HyenaDNA gene-expression prediction evaluation; Feng et al. 2025. Transcribed, not reproduced.
1 evaluation · 2 results. Different protocols are not a single leaderboard.
Protocol: Feng GTEx whole-blood expression prediction, all genes, 6 kb input · Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 3 kb
Sorted by MSE (mean across genes of per-gene MSE of covariate-corrected expression) (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 (mean across genes of per-gene MSE of covariate-corrected expression) | Pearson (mean across genes of per-gene Pearson correlation between predicted and observed expression) |
|---|---|---|
| HyenaDNA (GTEx whole-blood expression prediction)Evaluation | 0.235 | 0.122 |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: HyenaDNA (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, all genes, 6 kb input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 3 kb | 0.235 MSE (mean across genes of per-gene MSE of covariate-corrected expression) unit-unreported · lower Uncertainty: Not reported by the source: Table 4 prints averages only; per-gene spread is shown only as a histogram (Fig. 3). Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA GTEx whole-blood expression evaluation Table 4, frozen embeddings + per-gene random forest regression Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 4, row 'HyenaDNA', column 'Average Prediction MSE' |
| Configuration: HyenaDNA (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, all genes, 6 kb input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 3 kb | 0.122 Pearson (mean across genes of per-gene Pearson correlation between predicted and observed expression) unitless · higher Uncertainty: Not reported by the source: Table 4 prints averages only; per-gene spread is shown only as a histogram (Fig. 3). Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA GTEx whole-blood expression evaluation Table 4, frozen embeddings + per-gene random forest regression Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 4, row 'HyenaDNA', column 'Average Prediction Correlation' |
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Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified
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Table 4, frozen embeddings + per-gene random forest regression
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16 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Frozen pretrained representation plus a supervised random-forest regressor fitted per gene Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: aggregation Mean across genes of the per-gene test-set metric Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: budget Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: dataset version Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: inputs Subject-specific phased sequence centred on the TSS, 6000 bp input Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: metric implementation Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: population All 21,004 genes, 610 subjects Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: protocol id feng-dna-fm-20261013-protocol-gtex-wb-expression-6kb Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: split Per gene, subjects split 75:25; fivefold cross-validation for tuning Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Origin independent_paper Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: feng-dna-fm-20261013-eval-gtex-hyenadna