Evaluation

GENERATOR-v2-1.2B on NT benchmark H4 (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: GENERATOR-v2-1.2B, 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)	0.815 MCC (NT benchmark H4, reference fine-tuned score) unitless · higher Uncertainty: Not reported by the source 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 GENERATOR-v2-1.2B on NT benchmark H4 (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 'H4', column 'GENERATOR-v2', FT value

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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: GENERATOR-v2-1.2B, 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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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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 'H4', column 'GENERATOR-v2', 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-generator-v2-h4-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 'H4', column 'GENERATOR-v2', 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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