SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
lncRNA: per-nucleotide annotation (auPRC). Scored with Area under precision-recall curve on Human genome lncRNA test chromosomes 20 and 21. 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.
Overview
lncRNA: per-nucleotide annotation (auPRC). Scored with Area under precision-recall curve on Human genome lncRNA test chromosomes 20 and 21. 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.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
auprc (dimensionless) · Higher values are better.
Every method SegmentNT human genome annotation reports on lncRNA: per-nucleotide annotation (auPRC), scored with Area under precision-recall curve on Human genome lncRNA test chromosomes 20 and 21.
SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC) · Human genome lncRNA test chromosomes 20 and 21 (SegmentNT human genome annotation split)
Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.
SegmentNT supplementary information: complete Tables 2 and 3 · Supplementary Table 3, lncRNA column; primary article Sec16–17Ten test-set samplings with sliding windows beginning at different genomic starting positions. Mean plus reported standard deviation; not ten training seeds.
All comparison limitations (5)
- Ten test-set samplings with sliding windows beginning at different genomic starting positions. Mean plus reported standard deviation; not ten training seeds.
- Table names the v1 backbone NTv1 human; 2.5B; Sec17 describes NT v1 2.5B 1000G. Preserve exact table label and methods context.
- Source excludes homologous test genes but not homologous distal regulatory elements, which may inflate those region scores.
- Input lengths and training setups differ. Architecture baselines are newly trained from random initialization, not original pretrained checkpoint results.
- No aggregation across genomic elements or metrics. Split manifests and checkpoint revisions remain unextracted.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
Showing 12 of 21 matching rows.
- SegmentBorzoi-524kb0.40 (± 0.100)
- SegmentEnformer-196kb0.35 (± 0.017)
- SegmentBorzoi-30kb0.29 (± 0.008)
- SegmentEnformer-30kb0.27 (± 0.008)
- SegmentNT-30kb0.25 (± 0.003)
- SpliceAI arch.0.23 (± 0.001)
- SegmentNT-10kb0.23 (± 0.007)
- SegmentNT-20kb0.23 (± 0.005)
- BPNet arch.0.22 (± 0.001)
- SegmentNT-3kb (only head)0.22 (± 0.001)
- SegmentNT-3kb-single-task (x14)0.22 (± 0.001)
- BPNet arch. large0.21 (± 0.001)
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- BPNet arch. large on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- BPNet arch. on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- Random-Init on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- Random-Init (only head) on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentBorzoi-30kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentBorzoi-524kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentEnformer-196kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentEnformer-30kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentNT-10kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentNT-20kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentNT-30kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- SegmentNT-3kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 21
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of segmentnt-human-genome-annotation-2025 Individual claims | SegmentNT supplementary information: complete Tables 2 and 3 Supplementary Table 3, lncRNA column; primary article Sec16–17 Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | source checked automated source review · 2026-09-23 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: segmentnt-supplement-2025-association-lncrna-auprc Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
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-task-lncrna-auprc
- areas
- genomics
- tasks
- lncRNA: per-nucleotide annotation (auPRC)
- metric
- Area under precision-recall curve
- metric direction
- higher
- dataset
- Human genome lncRNA test chromosomes 20 and 21
- 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.
- source locator
- Supplementary Table 3, lncRNA column; primary article Sec16–17
- comparison panels
- id: segmentnt-supplement-2025-panel-lncrna-auprc; title: SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC); protocol id: segmentnt-supplement-2025-task-lncrna-auprc; dataset id: segmentnt-supplement-2025-dataset-human-genome-lncrna-test-chromosomes-20-and-21; metric: auprc; unit: dimensionless; direction: higher; result ids: segmentnt-supplement-2025-result-bpnet-arch-lncrna-auprc-auprc; segmentnt-supplement-2025-result-bpnet-arch-large-lncrna-auprc-auprc; segmentnt-supplement-2025-result-spliceai-arch-lncrna-auprc-auprc; segmentnt-supplement-2025-result-spliceai-arch-large-lncrna-auprc-auprc; segmentnt-supplement-2025-result-spliceai-arch-extra-large-lncrna-auprc-auprc; segmentnt-supplement-2025-result-unet-lncrna-auprc-auprc; segmentnt-supplement-2025-result-unet-1024-embedding-lncrna-auprc-auprc; segmentnt-supplement-2025-result-unet-large-lncrna-auprc-auprc; segmentnt-supplement-2025-result-random-init-only-head-lncrna-auprc-auprc; segmentnt-supplement-2025-result-random-init-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentnt-3kb-only-head-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentnt-3kb-ntv1-human-2-5b-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentnt-3kb-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentnt-3kb-single-task-x14-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentnt-10kb-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentnt-20kb-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentnt-30kb-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentenformer-30kb-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentenformer-196kb-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentborzoi-30kb-lncrna-auprc-auprc; segmentnt-supplement-2025-result-segmentborzoi-524kb-lncrna-auprc-auprc; source ids: coverage-segmentnt-2025-supplement; source locator: Supplementary Table 3, lncRNA column; primary article Sec16–17; context: Every method SegmentNT human genome annotation reports on lncRNA: per-nucleotide annotation (auPRC), scored with Area under precision-recall curve on Human genome lncRNA test chromosomes 20 and 21.; caveats: Ten test-set samplings with sliding windows beginning at different genomic starting positions. Mean plus reported standard deviation; not ten training seeds.; Table names the v1 backbone NTv1 human; 2.5B; Sec17 describes NT v1 2.5B 1000G. Preserve exact table label and methods context.; Source excludes homologous test genes but not homologous distal regulatory elements, which may inflate those region scores.; Input lengths and training setups differ. Architecture baselines are newly trained from random initialization, not original pretrained checkpoint results.; No aggregation across genomic elements or metrics. Split manifests and checkpoint revisions remain unextracted.; review: method: automated_source_review; date: 2026-09-23
- entity level
- protocol
Related records
- part of: SegmentNT human genome annotation
- subject: SegmentNT human genome annotation lncRNA auPRC: part of segmentnt-human-genome-annotation-2025
- benchmark: BPNet arch. large on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: BPNet arch. on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: Random-Init on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: Random-Init (only head) on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentBorzoi-30kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentBorzoi-524kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentEnformer-196kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentEnformer-30kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentNT-10kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentNT-20kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentNT-30kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentNT-3kb on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentNT-3kb (NTv1 human; 2.5B) on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentNT-3kb (only head) on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SegmentNT-3kb-single-task (x14) on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SpliceAI arch. extra-large on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SpliceAI arch. large on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: SpliceAI arch. on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: UNet 1024-embedding on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: UNet large on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)
- benchmark: UNet on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)