Evidence claim

Relevance of GenomeOcean embedding extraction throughput and peak VRAM, BF16 versus FP8 (Yu et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics"

Use case: Select an execution workflow for large-scale diagnostic genomics
Assessed by: GenomeOcean embedding extraction throughput, peak VRAM and binning fidelity, BF16 versus FP8 weights (Yu et al. 2026 Table 3)
Relevance: Proxy evidence
Endpoint: Embedding throughput (tokens per second, mean and SD over five trials), peak GPU memory and binning ARI for GenomeOcean-100M, -500M and -4B in BF16 and FP8 on one H100

Measures inference throughput and peak GPU memory of a genomic foundation model at three sizes and two precisions on stated hardware, with spread over five trials, which no previously linked source does. Proxy: microbial genomes rather than diagnostic human data, an embedding workload rather than a diagnostic pipeline, and author-reported by the model's developing institute.

6 reviewed evaluations

Evidence

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Evidence table

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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.

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20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Citation locations 1 values source id model-execution-20261011-source-yu2026-fp8-genomeocean locator Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Comparison group yu2026-genomeocean-fp8 Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Comparison title GenomeOcean inference on one H100, BF16 versus FP8 (Yu et al. 2026) Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Constraints 2 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. Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Endpoint Embedding throughput (tokens per second, mean and SD over five trials), peak GPU memory and binning ARI for GenomeOcean-100M, -500M and -4B in BF16 and FP8 on one H100 Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Claimed field links:assessed_by:model-execution-20261011-protocol-yu2026-genomeocean-embedding-fp8 Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Headline metric inference-throughput Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Limitations 5 values Author-reported: two authors are at the DOE Joint Genome Institute, which develops GenomeOcean; no competing-interest statement is printed. Microbial genomes and a metagenomic-binning fidelity check, not human diagnostic sequence; the paper says the fidelity metrics are benchmark-specific (Section 4.4). Throughput is measured at one fixed batch size per model scale, which is not printed. Peak VRAM is printed without spread; throughput and ARI are mean and standard deviation over five trials. One GPU type (H100 SXM5); the paper says results for other GPUs and engines need their own evaluation. Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
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Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact
Rationale Measures inference throughput and peak GPU memory of a genomic foundation model at three sizes and two precisions on stated hardware, with spread over five trials, which no previously linked source does. Proxy: microbial genomes rather than diagnostic human data, an embedding workload rather than a diagnostic pipeline, and author-reported by the model's developing institute. Context-only references	FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Original source ↗ model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `ca54817d1f1a308f09bd3022e56cf6f8b86a875b110da0a38fe31236e39ca076` Hash scope: bioRxiv stamps each PDF download, so artifact_sha256 describes one retrieval (a second download differed in 40 bytes). The pdftotext -layout text layer (poppler) of both downloads has SHA-256 bec6e695ce46c4ebd6692e01a1a93167e212dffbb97b6558f1da88b1eb453501. Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean · Original source · bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-model-execution-20261011-yu2026-genomeocean-embedding-fp8

field: links:assessed_by:model-execution-20261011-protocol-yu2026-genomeocean-embedding-fp8
value: model-execution-20261011-protocol-yu2026-genomeocean-embedding-fp8
relevance: proxy
endpoint: Embedding throughput (tokens per second, mean and SD over five trials), peak GPU memory and binning ARI for GenomeOcean-100M, -500M and -4B in BF16 and FP8 on one H100
rationale: Measures inference throughput and peak GPU memory of a genomic foundation model at three sizes and two precisions on stated hardware, with spread over five trials, which no previously linked source does. Proxy: microbial genomes rather than diagnostic human data, an embedding workload rather than a diagnostic pipeline, and author-reported by the model's developing institute.
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.
limitations: Author-reported: two authors are at the DOE Joint Genome Institute, which develops GenomeOcean; no competing-interest statement is printed.; Microbial genomes and a metagenomic-binning fidelity check, not human diagnostic sequence; the paper says the fidelity metrics are benchmark-specific (Section 4.4).; Throughput is measured at one fixed batch size per model scale, which is not printed.; Peak VRAM is printed without spread; throughput and ARI are mean and standard deviation over five trials.; One GPU type (H100 SXM5); the paper says results for other GPUs and engines need their own evaluation.
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-yu2026-fp8-genomeocean; locator: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions
source locator: model-execution-20261011-source-yu2026-fp8-genomeocean: Sections 2.2-2.7; Tables 3 and 4; Funding Statement and Author Contributions
comparison group: yu2026-genomeocean-fp8
comparison title: GenomeOcean inference on one H100, BF16 versus FP8 (Yu et al. 2026)
headline metric: inference-throughput
stratum label: Embedding extraction
stratum order: 1
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-yu2026-genomeocean-100m-bf16-embedding; model-execution-20261011-eval-yu2026-genomeocean-100m-fp8-weights-embedding; model-execution-20261011-eval-yu2026-genomeocean-4b-bf16-embedding; model-execution-20261011-eval-yu2026-genomeocean-4b-fp8-weights-embedding; model-execution-20261011-eval-yu2026-genomeocean-500m-bf16-embedding; model-execution-20261011-eval-yu2026-genomeocean-500m-fp8-weights-embedding
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