Feng Promoter Arabidopsis TATA sequence classification
Table 2 sequence classification; Feng et al. 2025 source-reported protocol.
Overview
Table 2 sequence classification; Feng et al. 2025 source-reported protocol.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
5 recorded evaluations, 5 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
5 evaluations · 5 results. Different protocols are not a single leaderboard.
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Caduceus-Ph (Promoter Arabidopsis TATA classification) | Protocol: Feng Promoter Arabidopsis TATA sequence classification Dataset: Feng Promoter Arabidopsis TATA dataset | 0.937 Promoter Arabidopsis TATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph Promoter Arabidopsis TATA evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, Promoter Arabidopsis TATA row, Caduceus-Ph column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: DNABERT-2 (Promoter Arabidopsis TATA classification) | Protocol: Feng Promoter Arabidopsis TATA sequence classification Dataset: Feng Promoter Arabidopsis TATA dataset | 0.951 Promoter Arabidopsis TATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 Promoter Arabidopsis TATA evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, Promoter Arabidopsis TATA row, DNABERT-2 column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: GROVER (Promoter Arabidopsis TATA classification) | Protocol: Feng Promoter Arabidopsis TATA sequence classification Dataset: Feng Promoter Arabidopsis TATA dataset | 0.949 Promoter Arabidopsis TATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGROVER Promoter Arabidopsis TATA evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, Promoter Arabidopsis TATA row, GROVER column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: HyenaDNA (Promoter Arabidopsis TATA classification) | Protocol: Feng Promoter Arabidopsis TATA sequence classification Dataset: Feng Promoter Arabidopsis TATA dataset | 0.961 Promoter Arabidopsis TATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA Promoter Arabidopsis TATA evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, Promoter Arabidopsis TATA row, HyenaDNA column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: NT-v2 (Promoter Arabidopsis TATA classification) | Protocol: Feng Promoter Arabidopsis TATA sequence classification Dataset: Feng Promoter Arabidopsis TATA dataset | 0.95 Promoter Arabidopsis TATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT-v2 Promoter Arabidopsis TATA evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, Promoter Arabidopsis TATA row, NT-v2 column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
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Baseline coverage
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- External evaluations
- 5
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Null control
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Conventional reference
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Regularised classifier on simple permitted features, or protocol's conventional reference
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
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Release 2026-10-07-1448159e6a81 · Record review: source checked
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Download this releaseTechnical metadata and extraction receipts
Stable ID: amp-feng-20261007-protocol-promoter-tata
- areas
- dna-genomes
- missing metadata
- None recorded
- scope note
- Frozen last-layer mean token embeddings from each pretrained model, scored by a supervised random forest classifier fitted for this exact task (not label-free prediction). Original predefined split retained where clearly defined; otherwise a random 70:30 train/test split, tuned by fivefold cross-validation. This ref34 multispecies promoter benchmark's own partitioning is not asserted to follow the DNABERT-2/NT reshuffle rule absent explicit confirmation. Exact per-task split sizes/counts (identified in Supplementary Data 6, not inspected by this intake) and immutable checkpoint/head revisions are unextracted from the inspected main text; not asserted absent from the article.
- task
- Promoter Arabidopsis TATA sequence classification (AUC)
- version
- Table 2