Evaluation

HyenaDNA-436K on NT benchmark H3K4me3 (reference fine-tuned)

Evidence concern: excluded from comparisons

Table 1 prints the same frozen value and spread (.5252+-.0262) for NT on both 'Enhancer' and 'Enhancer Types', while the fine-tuned references differ (.548 and .424). One of the two frozen cells is likely a transcription error in the source; both are kept as printed and should not support comparison until the authors clarify.Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models · Table 1, column 'NT', rows 'Enhancer' and 'Enhancer Types'

Table 1 and Table 4 disagree for HyenaDNA Splice Acceptor: Table 1 prints .4752±.0108 (recovery 50), while Table 4 prints 0.7308 ± 0.0033 (validation-selected) and 0.7360 ± 0.0052 (diagnostic grid-best). Five other HyenaDNA cells of Table 1 equal Table 4's grid-best values, but Splice Donor (.7247±.0087) equals the validation-selected value instead. Table 3 and Table 4 also name different grid-best readouts for HyenaDNA Splice All (MLP+Mean against MLP+Attn). Table 1 values are kept as printed.Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models · Table 1, column 'HyenaDNA', rows 'Splice Acceptor' and 'Splice Donor'; Table 4; Table 3, row 'Splice All'

Published comparison; transcribed, not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: HyenaDNA-436K, fine-tuned reference score (Datta et al. 2026)	Protocol: Nucleotide Transformer benchmark, reference fine-tuned scores (Datta et al. 2026 Table 1) Dataset: Nucleotide Transformer benchmark task data (Datta et al. 2026)	0.549 MCC (NT benchmark H3K4me3, reference fine-tuned score) unitless · higher Uncertainty: ± 0.056 (type not stated). Table 1 does not define the spread on reference fine-tuned scores; Section 3.3 defines only the frozen-probe spread Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Evidence concern: excluded from comparisons Table 1 prints the same frozen value and spread (.5252+-.0262) for NT on both 'Enhancer' and 'Enhancer Types', while the fine-tuned references differ (.548 and .424). One of the two frozen cells is likely a transcription error in the source; both are kept as printed and should not support comparison until the authors clarify.Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models · Table 1, column 'NT', rows 'Enhancer' and 'Enhancer Types' Table 1 and Table 4 disagree for HyenaDNA Splice Acceptor: Table 1 prints .4752±.0108 (recovery 50), while Table 4 prints 0.7308 ± 0.0033 (validation-selected) and 0.7360 ± 0.0052 (diagnostic grid-best). Five other HyenaDNA cells of Table 1 equal Table 4's grid-best values, but Splice Donor (.7247±.0087) equals the validation-selected value instead. Table 3 and Table 4 also name different grid-best readouts for HyenaDNA Splice All (MLP+Mean against MLP+Attn). Table 1 values are kept as printed.Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models · Table 1, column 'HyenaDNA', rows 'Splice Acceptor' and 'Splice Donor'; Table 4; Table 3, row 'Splice All' Methods, coverage and source HyenaDNA-436K on NT benchmark H3K4me3 (reference fine-tuned) gfm2-20261011-datta2026-protocol-fine-tuned-reference Aggregation: Not reported Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models · Table 1, row 'H3K4me3', column 'HyenaDNA', FT value

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

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

Nucleotide Transformer benchmark, reference fine-tuned scores (Datta et al. 2026 Table 1)

Configuration: HyenaDNA-436K, fine-tuned reference score (Datta et al. 2026)
Protocol: Nucleotide Transformer benchmark, reference fine-tuned scores (Datta et al. 2026 Table 1)
Dataset: Nucleotide Transformer benchmark task data (Datta et al. 2026)

origin: Evaluation origin not reported
configuration: Primary source as retrieved 2026-10-11
protocol id: gfm2-20261011-datta2026-protocol-fine-tuned-reference
dataset version: Nucleotide Transformer benchmark as distributed
split: Benchmark train/test split
inputs: DNA sequence for the histone mark task
adaptation: Fine-tuning; protocol not printed in this source
metric implementation: MCC
aggregation: As reported by the cited source
population: Not reported
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Benchmark train/test split
Adaptation: Fine-tuning; protocol not printed in this source
Scoring implementation: MCC

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Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

19 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
Comparison: adaptation Fine-tuning; protocol not printed in this source Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation As reported by the cited source Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	missing or unspecified No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version Nucleotide Transformer benchmark as distributed Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs DNA sequence for the histone mark task Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation MCC Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population Not reported Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	missing or unspecified No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id gfm2-20261011-datta2026-protocol-fine-tuned-reference Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split Benchmark train/test split Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 3 values Frozen-probe scores come from the authors' unified protocol; the fine-tuned column is benchmark- or model-reported where available and the authors mark it as a reference value, not a matched head-to-head comparison (Sections 2.7 and 3.3). Frozen scores are mean and standard deviation over five seeds with the probe selected on the diagnostic test grid for most tables; the authors treat grid-best figures as readout-sensitivity analyses rather than unbiased model selection (Sections 2.5 and 3.3). Table 1 covers four of the five models in the study; DNABERT-2 is absent from it and appears in Tables 2, 7, 8 and 9. Context-only references	Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models Original source ↗ Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell Version: arXiv:2608.05329v1, submitted 2026-08-05 Retrieved: 2026-10-11T00:51:27Z	not individually reviewed No individual claim review recorded unreported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.limitations` Source artifact SHA-256: `df36e4772562329550c924004a546812c8d76149a1b5238e4d0b0cfa8a82bb5c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

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

1 source record and release history

Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models · Original source · arXiv:2608.05329v1, submitted 2026-08-05

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Technical metadata and extraction receipts

Stable ID: gfm2-20261011-datta2026-eval-hyenadna-h3k4me3-ft

areas: dna-genomes
contexts: research
origin: unreported
protocol: gfm2-20261011-datta2026-protocol-fine-tuned-reference
version: Primary source as retrieved 2026-10-11
comparison: protocol id: gfm2-20261011-datta2026-protocol-fine-tuned-reference; dataset version: Nucleotide Transformer benchmark as distributed; split: Benchmark train/test split; inputs: DNA sequence for the histone mark task; adaptation: Fine-tuning; protocol not printed in this source; metric implementation: MCC; aggregation: As reported by the cited source; population: Not reported; budget: Not reported
source locator: Table 1, row 'H3K4me3', column 'HyenaDNA', second value of the cell
limitations: Frozen-probe scores come from the authors' unified protocol; the fine-tuned column is benchmark- or model-reported where available and the authors mark it as a reference value, not a matched head-to-head comparison (Sections 2.7 and 3.3).; Frozen scores are mean and standard deviation over five seeds with the probe selected on the diagnostic test grid for most tables; the authors treat grid-best figures as readout-sensitivity analyses rather than unbiased model selection (Sections 2.5 and 3.3).; Table 1 covers four of the five models in the study; DNABERT-2 is absent from it and appears in Tables 2, 7, 8 and 9.

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