Result

AUROC (task: e.coli 4mc) of Caduceus-Ph (E.Coli 4mC classification) on Feng E.Coli 4mC dataset

0.628 AUROC (task: e.coli 4mc)

Methods

Tested configuration: Caduceus-Ph (E.Coli 4mC classification)
Protocol: Feng E.Coli 4mC sequence classification
Dataset: Feng E.Coli 4mC dataset
Procedure: Table 3, frozen embeddings + task-specific random forest classifier
Evaluation: Caduceus-Ph E.Coli 4mC evaluation
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source: Table 3 prints point AUCs only.
Evidence: Independent external evaluation · source checkedBenchmarking DNA foundation models for genomic and genetic tasks · Table 3, row 'E.Coli 4mC', column 'Caduceus-Ph'. Printed in bold (table footnote: 'Bolded: higher than at least two other AUCs, p < 0.01.').

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Original predefined split retained where clearly defined; otherwise a random 70:30 train/test split. DNABERT-2/NT-v2 benchmark datasets are re-split 70:30 keeping class proportions. Random forest hyperparameters tuned by fivefold cross-validation. No whole-chromosome holdout (Methods, 'Sequence classification benchmark'). Supplementary Data 6: 8681 training and 3721 test sequences.
Adaptation: Frozen pretrained representation plus a supervised random-forest classifier head fitted for this exact task
Scoring implementation: Not reported

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Reported result 0.6283 Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Table 3, row 'E.Coli 4mC', column 'Caduceus-Ph'. Printed in bold (table footnote: 'Bolded: higher than at least two other AUCs, p < 0.01.'). Version: PMC12663285.1 Retrieved: 2026-09-17T07:54:51.004119+00:00	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-14T15:00:00Z independent paper Audit details Extracted by extract/extract_feng.py (deterministic parse). Independent review: value, metric and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact Extraction artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Extraction artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record 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: feng-dna-fm-20261014-result-t3-e-coli-4mc-caduceus-ph-auc

metric: auroc
metric direction: higher
unit: unitless
printed value: 0.6283
numeric value: 0.6283
metric qualifier: task: e.coli 4mc
source locator: Table 3, row 'E.Coli 4mC', column 'Caduceus-Ph'. Printed in bold (table footnote: 'Bolded: higher than at least two other AUCs, p < 0.01.').
missing metadata: uncertainty: reason: unreported; note: Table 3 prints point AUCs only.
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the Europe PMC XML and matched the pinned SHA-256. Parsed Tables 2 and 3 with a separate ElementTree parser (review/signoff.py) and checked printed value, numeric value, metric, qualifier, unit, direction, locator (including bold marking), and the linked configuration, checkpoint, protocol and dataset.; reviewer: claude; reviewer note: Independent Claude (Opus 5.5) review agent for PR #157, separate from the extraction agent for issue #142 that built this batch. Automated review only; no human review claimed. Transcription, not reproduction.; reviewed at: 2026-10-14T15:00:00Z; artifact sha256: 5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12663285/fullTextXML; note: Extracted by extract/extract_feng.py (deterministic parse). Independent review: value, metric and identity match the source.

Related records

evaluation: Caduceus-Ph E.Coli 4mC evaluation

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