Sei, output tracks* (pathogenic/common SNP classification)
Sei, output tracks (pathogenic/common SNP classification): Sei, output tracks* (pathogenic/common SNP classification); Actual DNA input consumed by the model: 4096 bp (a crop of the dataset's generated window where smaller); Alternate-minus-reference frozen representation.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
2 evaluations · 5 results. Different protocols are not a single leaderboard.
Protocol: Feng pathogenic-versus-common SNP classification · Dataset: Feng pathogenic/common SNP short-window dataset
Sorted by AUROC (task: pathogenic vs common snp; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) (higher 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 | AUROC (task: pathogenic vs common snp; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) | AUROC (task: pathogenic vs common snp; outer test group 2 only (chromosomes 2, 5, 11, 14, 17, 20, 22, X), not averaged) | AUROC (task: pathogenic vs common snp; outer test group 3 only (chromosomes 1, 4, 7, 8, 10, 13, 15), not averaged) | AUROC (task: pathogenic vs common snp) | Cohen's d (task: pathogenic vs common snp) |
|---|---|---|---|---|---|
| Sei, output tracks* (pathogenic/common SNP classification)Evaluation | 0.675 | 0.649 | 0.667 | Not reported | Not reported |
| Sei, output tracks* (pathogenic/common SNP classification)Evaluation | Not reported | Not reported | Not reported | 0.664 | 0.605 |
All 5 result rows with coverage, uncertainty and sources
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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 AUROC (task: pathogenic vs common snp) unitless · higher Uncertainty: Not yet extracted 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 Cohen's d (task: pathogenic vs common snp) unitless · unknown Uncertainty: Not yet extracted 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. |
| Configuration: Sei, output tracks* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.675 AUROC (task: pathogenic vs common snp; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSei, output tracks Pathogenic variants vs common per-test-group evaluation Table 5 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'Pathogenic variants vs common', row 'Sei, output tracks', column 'Test Group 1 AUC' (cell B13). Test group 1 is chromosomes 3, 6, 9, 12, 16, 18, 19, 21 (Methods, 'Variant effect quantification benchmark'). |
| Configuration: Sei, output tracks* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.649 AUROC (task: pathogenic vs common snp; outer test group 2 only (chromosomes 2, 5, 11, 14, 17, 20, 22, X), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSei, output tracks Pathogenic variants vs common per-test-group evaluation Table 5 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'Pathogenic variants vs common', row 'Sei, output tracks', column 'Test Group 2 AUC' (cell C13). Test group 2 is chromosomes 2, 5, 11, 14, 17, 20, 22, X (Methods, 'Variant effect quantification benchmark'). |
| Configuration: Sei, output tracks* (pathogenic/common SNP classification) | Protocol: Feng pathogenic-versus-common SNP classification Dataset: Feng pathogenic/common SNP short-window dataset | 0.667 AUROC (task: pathogenic vs common snp; outer test group 3 only (chromosomes 1, 4, 7, 8, 10, 13, 15), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSei, output tracks Pathogenic variants vs common per-test-group evaluation Table 5 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'Pathogenic variants vs common', row 'Sei, output tracks', column 'Test Group 3 AUC' (cell D13). Test group 3 is chromosomes 1, 4, 7, 8, 10, 13, 15 (Methods, 'Variant effect quantification benchmark'). |
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Evidence
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Evidence table
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1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Facets: method types1 values
| Benchmarking DNA foundation models for genomic and genetic tasks The store's Enformer and Sei model records (regulatory-variant-20261009-model-enformer, regulatory-variant-20261009-model-sei) are supervised_machine_learning Version: PMC12663285.1 | conflicting claim ["automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from conventional_pipeline to supervised_machine_learning (use-case baseline review 2026-10-12, table 2). The review did not read the Feng source. These configurations have no method link. catalog-model-alphagenome is tagged foundation_model; Feng prints AlphaGenome with an asterisk as a non-DNA-foundation comparator. Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-f243e94c160e04f31a55 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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: amp-feng-20261007-config-variant-sei-output-tracks
- method types
- supervised_machine_learning
- actual input bp
- 4096
- foundation model eligible
- false
- head
- Supervised random forest fitted separately for this task
- missing metadata
- head revision: reason: unextracted; output aggregation bp: reason: unextracted; version: reason: unreported; note: Printed model name and input representation only; immutable checkpoint/head revision is unreported in the inspected primary text.
- reported name
- Sei, output tracks*
- representation
- Alternate-minus-reference frozen representation
- task
- pathogenic/common SNP classification
- provenance note
- Sei, output tracks* (pathogenic/common SNP classification); Feng et al. 2025 source-reported, task-scoped configuration. Printed in the source with an asterisk as a non-DNA-foundation specialised genomic comparator, not one of the paper's own DNA foundation models. Actual DNA input consumed by the model: 4096 bp (a crop of the dataset's generated window where smaller).