GenBench Mouse Transcription Factor Prediction, dataset 1; arXiv v2

Overview

An explanatory profile has not yet been reviewed for this record.

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

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.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

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

Protocol: GenBench Mouse Transcription Factor Prediction, dataset 1 · Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1

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
NT (GenBench)Evaluation	0.931 (best in column)
DNABERT2 (GenBench)Evaluation	0.919
GENA-LM (GenBench)Evaluation	0.908
DNABERT (GenBench)Evaluation	0.876
Caduceus (GenBench)Evaluation	0.739
HyenaDNA (GenBench)Evaluation	0.728
CNN (GenBench)Evaluation	0.702

All 7 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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 1 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1	0.739 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 1 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 1', column 'Caduceus'
Configuration: CNN (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 1 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1	0.702 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 1 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 1', column 'CNN'
Configuration: DNABERT (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 1 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1	0.876 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 1 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 1', column 'DNABERT'
Configuration: DNABERT2 (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 1 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1	0.919 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 1 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 1', column 'DNABERT2'
Configuration: GENA-LM (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 1 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1	0.908 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 1 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 1', column 'GENA-LM'
Configuration: HyenaDNA (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 1 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1	0.728 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 1 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 1', column 'HyenaDNA'
Configuration: NT (GenBench)	Protocol: GenBench Mouse Transcription Factor Prediction, dataset 1 Dataset: GenBench Mouse Transcription Factor Prediction, dataset 1	0.931 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 1 lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1 Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 10, row 'Mouse Transcription Factor Prediction, dataset 1', column 'Nucleotide Transformer'

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

External evaluations: 7

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

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.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

1 source record and release history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-genbench-protocol-short-mouse-transcription-factor-prediction-1

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 1
assessment: Caduceus on GenBench Mouse Transcription Factor Prediction, dataset 1
assessment: CNN on GenBench Mouse Transcription Factor Prediction, dataset 1
assessment: DNABERT on GenBench Mouse Transcription Factor Prediction, dataset 1
assessment: DNABERT2 on GenBench Mouse Transcription Factor Prediction, dataset 1
assessment: GENA-LM on GenBench Mouse Transcription Factor Prediction, dataset 1
assessment: HyenaDNA on GenBench Mouse Transcription Factor Prediction, dataset 1
assessment: Nucleotide Transformer on GenBench Mouse Transcription Factor Prediction, dataset 1