GenBench Mouse Transcription Factor Prediction, dataset 2; 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 Mouse Transcription Factor Prediction, dataset 2 · Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2

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
GENA-LM (GenBench)Evaluation	0.905 (best in column)
DNABERT2 (GenBench)Evaluation	0.897
NT (GenBench)Evaluation	0.888
DNABERT (GenBench)Evaluation	0.827
Caduceus (GenBench)Evaluation	0.749
HyenaDNA (GenBench)Evaluation	0.706
CNN (GenBench)Evaluation	0.658

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 Mouse Transcription Factor Prediction, dataset 2 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2	0.749 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 Mouse Transcription Factor Prediction, dataset 2 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-2 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 2', column 'Caduceus'
Configuration: CNN (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 2 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2	0.658 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 Mouse Transcription Factor Prediction, dataset 2 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-2 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 2', column 'CNN'
Configuration: DNABERT (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 2 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2	0.827 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 Mouse Transcription Factor Prediction, dataset 2 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-2 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 2', column 'DNABERT'
Configuration: DNABERT2 (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 2 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2	0.897 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 Mouse Transcription Factor Prediction, dataset 2 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-2 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 2', column 'DNABERT2'
Configuration: GENA-LM (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 2 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2	0.905 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 Mouse Transcription Factor Prediction, dataset 2 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-2 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 2', column 'GENA-LM'
Configuration: HyenaDNA (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 2 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2	0.706 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 Mouse Transcription Factor Prediction, dataset 2 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-2 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 2', column 'HyenaDNA'
Configuration: NT (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 2 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 2	0.888 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 Mouse Transcription Factor Prediction, dataset 2 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-2 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 2', 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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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-mouse-transcription-factor-prediction-2

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 Mouse Transcription Factor Prediction, dataset 2
assessment: Caduceus on GenBench Mouse Transcription Factor Prediction, dataset 2
assessment: CNN on GenBench Mouse Transcription Factor Prediction, dataset 2
assessment: DNABERT on GenBench Mouse Transcription Factor Prediction, dataset 2
assessment: DNABERT2 on GenBench Mouse Transcription Factor Prediction, dataset 2
assessment: GENA-LM on GenBench Mouse Transcription Factor Prediction, dataset 2
assessment: HyenaDNA on GenBench Mouse Transcription Factor Prediction, dataset 2
assessment: Nucleotide Transformer on GenBench Mouse Transcription Factor Prediction, dataset 2