GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3; arXiv v2

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7 recorded evaluations, 7 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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All evaluations

7 evaluations · 7 results. Different protocols are not a single leaderboard.

Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 · Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3

Sorted by Accuracy (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Accuracy
DNABERT2 (GenBench)Evaluation	0.841 (best in column)
GENA-LM (GenBench)Evaluation	0.832
NT (GenBench)Evaluation	0.812
DNABERT (GenBench)Evaluation	0.777
HyenaDNA (GenBench)Evaluation	0.659
Caduceus (GenBench)Evaluation	0.659
CNN (GenBench)Evaluation	0.623

All 7 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus (GenBench)	Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3	0.659 Accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Yeast Epigenetic Marks Prediction, dataset H3K79me3', column 'Caduceus'
Configuration: CNN (GenBench)	Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3	0.623 Accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNN on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Yeast Epigenetic Marks Prediction, dataset H3K79me3', column 'CNN'
Configuration: DNABERT (GenBench)	Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3	0.777 Accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Yeast Epigenetic Marks Prediction, dataset H3K79me3', column 'DNABERT'
Configuration: DNABERT2 (GenBench)	Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3	0.841 Accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT2 on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Yeast Epigenetic Marks Prediction, dataset H3K79me3', column 'DNABERT2'
Configuration: GENA-LM (GenBench)	Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3	0.832 Accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GENA-LM on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Yeast Epigenetic Marks Prediction, dataset H3K79me3', column 'GENA-LM'
Configuration: HyenaDNA (GenBench)	Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3	0.659 Accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Yeast Epigenetic Marks Prediction, dataset H3K79me3', column 'HyenaDNA'
Configuration: NT (GenBench)	Protocol: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 Dataset: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3	0.812 Accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Nucleotide Transformer on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3 lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Yeast Epigenetic Marks Prediction, dataset H3K79me3', column 'Nucleotide Transformer'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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External evaluations: 7

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Evidence table

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Original source · arXiv 2406.01627 version 2

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-genbench-protocol-short-yeast-epigenetic-marks-prediction-h3k79me3

areas: dna-genomes
contexts: research
protocol: Fine-tuning per dataset; 'Top-1' score as printed (not defined in the source).
version: arXiv v2
metric: accuracy
metric direction: higher
unit: fraction
limitations: 'Top-1' is not defined in the source; no uncertainty printed.
source locator: Table 10

Related records

part of: GenBench
uses data: GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3
assessment: Caduceus on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3
assessment: CNN on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3
assessment: DNABERT on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3
assessment: DNABERT2 on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3
assessment: GENA-LM on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3
assessment: HyenaDNA on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3
assessment: Nucleotide Transformer on GenBench Yeast Epigenetic Marks Prediction, dataset H3K79me3