Subject-specific phased sequences (TSS +/- 98 kb) for a random 768-gene subset of GTEx v8 whole blood; Feng et al. 2025.
3 evaluations · 6 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Caduceus-Ph Long Sequence Input (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes | 0.227 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 sourceCaduceus-Ph Long Sequence Input 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 'Caduceus-Ph Long Sequence Input*', column 'Average Prediction MSE' |
| Configuration: Caduceus-Ph Long Sequence Input (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes | 0.127 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 sourceCaduceus-Ph Long Sequence Input 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 'Caduceus-Ph Long Sequence Input*', column 'Average Prediction Correlation' |
| Configuration: Enformer (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes | 0.227 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 sourceEnformer 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 'Enformer*', column 'Average Prediction MSE' |
| Configuration: Enformer (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes | 0.129 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 sourceEnformer 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 'Enformer*', column 'Average Prediction Correlation' |
| Configuration: HyenaDNA-450K (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes | 0.226 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-450K 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-450K*', column 'Average Prediction MSE' |
| Configuration: HyenaDNA-450K (GTEx whole-blood expression prediction) | Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes | 0.137 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-450K 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-450K*', column 'Average Prediction Correlation' |
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8 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Access Individual-level GTEx v8 whole-genome sequences and expression are protected human-participant data: per the Data availability statement, raw individual WGS must be requested through the GTEx Protected Data Access portal, and the processed expression benchmark is not deposited with the other processed datasets on Hugging Face. Only aggregated GTEx releases are public. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Population GTEx v8 whole blood, 610 subjects; 1,000 randomly selected genes reduced to 768 after excluding genes absent from the whole-blood data or whose TSS +/- 98 kb window exceeds the chromosome. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Private data not included true Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Source location Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Species Homo sapiens Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Split Per gene, subjects split 75:25 into training and test; fivefold cross-validation within training for tuning. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Description Subject-specific phased sequences (TSS +/- 98 kb) for a random 768-gene subset of GTEx v8 whole blood; Feng et al. 2025. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Name Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Methods, 'Gene expression prediction datasets' (paragraphs 2 and 3); Table 4 footnote Version: PMC12663285.1 | not individually reviewed No individual claim review recorded 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-dataset-gtex-wb-expression-long-768