Evidence claim

Relevance of DNA language model inference throughput and maximum batch size on one A100 (Aspidova et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics"

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

Use case: Select an execution workflow for large-scale diagnostic genomics
Assessed by: DNA language model inference throughput and maximum batch size on one A100 80 GB by sequence length (Aspidova et al. 2026 Table 2)
Relevance: Proxy evidence
Endpoint: Maximum batch size and mean inference throughput by sequence length (256 to 8,192 tokens) for ModernGENA, GENA-LM, DNABERT-2 and NTv2 encoders on one A100 80 GB

Compares the inference throughput and memory-bound batch size of several genomic foundation models on the same stated GPU across input lengths, which bears on whether a team's hardware can run such a model at the needed throughput. Proxy: a timing benchmark of forward passes, not a diagnostic workflow, author-reported for two of the four families, and with a printed throughput unit that is inconsistent with its batch sizes (source evidence concern).

9 reviewed evaluations

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

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Citation locations 1 values source id model-execution-20261011-source-aspidova2026-moderngena locator Section 3.3-3.4; Appendix B Table 2 Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Comparison group aspidova2026-a100-inference Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Comparison title DNA language model inference throughput on one A100 (Aspidova et al. 2026) Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Constraints 3 values 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. Compare throughput only within this table; the printed scale is uncertain. Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.constraints` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Endpoint Maximum batch size and mean inference throughput by sequence length (256 to 8,192 tokens) for ModernGENA, GENA-LM, DNABERT-2 and NTv2 encoders on one A100 80 GB Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.endpoint` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Claimed field links:assessed_by:model-execution-20261011-protocol-aspidova2026-a100-inference-throughput Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Headline metric inference-throughput Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Limitations 6 values Author-reported: the authors develop ModernGENA and GENA-LM; DNABERT-2 and NTv2 were run by them. The printed tokens/s values are inconsistent with the printed batch sizes and the stated pretraining throughput (1.33M tokens/s on eight A100s, Section 3.2.4); the source carries an evidence concern, and values are kept as printed. Inputs are fixed-length sequences whose content is not described; throughput does not depend on biology, but the input source is not stated. Throughput is the mean of 10 timing runs; no spread is printed. Models tokenize differently (BPE, 6-mer), so the same token length covers different numbers of base pairs. GENA base and large print no values from 1,024 tokens upwards. Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.limitations` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
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attributes.clinical_scope attributes.intended_users sha256 1c2a12431556cc6581f5aab019cf91576d2393387b88a8a2bea35ea2a3ee4a70 Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.pins` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact
Rationale Compares the inference throughput and memory-bound batch size of several genomic foundation models on the same stated GPU across input lengths, which bears on whether a team's hardware can run such a model at the needed throughput. Proxy: a timing benchmark of forward passes, not a diagnostic workflow, author-reported for two of the four families, and with a printed throughput unit that is inconsistent with its batch sizes (source evidence concern). Context-only references	Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models Original source ↗ model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2 Version: bioRxiv preprint version 1, posted 2026-04-23 Retrieved: 2026-10-11T21:39:38Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.rationale` Source artifact SHA-256: `238ab9916d54b419bf31fd79ecf146d654eb6574d3b441aa2043d39632e709fa` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval; retrieved_at is the file's modification time. The pdftotext -layout text layer has SHA-256 ebaf0541c173359940737efde2c15d4ab4aa37d7cc323b3922a818feb5be6b4b. A second download at 21:43Z was refused with HTTP 429. Inspected artifact

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Release 2026-10-23-5347695500ed · Record review: source checked

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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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Technical metadata and extraction receipts

Stable ID: use-case-mapping-model-execution-20261011-aspidova2026-a100-inference-throughput

field: links:assessed_by:model-execution-20261011-protocol-aspidova2026-a100-inference-throughput
value: model-execution-20261011-protocol-aspidova2026-a100-inference-throughput
relevance: proxy
endpoint: Maximum batch size and mean inference throughput by sequence length (256 to 8,192 tokens) for ModernGENA, GENA-LM, DNABERT-2 and NTv2 encoders on one A100 80 GB
rationale: Compares the inference throughput and memory-bound batch size of several genomic foundation models on the same stated GPU across input lengths, which bears on whether a team's hardware can run such a model at the needed throughput. Proxy: a timing benchmark of forward passes, not a diagnostic workflow, author-reported for two of the four families, and with a printed throughput unit that is inconsistent with its batch sizes (source evidence concern).
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.; Compare throughput only within this table; the printed scale is uncertain.
limitations: Author-reported: the authors develop ModernGENA and GENA-LM; DNABERT-2 and NTv2 were run by them.; The printed tokens/s values are inconsistent with the printed batch sizes and the stated pretraining throughput (1.33M tokens/s on eight A100s, Section 3.2.4); the source carries an evidence concern, and values are kept as printed.; Inputs are fixed-length sequences whose content is not described; throughput does not depend on biology, but the input source is not stated.; Throughput is the mean of 10 timing runs; no spread is printed.; Models tokenize differently (BPE, 6-mer), so the same token length covers different numbers of base pairs.; GENA base and large print no values from 1,024 tokens upwards.
revision: 1
reason: Add primary-source execution evidence from the diagnostic genomics execution literature pass (2026-10-11).
citation locators: source id: model-execution-20261011-source-aspidova2026-moderngena; locator: Section 3.3-3.4; Appendix B Table 2
source locator: model-execution-20261011-source-aspidova2026-moderngena: Section 3.3-3.4; Appendix B Table 2
comparison group: aspidova2026-a100-inference
comparison title: DNA language model inference throughput on one A100 (Aspidova et al. 2026)
headline metric: inference-throughput
review: method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent uc-execution extracted and drafted; Claude (Opus 5.5) review agent reviewer-exec checked every value and this judgement against the pinned sources; reviewed at: 2026-10-12T07:50:32Z; note: Bounded primary-source transcription with independent cell check and relevance review. No execution, reproduction, qualified human scientific review or clinical validation.
reviewed evaluations: model-execution-20261011-eval-aspidova2026-dnabert-2; model-execution-20261011-eval-aspidova2026-gena-base; model-execution-20261011-eval-aspidova2026-gena-large; model-execution-20261011-eval-aspidova2026-moderngena-base; model-execution-20261011-eval-aspidova2026-moderngena-base-fa2-bf16; model-execution-20261011-eval-aspidova2026-moderngena-large; model-execution-20261011-eval-aspidova2026-moderngena-large-fa2-bf16; model-execution-20261011-eval-aspidova2026-ntv2-100m; model-execution-20261011-eval-aspidova2026-ntv2-250m
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