GenomeOcean-500M, BF16, PyTorch embedding extraction (Yu et al. 2026)
Protocol A baseline: BF16 weights, single causal forward pass, mean-pooled final-layer hidden states.
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Evaluations and results
1 evaluation · 3 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) |
|---|---|---|---|
| GenomeOcean-500M, BF16, PyTorch embedding extraction (Yu et al. 2026)Evaluation | 0.3345 ± 0.0479 | 230,523 ± 651 | 47.2 |
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Sources and history
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
Technical metadata and extraction receipts
Stable ID: model-execution-20261011-config-yu2026-genomeocean-500m-bf16-embedding
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- 500M BF16
- foundation model eligible
- true
- version
- GenomeOcean-500M
- parameters
- 500M parameters
- access reuse
- Checkpoint release not stated in this source; benchmarking code at https://github.com/jgi-genomeocean/genomeocean_efficiency (not pinned)
- hardware
- description: One NVIDIA H100 SXM5 GPU, 80 GB HBM3 (Section 2.2)
- protocol
- Protocol A baseline: BF16 weights, single causal forward pass, mean-pooled final-layer hidden states.
- source locator
- Sections 2.1-2.4; Table 1; Table 2
Related records
- configuration of: GenomeOcean
- system: GenomeOcean-500M BF16 embedding extraction (Yu et al. 2026)