Dataset subset reported in SegmentNT supplementary information: complete Tables 2 and 3. Exact split manifest remains unextracted; source-table identity is retained.
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21 evaluations · 42 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: BPNet arch. large | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.45 (± 0.007) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.007 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 3; PDF page 5 (printed 4); block 2; data row 2; model BPNet arch. large; column promoter tissue-invariant |
| Configuration: BPNet arch. large | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.40 (± 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 2; data row 2; model BPNet arch. large; column promoter tissue-invariant |
| Configuration: BPNet arch. | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.29 (± 0.006) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.006 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 3; PDF page 5 (printed 4); block 2; data row 1; model BPNet arch.; column promoter tissue-invariant |
| Configuration: BPNet arch. | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.26 (± 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 2; data row 1; model BPNet arch.; column promoter tissue-invariant |
| Configuration: Random-Init (only head) | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.00 (± 0.000) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.000 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 3; PDF page 5 (printed 4); block 2; data row 9; model Random-Init (only head); column promoter tissue-invariant |
| Configuration: Random-Init (only head) | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.00 (± 0.001) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.001 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 2; data row 9; model Random-Init (only head); column promoter tissue-invariant |
| Configuration: Random-Init | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.35 (± 0.015) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.015 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 3; PDF page 5 (printed 4); block 2; data row 10; model Random-Init; column promoter tissue-invariant |
| Configuration: Random-Init | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.40 (± 0.011) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.011 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 2; data row 10; model Random-Init; column promoter tissue-invariant |
| Configuration: SegmentBorzoi-30kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.66 (± 0.007) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.007 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 3; PDF page 5 (printed 4); block 2; data row 20; model SegmentBorzoi-30kb; column promoter tissue-invariant |
| Configuration: SegmentBorzoi-30kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.64 (± 0.008) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.008 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 2; data row 20; model SegmentBorzoi-30kb; column promoter tissue-invariant |
| Configuration: SegmentBorzoi-524kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.46 (± 0.305) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.305 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 3; PDF page 5 (printed 4); block 2; data row 21; model SegmentBorzoi-524kb; column promoter tissue-invariant |
| Configuration: SegmentBorzoi-524kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.28 (± 0.306) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.306 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 2; data row 21; model SegmentBorzoi-524kb; column promoter tissue-invariant |
| Configuration: SegmentEnformer-196kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.55 (± 0.041) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.041 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 3; PDF page 5 (printed 4); block 2; data row 19; model SegmentEnformer-196kb; column promoter tissue-invariant |
| Configuration: SegmentEnformer-196kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.59 (± 0.042) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.042 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 2; data row 19; model SegmentEnformer-196kb; column promoter tissue-invariant |
| Configuration: SegmentEnformer-30kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.66 (± 0.012) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.012 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 3; PDF page 5 (printed 4); block 2; data row 18; model SegmentEnformer-30kb; column promoter tissue-invariant |
| Configuration: SegmentEnformer-30kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.65 (± 0.011) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.011 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 2; data row 18; model SegmentEnformer-30kb; column promoter tissue-invariant |
| Configuration: SegmentNT-10kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.57 (± 0.012) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.012 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 3; PDF page 5 (printed 4); block 2; data row 15; model SegmentNT-10kb; column promoter tissue-invariant |
| Configuration: SegmentNT-10kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.58 (± 0.009) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.009 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 2; data row 15; model SegmentNT-10kb; column promoter tissue-invariant |
| Configuration: SegmentNT-20kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.58 (± 0.013) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.013 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 3; PDF page 5 (printed 4); block 2; data row 16; model SegmentNT-20kb; column promoter tissue-invariant |
| Configuration: SegmentNT-20kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.59 (± 0.009) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.009 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 2; data row 16; model SegmentNT-20kb; column promoter tissue-invariant |
| Configuration: SegmentNT-30kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.55 (± 0.012) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.012 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 3; PDF page 5 (printed 4); block 2; data row 17; model SegmentNT-30kb; column promoter tissue-invariant |
| Configuration: SegmentNT-30kb | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.58 (± 0.007) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.007 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 2; data row 17; model SegmentNT-30kb; column promoter tissue-invariant |
| Configuration: SegmentNT-3kb (NTv1 human; 2.5B) | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.55 (± 0.007) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.007 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 3; PDF page 5 (printed 4); block 2; data row 12; model SegmentNT-3kb (NTv1 human; 2.5B); column promoter tissue-invariant |
| Configuration: SegmentNT-3kb (NTv1 human; 2.5B) | Protocol: SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.56 (± 0.007) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.007 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 2; data row 12; model SegmentNT-3kb (NTv1 human; 2.5B); column promoter tissue-invariant |
| Configuration: SegmentNT-3kb (only head) | Protocol: SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC) Dataset subset: Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.55 (± 0.006) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.006 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 3; PDF page 5 (printed 4); block 2; data row 11; model SegmentNT-3kb (only head); column promoter tissue-invariant |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description Dataset subset reported in SegmentNT supplementary information: complete Tables 2 and 3. Exact split manifest remains unextracted; source-table identity is retained. Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 No field-specific location recorded Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name Human genome promoter tissue-invariant test chromosomes 20 and 21 (SegmentNT human genome annotation split) Context-only references | SegmentNT supplementary information: complete Tables 2 and 3 No field-specific location recorded Version: Published supplementary information to s41592-025-02881-2; SHA-256 pinned snapshot | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Stable ID: segmentnt-supplement-2025-dataset-human-genome-promoter-tissue-invariant-test-chromosomes-20-and-21