Caduceus-Ph Long Sequence Input* 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, 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 |
Applied filters: All linked evaluations
| 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.
0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.
Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified
Exact outcomes, predictions, identifiers and evaluator are connected.
Missing or unresolved evidence
Verified: Not verified
Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.
Missing or unresolved evidence
Verified: Not verified
A pinned recipe describes the inputs, environment and resource requirements.
Missing or unresolved evidence
Verified: Not verified
Separate data and exposure records support an independent test.
Missing or unresolved evidence
Verified: Not verified
Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.
No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.
Table 4, frozen embeddings + per-gene random forest regression
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
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.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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, 131K 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 768-gene long-context subset, 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-long-768 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-caduceus-ph-long-sequence-input