SegmentNT-3kb (only head) on SegmentNT human genome annotation enhancer tissue-invariant MCC: enhancer tissue-invariant: per-nucleotide annotation (MCC)
SegmentNT human genome annotation evaluation of SegmentNT-3kb (only head) on enhancer tissue-invariant: per-nucleotide annotation (MCC), scored with Matthews correlation coefficient.
Evaluation results
1 evaluation · 1 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: SegmentNT-3kb (only head) | Protocol: SegmentNT human genome annotation enhancer tissue-invariant MCC: enhancer tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.16 (± 0.005) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.005 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceTest chromosomes 20 and 21; validation chromosome 22; training remaining chromosomes. Test chunks with genes homologous to train/validation genes excluded using Ensembl BioMart accessed 2024-05-08; homologous distal regulatory elements not excluded. Ten test-set samplings with sliding windows beginning at different genomic starting positions. Mean plus reported standard deviation; not ten training seeds. Best validation checkpoint by average MCC across 14 elements. Per-nucleotide predictions pooled across test sequences separately for each genomic element. MCC and auPRC are separate metrics, not cross-element or cross-table pooled comparisons. Aggregation: Not reported SegmentNT supplementary information: complete Tables 2 and 3 · Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Evaluation procedure
Test chromosomes 20 and 21; validation chromosome 22; training remaining chromosomes. Test chunks with genes homologous to train/validation genes excluded using Ensembl BioMart accessed 2024-05-08; homologous distal regulatory elements not excluded. Ten test-set samplings with sliding windows beginning at different genomic starting positions. Mean plus reported standard deviation; not ten training seeds. Best validation checkpoint by average MCC across 14 elements. Per-nucleotide predictions pooled across test sequences separately for each genomic element. MCC and auPRC are separate metrics, not cross-element or cross-table pooled comparisons.
- Configuration
- SegmentNT-3kb (only head)
- Protocol
- SegmentNT human genome annotation enhancer tissue-invariant MCC: enhancer tissue-invariant: per-nucleotide annotation (MCC)
- Dataset subset
- Human genome enhancer tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split)
- origin
- Author-reported evaluation
- configuration
- Not reported
- protocol id
- segmentnt-supplement-2025-task-enhancer-tissue-invariant-mcc
- metric implementation
- Matthews correlation coefficient
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Reproduction
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- Matthews correlation coefficient
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.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
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16 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation Only segmentation head fine-tuned; encoder frozen. Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation Matthews correlation coefficient Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id segmentnt-supplement-2025-task-enhancer-tissue-invariant-mcc Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.evaluation_group_id segmentnt-supplement-2025-method-segmentnt-3kb-only-head-segmentnt-supplement-2025-dataset-human-genome-enhancer-tissue-invariant-test-chromosomes-20-and-21-evaluation-setup Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.evidence_overlap Tables 2 and 3 report different metrics over the same paper experiment set. They are not independent reproductions or replications. Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin author_reported Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.protocol Test chromosomes 20 and 21; validation chromosome 22; training remaining chromosomes. Test chunks with genes homologous to train/validation genes excluded using Ensembl BioMart accessed 2024-05-08; homologous distal regulatory elements not excluded. Ten test-set samplings with sliding windows beginning at different genomic starting positions. Mean plus reported standard deviation; not ten training seeds. Best validation checkpoint by average MCC across 14 elements. Per-nucleotide predictions pooled across test sequences separately for each genomic element. MCC and auPRC are separate metrics, not cross-element or cross-table pooled comparisons. Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.published_score_reproduction false Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.same_paper_experiment_set segmentnt-2025-human-genome-14-elements Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
1 source records and release history
- SegmentNT supplementary information: complete Tables 2 and 3 · Original source · Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot
Technical metadata and extraction receipts
Stable ID: segmentnt-supplement-2025-evaluation-segmentnt-3kb-only-head-enhancer-tissue-invariant-mcc
- areas
- genomics
- tasks
- enhancer tissue-invariant: per-nucleotide annotation (MCC)
- origin
- author_reported
- protocol
- Test chromosomes 20 and 21; validation chromosome 22; training remaining chromosomes. Test chunks with genes homologous to train/validation genes excluded using Ensembl BioMart accessed 2024-05-08; homologous distal regulatory elements not excluded. Ten test-set samplings with sliding windows beginning at different genomic starting positions. Mean plus reported standard deviation; not ten training seeds. Best validation checkpoint by average MCC across 14 elements. Per-nucleotide predictions pooled across test sequences separately for each genomic element. MCC and auPRC are separate metrics, not cross-element or cross-table pooled comparisons.
- comparison
- protocol id: segmentnt-supplement-2025-task-enhancer-tissue-invariant-mcc; metric implementation: Matthews correlation coefficient
- missing metadata
- checkpoint revision: unreported; seeds: unreported; budget: unreported; split manifest: unextracted
- source locator
- Supplementary Table 2; PDF page 4 (printed 3); block 1; data row 11; model SegmentNT-3kb (only head); column enhancer tissue-invariant
- same paper experiment set
- segmentnt-2025-human-genome-14-elements
- adaptation
- Only segmentation head fine-tuned; encoder frozen.
- evidence overlap
- Tables 2 and 3 report different metrics over the same paper experiment set. They are not independent reproductions or replications.
- published score reproduction
- false
- suite complete
- false
- evaluation group id
- segmentnt-supplement-2025-method-segmentnt-3kb-only-head-segmentnt-supplement-2025-dataset-human-genome-enhancer-tissue-invariant-test-chromosomes-20-and-21-evaluation-setup
Related records
- benchmark: SegmentNT human genome annotation enhancer tissue-invariant MCC: enhancer tissue-invariant: per-nucleotide annotation (MCC)
- model: SegmentNT-3kb (only head)
- dataset: Human genome enhancer tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split)
- evaluation: SegmentNT-3kb (only head) · SegmentNT human genome annotation enhancer tissue-invariant MCC · Matthews correlation coefficient