GUE EPIGENETIC-MARKS-PREDICTION-H3: Epigenetic marks prediction, dataset H3

Overview

Epigenetic marks prediction, dataset H3. Scored with MCC on GUE Epigenetic marks prediction, H3. Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.

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

Results

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Evaluation scope and datasetMetric and reported setup

GUE EPIGENETIC-MARKS-PREDICTION-H3: Epigenetic marks prediction, dataset H3

mcc (percent) · Higher values are better.

GUE EPIGENETIC-MARKS-PREDICTION-H3: Epigenetic marks prediction, dataset H3 · GUE Epigenetic marks prediction, H3 (GUE split)

Evidence origin: Author-reported evaluation.

DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 12, row(Epigenetic marks prediction)

Scores are MCC, except Covid variant classification which is F1, both on a 0 to 100 scale.
The diamond entry is DNABERT-2 with further pre-training on the GUE training sets, so it is not directly comparable to the others.

Comparison details and limitations

Every method GUE reports on Epigenetic marks prediction, dataset H3, scored with MCC on GUE Epigenetic marks prediction, H3.

Author-reported numbers, source checked but not independently reproduced.

Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

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Tested configuration

-119.339.659.980.2

Reported score

Methods and evaluation design

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Evaluation design

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Benchmarks

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Evidence

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Evidence table

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1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Relationship: part of discovery-benchmark-gue Individual claims	DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes Original source ↗ Table 12, row(Epigenetic marks prediction) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 Retrieved: 2026-09-17T08:06:28.183387+00:00	source checked automated source review · 2026-09-18 Audit details Primary-source transcription with no human sign-off and no independent reproduction. Field: `links:part_of:discovery-benchmark-gue` Claim: gue-association-epigenetic-marks-prediction-h3 Source artifact SHA-256: `49300acee3e4afd44bebc3de9893c3bc310d331bd4805374e0952fdfbf366f06` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: source checked

1 source records and release history

DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256

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Technical metadata and extraction receipts

Stable ID: gue-task-epigenetic-marks-prediction-h3

areas: dna-genomes
tasks: Epigenetic marks prediction, dataset H3
metric: MCC
metric direction: higher
dataset: GUE Epigenetic marks prediction, H3
protocol: Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.
source locator: Table 12, row(Epigenetic marks prediction)
comparison panels: id: gue-panel-epigenetic-marks-prediction-h3; title: GUE EPIGENETIC-MARKS-PREDICTION-H3: Epigenetic marks prediction, dataset H3; protocol id: gue-task-epigenetic-marks-prediction-h3; dataset id: gue-dataset-gue-epigenetic-marks-prediction-h3; metric: mcc; unit: percent; direction: higher; result ids: gue-result-dnabert-3-mer-epigenetic-marks-prediction-h3-mcc; gue-result-dnabert-4-mer-epigenetic-marks-prediction-h3-mcc; gue-result-dnabert-5-mer-epigenetic-marks-prediction-h3-mcc; gue-result-dnabert-6-mer-epigenetic-marks-prediction-h3-mcc; gue-result-nt-500m-human-epigenetic-marks-prediction-h3-mcc; gue-result-nt-500m-1000g-epigenetic-marks-prediction-h3-mcc; gue-result-nt-2500m-1000g-epigenetic-marks-prediction-h3-mcc; gue-result-nt-2500m-multi-epigenetic-marks-prediction-h3-mcc; gue-result-dnabert-2-epigenetic-marks-prediction-h3-mcc; gue-result-dnabert-2-further-pre-trained-on-gue-epigenetic-marks-prediction-h3-mcc; source ids: evidence-expansion-gue-49300ace; source locator: Table 12, row(Epigenetic marks prediction); context: Every method GUE reports on Epigenetic marks prediction, dataset H3, scored with MCC on GUE Epigenetic marks prediction, H3.; caveats: Author-reported numbers, source checked but not independently reproduced.; Scores are MCC, except Covid variant classification which is F1, both on a 0 to 100 scale.; The diamond entry is DNABERT-2 with further pre-training on the GUE training sets, so it is not directly comparable to the others.; review: method: automated_source_review; date: 2026-09-18

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