Configuration

GENA base on one A100 80 GB (Aspidova et al. 2026)

Evidence concern: excluded from comparisons

Appendix B Table 2 and Figure 1 (axis 'Inference speed (tokens/s)') give throughput in tokens/s, but the printed values are inconsistent with the printed batch sizes: ModernGENA base (FA2 + autocast bf16) at L = 256 prints 552.44 tokens/s with a batch of 3,631 sequences (929,536 tokens), about 28 minutes per batch, and ModernGENA base without FA2 at L = 8192 prints 71.15 tokens/s with a batch of 92 (753,664 tokens), about 2.9 hours per batch, against a stated pretraining throughput of 1.33M tokens/s on eight A100 GPUs (Section 3.2.4). The unit or scale of the throughput column is unclear. Batch sizes share the table. Values are recorded as printed.Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9); Figure 1 (page 4); Section 3.2.4

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1 evaluation · 4 results

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1 evaluation · 4 results. Different protocols are not a single leaderboard.

Protocol: DNA language model inference throughput and maximum batch size on one A100 80 GB by sequence length (Aspidova et al. 2026 Table 2) · Dataset: Fixed-length token sequences of 256 to 8,192 tokens (Aspidova et al. 2026)

Sorted by Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 256 tokens) (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	Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 256 tokens)	Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 512 tokens)	Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 256 tokens)	Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 512 tokens)
GENA base on one A100 80 GB (Aspidova et al. 2026)Evaluation	91.8	82	6637	2206

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GENA base on one A100 80 GB (Aspidova et al. 2026)	Protocol: DNA language model inference throughput and maximum batch size on one A100 80 GB by sequence length (Aspidova et al. 2026 Table 2) Dataset: Fixed-length token sequences of 256 to 8,192 tokens (Aspidova et al. 2026)	6640 Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 256 tokens) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Appendix B Table 2 and Figure 1 (axis 'Inference speed (tokens/s)') give throughput in tokens/s, but the printed values are inconsistent with the printed batch sizes: ModernGENA base (FA2 + autocast bf16) at L = 256 prints 552.44 tokens/s with a batch of 3,631 sequences (929,536 tokens), about 28 minutes per batch, and ModernGENA base without FA2 at L = 8192 prints 71.15 tokens/s with a batch of 92 (753,664 tokens), about 2.9 hours per batch, against a stated pretraining throughput of 1.33M tokens/s on eight A100 GPUs (Section 3.2.4). The unit or scale of the throughput column is unclear. Batch sizes share the table. Values are recorded as printed.Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9); Figure 1 (page 4); Section 3.2.4 Methods, coverage and source GENA base (110M) inference throughput on one A100 (Aspidova et al. 2026) model-execution-20261011-protocol-aspidova2026-a100-inference-throughput Aggregation: Not reported Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9), row 'GENA base (110M)', sequence length L = 256, column 'bs'
Configuration: GENA base on one A100 80 GB (Aspidova et al. 2026)	Protocol: DNA language model inference throughput and maximum batch size on one A100 80 GB by sequence length (Aspidova et al. 2026 Table 2) Dataset: Fixed-length token sequences of 256 to 8,192 tokens (Aspidova et al. 2026)	91.8 Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 256 tokens) sample-per-second · higher Uncertainty: Not reported by the source: Mean of 10 timing runs; spread not printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Appendix B Table 2 and Figure 1 (axis 'Inference speed (tokens/s)') give throughput in tokens/s, but the printed values are inconsistent with the printed batch sizes: ModernGENA base (FA2 + autocast bf16) at L = 256 prints 552.44 tokens/s with a batch of 3,631 sequences (929,536 tokens), about 28 minutes per batch, and ModernGENA base without FA2 at L = 8192 prints 71.15 tokens/s with a batch of 92 (753,664 tokens), about 2.9 hours per batch, against a stated pretraining throughput of 1.33M tokens/s on eight A100 GPUs (Section 3.2.4). The unit or scale of the throughput column is unclear. Batch sizes share the table. Values are recorded as printed.Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9); Figure 1 (page 4); Section 3.2.4 Methods, coverage and source GENA base (110M) inference throughput on one A100 (Aspidova et al. 2026) model-execution-20261011-protocol-aspidova2026-a100-inference-throughput Aggregation: Not reported Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9), row 'GENA base (110M)', sequence length L = 256, column 'tokens/s'
Configuration: GENA base on one A100 80 GB (Aspidova et al. 2026)	Protocol: DNA language model inference throughput and maximum batch size on one A100 80 GB by sequence length (Aspidova et al. 2026 Table 2) Dataset: Fixed-length token sequences of 256 to 8,192 tokens (Aspidova et al. 2026)	2210 Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 512 tokens) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Appendix B Table 2 and Figure 1 (axis 'Inference speed (tokens/s)') give throughput in tokens/s, but the printed values are inconsistent with the printed batch sizes: ModernGENA base (FA2 + autocast bf16) at L = 256 prints 552.44 tokens/s with a batch of 3,631 sequences (929,536 tokens), about 28 minutes per batch, and ModernGENA base without FA2 at L = 8192 prints 71.15 tokens/s with a batch of 92 (753,664 tokens), about 2.9 hours per batch, against a stated pretraining throughput of 1.33M tokens/s on eight A100 GPUs (Section 3.2.4). The unit or scale of the throughput column is unclear. Batch sizes share the table. Values are recorded as printed.Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9); Figure 1 (page 4); Section 3.2.4 Methods, coverage and source GENA base (110M) inference throughput on one A100 (Aspidova et al. 2026) model-execution-20261011-protocol-aspidova2026-a100-inference-throughput Aggregation: Not reported Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9), row 'GENA base (110M)', sequence length L = 512, column 'bs'
Configuration: GENA base on one A100 80 GB (Aspidova et al. 2026)	Protocol: DNA language model inference throughput and maximum batch size on one A100 80 GB by sequence length (Aspidova et al. 2026 Table 2) Dataset: Fixed-length token sequences of 256 to 8,192 tokens (Aspidova et al. 2026)	82 Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 512 tokens) sample-per-second · higher Uncertainty: Not reported by the source: Mean of 10 timing runs; spread not printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Appendix B Table 2 and Figure 1 (axis 'Inference speed (tokens/s)') give throughput in tokens/s, but the printed values are inconsistent with the printed batch sizes: ModernGENA base (FA2 + autocast bf16) at L = 256 prints 552.44 tokens/s with a batch of 3,631 sequences (929,536 tokens), about 28 minutes per batch, and ModernGENA base without FA2 at L = 8192 prints 71.15 tokens/s with a batch of 92 (753,664 tokens), about 2.9 hours per batch, against a stated pretraining throughput of 1.33M tokens/s on eight A100 GPUs (Section 3.2.4). The unit or scale of the throughput column is unclear. Batch sizes share the table. Values are recorded as printed.Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9); Figure 1 (page 4); Section 3.2.4 Methods, coverage and source GENA base (110M) inference throughput on one A100 (Aspidova et al. 2026) model-execution-20261011-protocol-aspidova2026-a100-inference-throughput Aggregation: Not reported Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Appendix B Table 2 (page 9), row 'GENA base (110M)', sequence length L = 512, column 'tokens/s'

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Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models · Original source · bioRxiv preprint version 1, posted 2026-04-23

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Stable ID: model-execution-20261011-config-aspidova2026-gena-base

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: GENA base (110M)
foundation model eligible: true
parameters: 110M parameters
version: GENA-LM base
hardware: description: One NVIDIA A100 80 GB GPU (Section 3.4)
protocol: As provided
access reuse: Pretrained checkpoint; access not stated in this source
source locator: Appendix B Table 2 row 'GENA base (110M)'

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configuration of: GENA-LM
system: GENA base (110M) inference throughput on one A100 (Aspidova et al. 2026)

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