Protocol

Feng Acceptor sequence classification

Table 1 sequence classification; Feng et al. 2025 source-reported protocol.

Overview

Table 1 sequence classification; Feng et al. 2025 source-reported protocol.

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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.

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Results

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5 evaluations · 5 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ph (Acceptor classification)	Protocol: Feng Acceptor sequence classification Dataset: Feng Acceptor dataset	0.845 Acceptor AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph Acceptor evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, Acceptor row, Caduceus-Ph column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json)
Configuration: DNABERT-2 (Acceptor classification)	Protocol: Feng Acceptor sequence classification Dataset: Feng Acceptor dataset	0.897 Acceptor AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 Acceptor evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, Acceptor row, DNABERT-2 column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json)
Configuration: GROVER (Acceptor classification)	Protocol: Feng Acceptor sequence classification Dataset: Feng Acceptor dataset	0.804 Acceptor AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GROVER Acceptor evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, Acceptor row, GROVER column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json)
Configuration: HyenaDNA (Acceptor classification)	Protocol: Feng Acceptor sequence classification Dataset: Feng Acceptor dataset	0.795 Acceptor AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA Acceptor evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, Acceptor row, HyenaDNA column (deterministic XML extraction; see data/omics/amp-coverage-20261007/feng/selected-rows.json)
Configuration: NT-v2 (Acceptor classification)	Protocol: Feng Acceptor sequence classification Dataset: Feng Acceptor dataset	0.793 Acceptor AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT-v2 Acceptor evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, Acceptor 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

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Recorded evaluations

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Baseline coverage

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External evaluations: 5

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Regularised classifier on simple permitted features, or protocol's conventional reference

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Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-10-07-1448159e6a81. 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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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

1 source records and release history

Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1

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Technical metadata and extraction receipts

Stable ID: amp-feng-20261007-protocol-splice-acceptor

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. DNABERT-2/NT benchmark datasets are reshuffled unless an explicit source exception applies. 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: Acceptor sequence classification (AUC)
version: Table 1

Related records

protocol: Caduceus-Ph Acceptor evaluation
protocol: DNABERT-2 Acceptor evaluation
protocol: GROVER Acceptor evaluation
protocol: HyenaDNA Acceptor evaluation
protocol: NT-v2 Acceptor evaluation

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