Protocol

Feng pathogenic-versus-common SNP classification

Table 5 pathogenic-versus-common SNP classification; Feng et al. 2025 source-reported protocol.

Overview

Table 5 pathogenic-versus-common SNP classification; Feng et al. 2025 source-reported protocol.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

11 recorded evaluations, 22 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

11 evaluations · 22 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
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 checked Methods, coverage and source Caduceus-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 checked Methods, coverage and source Caduceus-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: 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 checked Methods, coverage and source Caduceus-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 checked Methods, coverage and source Caduceus-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: 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 checked Methods, coverage and source DNABERT-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 checked Methods, coverage and source DNABERT-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: 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 checked Methods, coverage and source Enformer, 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 checked Methods, coverage and source Enformer, 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 checked Methods, coverage and source Enformer, 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 checked Methods, coverage and source Enformer, 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: 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 checked Methods, coverage and source GROVER 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 checked Methods, coverage and source GROVER 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-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 checked Methods, coverage and source HyenaDNA-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 checked Methods, coverage and source HyenaDNA-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.
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 checked Methods, coverage and source HyenaDNA 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 checked Methods, coverage and source HyenaDNA 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 checked Methods, coverage and source NT-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 checked Methods, coverage and source NT-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 checked Methods, coverage and source Sei, 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 checked Methods, coverage and source Sei, 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 checked Methods, coverage and source Sei, 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 checked Methods, coverage and source Sei, 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.

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External evaluations: 11

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Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1

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Technical metadata and extraction receipts

Stable ID: amp-feng-20261007-protocol-pathogenic-common-variant-classification

areas: dna-genomes
missing metadata: None recorded
scope note: Alternate-minus-reference embedding representations scored by a supervised random forest classifier. 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. Short and long are separate scored populations by window-size boundary exclusion, never pooled; see each configuration/dataset for its exact window assignment. Exact immutable checkpoints are unreported; configurations retain the printed model name and input representation only.
task: Pathogenic-versus-common SNP discrimination (AUC, Cohen's d)
version: Table 5

Related records

protocol: Caduceus-Ph pathogenic/common SNP evaluation
protocol: Caduceus-Ph, long sequence pathogenic/common SNP evaluation
protocol: DNABERT-2 pathogenic/common SNP evaluation
protocol: Enformer, hidden states* pathogenic/common SNP evaluation
protocol: Enformer, output tracks* pathogenic/common SNP evaluation
protocol: GROVER pathogenic/common SNP evaluation
protocol: HyenaDNA pathogenic/common SNP evaluation
protocol: HyenaDNA-450K, long sequence pathogenic/common SNP evaluation
protocol: NT-v2 pathogenic/common SNP evaluation
protocol: Sei, hidden states* pathogenic/common SNP evaluation
protocol: Sei, output tracks* pathogenic/common SNP evaluation

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