Protocol
Nucleotide Transformer benchmark under frozen-embedding probing (Datta et al. 2026 Table 1)
Lightweight probes trained on frozen sequence embeddings, with the backbone in inference mode and no parameter update.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
72 recorded evaluations, 72 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
72 evaluations · 72 results. Different protocols are not a single leaderboard.
Protocol: Nucleotide Transformer benchmark under frozen-embedding probing (Datta et al. 2026 Table 1) · Dataset: Nucleotide Transformer benchmark task data (Datta et al. 2026)
Sorted by F1 (NT benchmark Promoter All, frozen-embedding probe) (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 | F1 (NT benchmark Promoter All, frozen-embedding probe) | F1 (NT benchmark Promoter Non-TATA, frozen-embedding probe) | F1 (NT benchmark Promoter TATA, frozen-embedding probe) | F1 (NT benchmark Splice Acceptor, frozen-embedding probe) | F1 (NT benchmark Splice All, frozen-embedding probe) | F1 (NT benchmark Splice Donor, frozen-embedding probe) | MCC (NT benchmark Enhancer Types, frozen-embedding probe) | MCC (NT benchmark Enhancer, frozen-embedding probe) | MCC (NT benchmark H3, frozen-embedding probe) | MCC (NT benchmark H3K14ac, frozen-embedding probe) | MCC (NT benchmark H3K36me3, frozen-embedding probe) | MCC (NT benchmark H3K4me1, frozen-embedding probe) | MCC (NT benchmark H3K4me2, frozen-embedding probe) | MCC (NT benchmark H3K4me3, frozen-embedding probe) | MCC (NT benchmark H3K79me3, frozen-embedding probe) | MCC (NT benchmark H3K9ac, frozen-embedding probe) | MCC (NT benchmark H4, frozen-embedding probe) | MCC (NT benchmark H4ac, frozen-embedding probe) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | 0.963 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | 0.952 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | 0.933 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | 0.928 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.531 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.43 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.738 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.504 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.567 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.5 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.316 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.382 (best in column) | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.562 | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.61 (best in column) | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.793 (best in column) | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.444 (best in column) |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | 0.966 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.953 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.909 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.775 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.909 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.524 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.371 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.693 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.33 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.396 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.332 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.279 | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.222 | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.55 | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.43 | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.727 | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.304 |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | 0.935 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.934 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.475 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.524 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.725 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.525 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.525 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.695 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.332 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.4 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.328 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.254 | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.204 | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.566 (best in column) | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.399 | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.714 | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.302 |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | 0.937 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.918 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.86 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.687 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.81 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.495 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.413 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.722 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.387 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.474 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.379 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.266 | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.251 | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.562 | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.455 | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.75 | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.322 |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | 0.954 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.954 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.815 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.422 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, frozen embeddings with a lightweight probe (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.808 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
All 72 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- GENERATOR-v2-1.2B on NT benchmark Enhancer (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark Enhancer Types (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3 (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3K14ac (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3K36me3 (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3K4me1 (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3K4me2 (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3K4me3 (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3K79me3 (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H3K9ac (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H4 (frozen probe)
- GENERATOR-v2-1.2B on NT benchmark H4ac (frozen probe)
Baseline coverage
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- External evaluations
- 72
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
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Conventional reference
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models · Original source · arXiv:2608.05329v1, submitted 2026-08-05
Technical metadata and extraction receipts
Stable ID: gfm2-20261011-datta2026-protocol-frozen-probe
- areas
- dna-genomes
- contexts
- research
- protocol
- Extract a sequence embedding from the frozen backbone (gradients disabled), standardise with training-set statistics, and train a logistic-regression or MLP probe on each readout of the grid {mean, max, CLS, last, attn, top-k} x {LR, MLP} (Section 2.5); report the best configuration over the diagnostic test grid, as mean and standard deviation over five seeds.
- version
- Table 1, 'Frozen' value of each cell
- metric implementation
- MCC for enhancer and histone-mark tasks, F1 for promoter and splice-site tasks (Section 3.2)
- aggregation
- Mean over five seeds
- replicates
- Five seeds
- limitations
- Frozen-probe scores come from the authors' unified protocol; the fine-tuned column is benchmark- or model-reported where available and the authors mark it as a reference value, not a matched head-to-head comparison (Sections 2.7 and 3.3).; Frozen scores are mean and standard deviation over five seeds with the probe selected on the diagnostic test grid for most tables; the authors treat grid-best figures as readout-sensitivity analyses rather than unbiased model selection (Sections 2.5 and 3.3).; Table 1 covers four of the five models in the study; DNABERT-2 is absent from it and appears in Tables 2, 7, 8 and 9.; Table 4 shows that Table 1's frozen values are diagnostic test-set grid-best scores: five of seven HyenaDNA tasks match the grid-best column exactly. They are maxima over the test grid, not validation-selected estimates.
- source locator
- Table 1; Sections 2.3-2.5, 3.2 and 3.3
Related records
- uses data: Nucleotide Transformer benchmark task data (Datta et al. 2026)
- subject: recovery_definition: gfm2-20261011-datta2026-protocol-frozen-probe
- assessment: GENERATOR-v2-1.2B on NT benchmark Enhancer (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark Enhancer Types (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3 (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K14ac (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K36me3 (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K4me1 (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K4me2 (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K4me3 (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K79me3 (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K9ac (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H4 (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark H4ac (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark Promoter All (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark Promoter Non-TATA (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark Promoter TATA (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark Splice Acceptor (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark Splice All (frozen probe)
- assessment: GENERATOR-v2-1.2B on NT benchmark Splice Donor (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Enhancer (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Enhancer Types (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3 (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3K14ac (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3K36me3 (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3K4me1 (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3K4me2 (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3K4me3 (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3K79me3 (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H3K9ac (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H4 (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark H4ac (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Promoter All (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Promoter Non-TATA (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Promoter TATA (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Splice Acceptor (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Splice All (frozen probe)
- assessment: HyenaDNA-436K on NT benchmark Splice Donor (frozen probe)
- assessment: NT-500M on NT benchmark Enhancer (frozen probe)
- assessment: NT-500M on NT benchmark Enhancer Types (frozen probe)
- assessment: NT-500M on NT benchmark H3 (frozen probe)
- assessment: NT-500M on NT benchmark H3K14ac (frozen probe)
- assessment: NT-500M on NT benchmark H3K36me3 (frozen probe)
- assessment: NT-500M on NT benchmark H3K4me1 (frozen probe)
- assessment: NT-500M on NT benchmark H3K4me2 (frozen probe)
- assessment: NT-500M on NT benchmark H3K4me3 (frozen probe)
- assessment: NT-500M on NT benchmark H3K79me3 (frozen probe)
- assessment: NT-500M on NT benchmark H3K9ac (frozen probe)
- assessment: NT-500M on NT benchmark H4 (frozen probe)
- assessment: NT-500M on NT benchmark H4ac (frozen probe)
- assessment: NT-500M on NT benchmark Promoter All (frozen probe)
- assessment: NT-500M on NT benchmark Promoter Non-TATA (frozen probe)
- assessment: NT-500M on NT benchmark Promoter TATA (frozen probe)
- assessment: NT-500M on NT benchmark Splice Acceptor (frozen probe)
- assessment: NT-500M on NT benchmark Splice All (frozen probe)
- assessment: NT-500M on NT benchmark Splice Donor (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Enhancer (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Enhancer Types (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3 (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3K14ac (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3K36me3 (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3K4me1 (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3K4me2 (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3K4me3 (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3K79me3 (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H3K9ac (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H4 (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark H4ac (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Promoter All (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Promoter Non-TATA (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Promoter TATA (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Splice Acceptor (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Splice All (frozen probe)
- assessment: Omni-DNA-116M on NT benchmark Splice Donor (frozen probe)