Caduceus-Ph Long Sequence Input (GTEx whole-blood expression prediction)
Caduceus-Ph Long Sequence Input (GTEx whole-blood expression prediction): Frozen zero-shot embeddings computed per phased allele and the two averaged; Supervised random forest regressor fitted per gene.
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Evaluations and results
1 evaluation · 2 results. Different protocols are not a single leaderboard.
Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input · Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes
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) |
|---|---|---|
| Caduceus-Ph Long Sequence Input (GTEx whole-blood expression prediction)Evaluation | 0.227 | 0.127 |
All 2 result rows with coverage, uncertainty and sources
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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' |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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Evidence
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
Download this release (gzip)Technical metadata and extraction receipts
Stable ID: feng-dna-fm-20261013-config-gtex-caduceus-ph-long-sequence-input
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- foundation model eligible
- true
- head
- Supervised random forest regressor fitted per gene
- reported name
- Caduceus-Ph Long Sequence Input*
- task
- GTEx whole-blood gene expression prediction
- representation
- Frozen zero-shot embeddings computed per phased allele and the two averaged (Methods, Gene expression prediction benchmark). Token pooling for this task is not stated; the pinned HyenaDNA author script mean-pools tokens.
- limitations
- Input length printed as '131K bp'.
- checkpoint
- Caduceus-Ph-131K (Methods, 'Model configuration selection' paragraph)
- missing metadata
- actual input bp: reason: unreported; note: Printed as '131K bp'; the exact base-pair count is not printed in Table 4.; head revision: reason: unextracted; version: reason: unreported; note: Immutable checkpoint revision is not stated in the article.
- provenance note
- Caduceus-Ph Long Sequence Input* (GTEx whole-blood expression prediction); Feng et al. 2025 source-reported, task-scoped configuration.