Configuration

ModernGENA large (FA2 + autocast bf16) 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

FlashAttention 2 with bf16 autocast

1 evaluation · 12 results

Overview

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Evaluations and results

1 evaluation · 12 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 1024 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 1024 tokens)	Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 2048 tokens)	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 4096 tokens)	Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 512 tokens)	Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 8192 tokens)	Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 1024 tokens)	Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 2048 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 4096 tokens)	Maximum batch size (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 8192 tokens)
ModernGENA large (FA2 + autocast bf16) on one A100 80 GB (Aspidova et al. 2026)Evaluation	212	203	224	186	218	154	673	332	2721	161	1356	67

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	673 Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 1024 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 1024, column 'bs'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	212 Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 1024 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 1024, column 'tokens/s'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	332 Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 2048 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 2048, column 'bs'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	203 Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 2048 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 2048, column 'tokens/s'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	2720 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 256, column 'bs'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	224 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 256, column 'tokens/s'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	161 Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 4096 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 4096, column 'bs'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	186 Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 4096 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 4096, column 'tokens/s'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	1360 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 512, column 'bs'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	218 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 512, column 'tokens/s'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	67 Maximum batch size (Encoder forward pass on one A100 80 GB; sequence length 8192 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 8192, column 'bs'
Configuration: ModernGENA large (FA2 + autocast bf16) 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)	154 Inference throughput (Encoder forward pass on one A100 80 GB; sequence length 8192 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 ModernGENA large (FA2 + autocast bf16) (377M) 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 'ModernGENA large (FA2 + autocast bf16) (377M)', sequence length L = 8192, column 'tokens/s'

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Stable ID: model-execution-20261011-config-aspidova2026-moderngena-large-fa2-bf16

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: ModernGENA large (FA2 + autocast bf16) (377M)
foundation model eligible: true
parameters: 377M parameters
version: ModernGENA large
hardware: description: One NVIDIA A100 80 GB GPU (Section 3.4)
protocol: FlashAttention 2 with bf16 autocast
access reuse: Public pretrained checkpoint
source locator: Appendix B Table 2 row 'ModernGENA large (FA2 + autocast bf16) (377M)'

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configuration of: ModernGENA
system: ModernGENA large (FA2 + autocast bf16) (377M) inference throughput on one A100 (Aspidova et al. 2026)

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