Published inference benchmark; transcribed, not reproduced.
1 evaluation · 4 results. Different protocols are not a single leaderboard.
Protocol: GenomeOcean embedding extraction throughput, peak VRAM and binning fidelity, BF16 versus FP8 weights (Yu et al. 2026 Table 3) · Dataset: GTDB genome fragments for metagenomic binning, 20 of a pre-sampled pool of 50 bacterial genomes per trial (Yu et al. 2026)
Sorted by Adjusted rand index (DBSCAN clustering of embeddings against GTDB species labels) (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 | Adjusted rand index (DBSCAN clustering of embeddings against GTDB species labels) | Inference throughput (Embedding extraction; input tokens per second) | Peak memory (Embedding extraction; peak GPU memory allocated) | Throughput change (Embedding extraction; relative to the BF16 baseline of the same model scale) |
|---|---|---|---|---|
| GenomeOcean-4B, FP8 (E4M3) static weights, PyTorch with FBGEMM (Yu et al. 2026)Evaluation | 0.5280 ± 0.0653 | 22,401 ± 204 | 67.9 | 4.7% |
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation None (pretrained checkpoint, post-training quantization only) Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: aggregation Mean and standard deviation over five trials Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: budget One NVIDIA H100 SXM5 80 GB GPU Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: dataset version Not reported Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: inputs Tokenized DNA sequence Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: metric implementation Not reported Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: population GTDB bacterial genomes Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: protocol id model-execution-20261011-protocol-yu2026-genomeocean-embedding-fp8 Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Comparison: split Five trials, seeds 42-46 Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
| Origin author_reported Context-only references | FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean Table 3 row '4B FP8 (E4M3)' Version: bioRxiv preprint version 1, posted 2026-08-14 (PDF footer); bioRxiv API date 2026-08-18 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: 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. |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: model-execution-20261011-eval-yu2026-genomeocean-4b-fp8-weights-embedding