Feng pathogenic/common SNP short-window scored population; Feng et al. 2025.
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7 evaluations · 14 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 (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.696 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 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 row, AUC column (deterministic XML extraction) |
| Configuration: Caduceus-Ph (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.735 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 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 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: DNABERT-2 (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.538 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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, DNABERT-2 row, AUC column (deterministic XML extraction) |
| Configuration: DNABERT-2 (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.134 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 sourceDNABERT-2 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, DNABERT-2 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: GROVER (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.603 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGROVER 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, GROVER row, AUC column (deterministic XML extraction) |
| Configuration: GROVER (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.369 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 sourceGROVER 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, GROVER 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 (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.612 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA 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 row, AUC column (deterministic XML extraction) |
| Configuration: HyenaDNA (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.395 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 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 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: NT-v2 (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.732 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT-v2 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, NT-v2 row, AUC column (deterministic XML extraction) |
| Configuration: NT-v2 (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.881 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 sourceNT-v2 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, NT-v2 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: Sei, hidden states* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.66 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSei, 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, Sei, hidden states* row, AUC column (deterministic XML extraction) |
| Configuration: Sei, hidden states* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.557 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 sourceSei, 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, Sei, 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: Sei, output tracks* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.664 pathogenic/common SNP AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSei, 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, Sei, output tracks* row, AUC column (deterministic XML extraction) |
| Configuration: Sei, output tracks* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.605 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 sourceSei, 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, Sei, 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. |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
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.
5 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.population Short generated/chromosome-boundary-filtered window: 6,000 bp. 22,239 pathogenic/17,398 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 short-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 short-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-short