Feng Promoter Arabidopsis NonTATA 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
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All evaluations
5 evaluations · 5 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Caduceus-Ph (Promoter Arabidopsis NonTATA classification) | Protocol: Feng Promoter Arabidopsis NonTATA sequence classification Dataset: Feng Promoter Arabidopsis NonTATA dataset | 0.944 Promoter Arabidopsis NonTATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph Promoter Arabidopsis NonTATA 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 NonTATA row, Caduceus-Ph column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: DNABERT-2 (Promoter Arabidopsis NonTATA classification) | Protocol: Feng Promoter Arabidopsis NonTATA sequence classification Dataset: Feng Promoter Arabidopsis NonTATA dataset | 0.946 Promoter Arabidopsis NonTATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 Promoter Arabidopsis NonTATA 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 NonTATA row, DNABERT-2 column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: GROVER (Promoter Arabidopsis NonTATA classification) | Protocol: Feng Promoter Arabidopsis NonTATA sequence classification Dataset: Feng Promoter Arabidopsis NonTATA dataset | 0.949 Promoter Arabidopsis NonTATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGROVER Promoter Arabidopsis NonTATA 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 NonTATA row, GROVER column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: HyenaDNA (Promoter Arabidopsis NonTATA classification) | Protocol: Feng Promoter Arabidopsis NonTATA sequence classification Dataset: Feng Promoter Arabidopsis NonTATA dataset | 0.955 Promoter Arabidopsis NonTATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA Promoter Arabidopsis NonTATA 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 NonTATA row, HyenaDNA column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json) |
| Configuration: NT-v2 (Promoter Arabidopsis NonTATA classification) | Protocol: Feng Promoter Arabidopsis NonTATA sequence classification Dataset: Feng Promoter Arabidopsis NonTATA dataset | 0.94 Promoter Arabidopsis NonTATA AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT-v2 Promoter Arabidopsis NonTATA 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 NonTATA 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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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-nontata
- 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 NonTATA sequence classification (AUC)
- version
- Table 2