SegmentNT human genome annotation CTCF-bound MCC: CTCF-bound: per-nucleotide annotation (MCC)

Overview

CTCF-bound: per-nucleotide annotation (MCC). Scored with Matthews correlation coefficient on Human genome CTCF-bound 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.

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Evaluation scope and datasetMetric and reported setup

SegmentNT human genome annotation CTCF-bound MCC: CTCF-bound: per-nucleotide annotation (MCC)

mcc (dimensionless) · Higher values are better.

Every method SegmentNT human genome annotation reports on CTCF-bound: per-nucleotide annotation (MCC), scored with Matthews correlation coefficient on Human genome CTCF-bound test chromosomes 20 and 21.

SegmentNT human genome annotation CTCF-bound MCC: CTCF-bound: per-nucleotide annotation (MCC) · Human genome CTCF-bound 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 2, CTCF-bound column; primary article Sec16–17

Ten 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.

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SegmentNT human genome annotation

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Author-reported evaluations: 21

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Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
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 Original source ↗ Supplementary Table 2, CTCF-bound column; primary article Sec16–17 Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot Retrieved: 2026-09-23T11:23:43.985410+00:00	source checked automated source review · 2026-09-23 Audit details Primary-source transcription with no human sign-off and no independent reproduction. Field: `links:part_of:segmentnt-human-genome-annotation-2025` Claim: segmentnt-supplement-2025-association-ctcf-bound-mcc Source artifact SHA-256: `c4ad23a62ab161a464fe789e5dd167cf2bfe9f43a91a9c3fb1261b99a5594b0f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-09-23-2b89723c6dd9 · Record review: source checked

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SegmentNT supplementary information: complete Tables 2 and 3 · Original source · Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot

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Technical metadata and extraction receipts

Stable ID: segmentnt-supplement-2025-task-ctcf-bound-mcc

areas: genomics
tasks: CTCF-bound: per-nucleotide annotation (MCC)
metric: Matthews correlation coefficient
metric direction: higher
dataset: Human genome CTCF-bound 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 2, CTCF-bound column; primary article Sec16–17
comparison panels: id: segmentnt-supplement-2025-panel-ctcf-bound-mcc; title: SegmentNT human genome annotation CTCF-bound MCC: CTCF-bound: per-nucleotide annotation (MCC); protocol id: segmentnt-supplement-2025-task-ctcf-bound-mcc; dataset id: segmentnt-supplement-2025-dataset-human-genome-ctcf-bound-test-chromosomes-20-and-21; metric: mcc; unit: dimensionless; direction: higher; result ids: segmentnt-supplement-2025-result-bpnet-arch-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-bpnet-arch-large-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-spliceai-arch-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-spliceai-arch-large-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-spliceai-arch-extra-large-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-unet-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-unet-1024-embedding-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-unet-large-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-random-init-only-head-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-random-init-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentnt-3kb-only-head-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentnt-3kb-ntv1-human-2-5b-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentnt-3kb-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentnt-3kb-single-task-x14-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentnt-10kb-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentnt-20kb-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentnt-30kb-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentenformer-30kb-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentenformer-196kb-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentborzoi-30kb-ctcf-bound-mcc-mcc; segmentnt-supplement-2025-result-segmentborzoi-524kb-ctcf-bound-mcc-mcc; source ids: coverage-segmentnt-2025-supplement; source locator: Supplementary Table 2, CTCF-bound column; primary article Sec16–17; context: Every method SegmentNT human genome annotation reports on CTCF-bound: per-nucleotide annotation (MCC), scored with Matthews correlation coefficient on Human genome CTCF-bound 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
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