Protocol

GenBench Bulk RNA expression

GenBench task Bulk RNA expression.

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.

5 recorded evaluations, 10 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

5 evaluations · 10 results. Different protocols are not a single leaderboard.

Protocol: GenBench Bulk RNA expression · Dataset: GenBench Bulk RNA expression

Sorted by MSE (lower 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	MSE	Spearman
NT (GenBench)Evaluation	0.396 (best in column)	0.783 (best in column)
DNABERT2 (GenBench)Evaluation	0.451	0.767
HyenaDNA (GenBench)Evaluation	0.453	0.755
GENA-LM (GenBench)Evaluation	0.496	0.748
Caduceus (GenBench)Evaluation	0.51	0.746

All 10 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 Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.51 MSE unitless · lower 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'Caduceus MSE'
Configuration: Caduceus (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.746 Spearman unitless · 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'Caduceus Spearman'
Configuration: DNABERT2 (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.451 MSE unitless · lower 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'DNABERT2 MSE'
Configuration: DNABERT2 (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.767 Spearman unitless · 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'DNABERT2 Spearman'
Configuration: GENA-LM (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.496 MSE unitless · lower 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'GENA-LM MSE'
Configuration: GENA-LM (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.748 Spearman unitless · 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'GENA-LM Spearman'
Configuration: HyenaDNA (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.453 MSE unitless · lower 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'HyenaDNA MSE'
Configuration: HyenaDNA (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.755 Spearman unitless · 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'HyenaDNA Spearman'
Configuration: NT (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.396 MSE unitless · lower 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'Nucleotide Transformer MSE'
Configuration: NT (GenBench)	Protocol: GenBench Bulk RNA expression Dataset: GenBench Bulk RNA expression	0.783 Spearman unitless · 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 Bulk RNA expression lit-genomics-20261011-genbench-protocol-bulk-rna-expression Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 8, row 'Bulk RNA expression', column 'Nucleotide Transformer Spearman'

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: 5

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.

Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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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

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-genbench-protocol-bulk-rna-expression

areas: dna-genomes
contexts: research
protocol: Fine-tuning per dataset; 'Top-1' score as printed (not defined in the source).
version: arXiv v2
metric: spearman-correlation
metric direction: higher
unit: unitless
limitations: 'Top-1' is not defined in the source; no uncertainty printed.
source locator: Table 8

Related records

part of: GenBench
uses data: GenBench Bulk RNA expression
assessment: Caduceus on GenBench Bulk RNA expression
assessment: DNABERT2 on GenBench Bulk RNA expression
assessment: GENA-LM on GenBench Bulk RNA expression
assessment: HyenaDNA on GenBench Bulk RNA expression
assessment: Nucleotide Transformer on GenBench Bulk RNA expression

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