Feng pathogenic/common SNP long-window scored population; Feng et al. 2025.
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4 evaluations · 8 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Caduceus-Ph, long sequence (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.624 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph, long sequence pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, Caduceus-Ph, long sequence row, AUC column (deterministic XML extraction) |
| Configuration: Caduceus-Ph, long sequence (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.462 pathogenic/common SNP Cohen's d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph, long sequence pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, Caduceus-Ph, long sequence row, Cohen's d column (deterministic XML extraction). Signed effect size; the source does not state a universal desirable sign/direction, so direction is recorded as unknown rather than assumed higher-is-better. |
| Configuration: Enformer, hidden states* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.688 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, hidden states* pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, Enformer, hidden states* row, AUC column (deterministic XML extraction) |
| Configuration: Enformer, hidden states* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.727 pathogenic/common SNP Cohen's d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, hidden states* pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, Enformer, hidden states* row, Cohen's d column (deterministic XML extraction). Signed effect size; the source does not state a universal desirable sign/direction, so direction is recorded as unknown rather than assumed higher-is-better. |
| Configuration: Enformer, output tracks* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.666 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, output tracks* pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, Enformer, output tracks* row, AUC column (deterministic XML extraction) |
| Configuration: Enformer, output tracks* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.654 pathogenic/common SNP Cohen's d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, output tracks* pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, Enformer, output tracks* row, Cohen's d column (deterministic XML extraction). Signed effect size; the source does not state a universal desirable sign/direction, so direction is recorded as unknown rather than assumed higher-is-better. |
| Configuration: HyenaDNA-450K, long sequence (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.626 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-450K, long sequence pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, HyenaDNA-450K, long sequence row, AUC column (deterministic XML extraction) |
| Configuration: HyenaDNA-450K, long sequence (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP long-window dataset | 0.449 pathogenic/common SNP Cohen's d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-450K, long sequence pathogenic/common SNP evaluation Table 5, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 5, HyenaDNA-450K, long sequence row, Cohen's d column (deterministic XML extraction). Signed effect size; the source does not state a universal desirable sign/direction, so direction is recorded as unknown rather than assumed higher-is-better. |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
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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.
5 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.population Long generated/chromosome-boundary-filtered window: 196,608 bp. A model's actual_input_bp may crop a smaller region from this generated window (e.g. AlphaGenome and long-sequence Caduceus-Ph each crop the central 131,072 bp); exact realised per-model scored counts after that crop are unextracted, not asserted as zero. 22,222/17,374 pathogenic/common SNPs. 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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.split Three disjoint outer chromosome test groups (3/6/9/12/16/18/19/21; 2/5/11/14/17/20/22/X; 1/4/7/8/10/13/15), each held out in turn with fourfold inner-chromosome cross-validation for hyperparameter 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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| description Feng pathogenic/common SNP long-window scored population; Feng et al. 2025. 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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name Feng pathogenic/common SNP long-window dataset 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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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Release 2026-10-07-1448159e6a81 · Record review: source checked
Stable ID: amp-feng-20261007-dataset-variant-long