Protocol
Nucleotide Transformer benchmark, reference fine-tuned scores (Datta et al. 2026 Table 1)
Fine-tuned scores for the same tasks, taken from benchmark or model reports where available and marked by the authors as reference values.
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, reference fine-tuned scores (Datta et al. 2026 Table 1) · Dataset: Nucleotide Transformer benchmark task data (Datta et al. 2026)
Sorted by F1 (NT benchmark Promoter All, reference fine-tuned score) (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, reference fine-tuned score) | F1 (NT benchmark Promoter Non-TATA, reference fine-tuned score) | F1 (NT benchmark Promoter TATA, reference fine-tuned score) | F1 (NT benchmark Splice Acceptor, reference fine-tuned score) | F1 (NT benchmark Splice All, reference fine-tuned score) | F1 (NT benchmark Splice Donor, reference fine-tuned score) | MCC (NT benchmark Enhancer Types, reference fine-tuned score) | MCC (NT benchmark Enhancer, reference fine-tuned score) | MCC (NT benchmark H3, reference fine-tuned score) | MCC (NT benchmark H3K14ac, reference fine-tuned score) | MCC (NT benchmark H3K36me3, reference fine-tuned score) | MCC (NT benchmark H3K4me1, reference fine-tuned score) | MCC (NT benchmark H3K4me2, reference fine-tuned score) | MCC (NT benchmark H3K4me3, reference fine-tuned score) | MCC (NT benchmark H3K79me3, reference fine-tuned score) | MCC (NT benchmark H3K9ac, reference fine-tuned score) | MCC (NT benchmark H4, reference fine-tuned score) | MCC (NT benchmark H4ac, reference fine-tuned score) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | 0.976 (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, fine-tuned reference score (Datta et al. 2026)Evaluation | 0.973 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | 0.962 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | 0.96 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.58 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.477 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.806 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.605 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.657 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.553 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.424 | Not reported | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.512 | Not reported | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.67 | Not reported | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.612 | Not reported | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.815 (best in column) | Not reported |
| GENERATOR-v2-1.2B, fine-tuned reference score (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 | 0.592 |
| GENERATOR-v2-1.2B, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | 0.962 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.948 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.981 (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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.978 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.978 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.517 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.386 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.779 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.612 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.613 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.512 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.455 | Not reported | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.549 | Not reported | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.672 | Not reported | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.581 | Not reported | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.763 | Not reported |
| HyenaDNA-436K, fine-tuned reference score (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 | 0.564 |
| HyenaDNA-436K, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | 0.959 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.944 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.958 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.956 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.949 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.548 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.424 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.784 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.551 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.625 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.55 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.319 | Not reported | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.41 | Not reported | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.672 | Not reported | Not reported | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.562 | Not reported | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.799 | Not reported |
| NT-500M, fine-tuned reference score (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 | 0.495 |
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | 0.976 (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 |
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.966 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.981 (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 |
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.983 (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 |
| NT-500M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.985 (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 |
| Omni-DNA-116M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.593 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.498 (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 |
| Omni-DNA-116M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.818 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.685 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.661 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.577 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.576 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.587 (best in column) | Not reported | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.718 (best in column) | Not reported | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.658 (best in column) | Not reported | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.802 | Not reported |
| Omni-DNA-116M, fine-tuned reference score (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 | 0.663 (best in column) |
| Omni-DNA-116M, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | 0.972 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | 0.967 (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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | 0.968 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | 0.927 | 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, fine-tuned reference score (Datta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.951 | 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 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark Enhancer Types (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3K14ac (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3K36me3 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3K4me1 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3K4me2 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3K4me3 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3K79me3 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H3K9ac (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H4 (reference fine-tuned)
- GENERATOR-v2-1.2B on NT benchmark H4ac (reference fine-tuned)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- unreported
- 72
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
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.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
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-fine-tuned-reference
- areas
- dna-genomes
- contexts
- research
- protocol
- Fine-tuned scores as printed in the 'FT' position of each Table 1 cell. The authors state these are benchmark- or model-reported where available and are provenance-marked reference values rather than fully matched head-to-head comparisons.
- version
- Table 1, 'FT' value of each cell
- metric implementation
- MCC for enhancer and histone-mark tasks, F1 for promoter and splice-site tasks (Section 3.2)
- aggregation
- As reported by the cited benchmark or model source
- 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.; Who ran each fine-tuned score is not stated per cell, so these evaluations are recorded with origin 'unreported'.; Fine-tuning protocol, epochs and selection are not printed for these reference values.; 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 2.7 and 3.3
Related records
- uses data: Nucleotide Transformer benchmark task data (Datta et al. 2026)
- assessment: GENERATOR-v2-1.2B on NT benchmark Enhancer (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark Enhancer Types (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3 (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K14ac (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K36me3 (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K4me1 (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K4me2 (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K4me3 (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K79me3 (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H3K9ac (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H4 (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark H4ac (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark Promoter All (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark Promoter Non-TATA (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark Promoter TATA (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark Splice Acceptor (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark Splice All (reference fine-tuned)
- assessment: GENERATOR-v2-1.2B on NT benchmark Splice Donor (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Enhancer (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Enhancer Types (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3 (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3K14ac (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3K36me3 (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3K4me1 (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3K4me2 (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3K4me3 (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3K79me3 (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H3K9ac (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H4 (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark H4ac (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Promoter All (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Promoter Non-TATA (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Promoter TATA (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Splice Acceptor (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Splice All (reference fine-tuned)
- assessment: HyenaDNA-436K on NT benchmark Splice Donor (reference fine-tuned)
- assessment: NT-500M on NT benchmark Enhancer (reference fine-tuned)
- assessment: NT-500M on NT benchmark Enhancer Types (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3 (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3K14ac (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3K36me3 (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3K4me1 (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3K4me2 (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3K4me3 (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3K79me3 (reference fine-tuned)
- assessment: NT-500M on NT benchmark H3K9ac (reference fine-tuned)
- assessment: NT-500M on NT benchmark H4 (reference fine-tuned)
- assessment: NT-500M on NT benchmark H4ac (reference fine-tuned)
- assessment: NT-500M on NT benchmark Promoter All (reference fine-tuned)
- assessment: NT-500M on NT benchmark Promoter Non-TATA (reference fine-tuned)
- assessment: NT-500M on NT benchmark Promoter TATA (reference fine-tuned)
- assessment: NT-500M on NT benchmark Splice Acceptor (reference fine-tuned)
- assessment: NT-500M on NT benchmark Splice All (reference fine-tuned)
- assessment: NT-500M on NT benchmark Splice Donor (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Enhancer (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Enhancer Types (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3 (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3K14ac (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3K36me3 (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3K4me1 (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3K4me2 (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3K4me3 (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3K79me3 (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H3K9ac (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H4 (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark H4ac (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Promoter All (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Promoter Non-TATA (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Promoter TATA (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Splice Acceptor (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Splice All (reference fine-tuned)
- assessment: Omni-DNA-116M on NT benchmark Splice Donor (reference fine-tuned)