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DNABERT (6-mer)

Genome language model fine-tuned on each GUE dataset by the DNABERT-2 authors.

28 evaluations · 28 metric rows

Overview

Genome language model fine-tuned on each GUE dataset by the DNABERT-2 authors.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

Release 2026-09-17-134cd1815de8 · 28 evaluations · 28 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
DNABERT (6-mer) on GUE CORE-PROMOTER-DETECTION-ALL: Core promoter detection, dataset all

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

68.90% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Core promoter detection all)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE CORE-PROMOTER-DETECTION-NOTATA: Core promoter detection, dataset notata

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

70.47% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Core promoter detection notata)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE CORE-PROMOTER-DETECTION-TATA: Core promoter detection, dataset tata

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

76.06% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Core promoter detection tata)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE COVID-VARIANT-CLASSIFICATION-COVID: Covid variant classification, dataset Covid

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

55.50% f1

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Covid variant classification Covid)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3: Epigenetic marks prediction, dataset H3

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

73.10% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3K14AC: Epigenetic marks prediction, dataset H3K14ac

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

40.06% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3K14ac)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3K36ME3: Epigenetic marks prediction, dataset H3K36me3

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

47.25% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3K36me3)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3K4ME1: Epigenetic marks prediction, dataset H3K4me1

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

41.44% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3K4me1)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3K4ME2: Epigenetic marks prediction, dataset H3K4me2

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

32.27% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3K4me2)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3K4ME3: Epigenetic marks prediction, dataset H3K4me3

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

27.81% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3K4me3)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3K79ME3: Epigenetic marks prediction, dataset H3K79me3

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

61.17% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3K79me3)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H3K9AC: Epigenetic marks prediction, dataset H3K9ac

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

51.22% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H3K9ac)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H4: Epigenetic marks prediction, dataset H4

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

79.26% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H4)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE EPIGENETIC-MARKS-PREDICTION-H4AC: Epigenetic marks prediction, dataset H4ac

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

37.43% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Epigenetic marks prediction H4ac)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE PROMOTER-DETECTION-ALL: Promoter detection, dataset all

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

90.48% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Promoter detection all)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE PROMOTER-DETECTION-NOTATA: Promoter detection, dataset notata

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

93.05% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Promoter detection notata)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE PROMOTER-DETECTION-TATA: Promoter detection, dataset tata

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

61.56% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Promoter detection tata)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE SPLICE-SITE-PREDICTION-RECONSTRUCT: Splice site prediction, dataset Reconstruct

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

84.07% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Splice site prediction Reconstruct)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-0: Transcription factor prediction (human), dataset 0

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

66.84% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (human) 0)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-1: Transcription factor prediction (human), dataset 1

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

70.14% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (human) 1)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-2: Transcription factor prediction (human), dataset 2

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

61.03% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (human) 2)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-3: Transcription factor prediction (human), dataset 3

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

51.89% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (human) 3)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-4: Transcription factor prediction (human), dataset 4

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

70.97% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (human) 4)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-0: Transcription factor prediction (mouse), dataset 0

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

44.42% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (mouse) 0)

Source checking is not independent reproduction.

DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-1: Transcription factor prediction (mouse), dataset 1

Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

Author-reported evaluation · Evaluation metadata: source checked

78.94% mcc

Unit: percent · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (mouse) 1)

Source checking is not 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.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-134cd1815de8
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No evidence rows match these filters. Choose another scope or clear the search.

Sources and history

Release 2026-09-17-134cd1815de8 · Record review: source checked

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: gue-method-dnabert-6-mer

areas
dna-genomes
source locator
Table 6, row(DNABERT (6-mer))
missing metadata
checkpoint revision: unreported; parameters: unextracted
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