraining GPUs and runtime for short-range models (HyenaDNA Table A.2) Dataset: Pretraining corpora of the models in HyenaDNA Table A.2	28 Runtime (Pretraining, wall clock) day · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Evidence concern: excluded from comparisons Table A.2 GPU-hours for the DNABERT and Nucleotide Transformer columns do not equal the GPUs × wall clock printed in the same table: 8 GPUs × 25 days is 4,800 GPU-hours against 12,000 printed, and 128 GPUs × 28 days is 86,016 GPU-hours against 215,000 printed, both about 2.5 times higher. The HyenaDNA columns agree (1 GPU × 80 min, about 1.3 GPU-hours). The Nucleotide Transformer article (Methods 'Hardware') also gives 128 A100 GPUs for 28 days. The table cites no source for these columns. Values are kept as printed and should not be compared until the discrepancy is resolved.HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution, arXiv v2 · Table A.2 (page 17), rows 'GPUs', 'Wall clock' and 'GPU-hrs', columns 'DNABERT' and 'Nucleotide Transformer' Methods, coverage and source Nucleotide Transformer 2.5B pretraining compute (HyenaDNA Table A.2) gfm-guide-20261014-protocol-hyenadna-pretraining-compute Aggregation: Not reported HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution, arXiv v2 · Table A.2 (page 17), row 'Wall clock', column 2 of 4 ('Nucleotide Transformer', 2.5B)

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HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution, arXiv v2 · Original source · arXiv 2306.15794v2

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Stable ID: gfm-guide-20261014-config-hyenadna-table-a2-nt-2-5b-pretraining

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: Nucleotide Transformer (2.5B)
parameters: 2.5B
hardware: description: 128 × NVIDIA A100 80GB (printed '128-A100-80GB')
source locator: Table A.2 (page 17)
missing metadata: version: reason: unreported
provenance note: Pretraining run of Nucleotide Transformer 2.5B as listed in HyenaDNA Table A.2.

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configuration of: Nucleotide Transformer
system: Nucleotide Transformer 2.5B pretraining compute (HyenaDNA Table A.2)

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