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. | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.23 (± 0.001) auprc 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 3; PDF page 5 (printed 4); block 1; data row 1; model BPNet arch.; column enhancer tissue-specific |
| Configuration: BPNet arch. | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.04 (± 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 1; data row 1; model BPNet arch.; column enhancer tissue-specific |
| Configuration: BPNet arch. large | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.30 (± 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 1; data row 2; model BPNet arch. large; column enhancer tissue-specific |
| Configuration: BPNet arch. large | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.20 (± 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 1; data row 2; model BPNet arch. large; column enhancer tissue-specific |
| Configuration: Random-Init | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.18 (± 0.001) auprc 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 3; PDF page 5 (printed 4); block 1; data row 10; model Random-Init; column enhancer tissue-specific |
| Configuration: Random-Init | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.14 (± 0.002) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.002 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 10; model Random-Init; column enhancer tissue-specific |
| Configuration: Random-Init (only head) | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.08 (± 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 1; data row 9; model Random-Init (only head); column enhancer tissue-specific |
| Configuration: Random-Init (only head) | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.01 (± 0.000) mcc 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 2; PDF page 4 (printed 3); block 1; data row 9; model Random-Init (only head); column enhancer tissue-specific |
| Configuration: SegmentBorzoi-30kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.50 (± 0.003) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.003 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 1; data row 20; model SegmentBorzoi-30kb; column enhancer tissue-specific |
| Configuration: SegmentBorzoi-30kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.42 (± 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 1; data row 20; model SegmentBorzoi-30kb; column enhancer tissue-specific |
| Configuration: SegmentBorzoi-524kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.38 (± 0.025) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.025 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 1; data row 21; model SegmentBorzoi-524kb; column enhancer tissue-specific |
| Configuration: SegmentBorzoi-524kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.37 (± 0.022) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.022 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 21; model SegmentBorzoi-524kb; column enhancer tissue-specific |
| Configuration: SegmentEnformer-196kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.45 (± 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 1; data row 19; model SegmentEnformer-196kb; column enhancer tissue-specific |
| Configuration: SegmentEnformer-196kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.42 (± 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 19; model SegmentEnformer-196kb; column enhancer tissue-specific |
| Configuration: SegmentEnformer-30kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.53 (± 0.003) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.003 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 1; data row 18; model SegmentEnformer-30kb; column enhancer tissue-specific |
| Configuration: SegmentEnformer-30kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.44 (± 0.002) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.002 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 18; model SegmentEnformer-30kb; column enhancer tissue-specific |
| Configuration: SegmentNT-10kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.31 (± 0.001) auprc 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 3; PDF page 5 (printed 4); block 1; data row 15; model SegmentNT-10kb; column enhancer tissue-specific |
| Configuration: SegmentNT-10kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.27 (± 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 1; data row 15; model SegmentNT-10kb; column enhancer tissue-specific |
| Configuration: SegmentNT-20kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.30 (± 0.001) auprc 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 3; PDF page 5 (printed 4); block 1; data row 16; model SegmentNT-20kb; column enhancer tissue-specific |
| Configuration: SegmentNT-20kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.27 (± 0.002) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.002 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 16; model SegmentNT-20kb; column enhancer tissue-specific |
| Configuration: SegmentNT-30kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.29 (± 0.002) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.002 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 1; data row 17; model SegmentNT-30kb; column enhancer tissue-specific |
| Configuration: SegmentNT-30kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.27 (± 0.002) mcc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.002 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 17; model SegmentNT-30kb; column enhancer tissue-specific |
| Configuration: SegmentNT-3kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.30 (± 0.001) auprc 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 3; PDF page 5 (printed 4); block 1; data row 13; model SegmentNT-3kb; column enhancer tissue-specific |
| Configuration: SegmentNT-3kb | Protocol: SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.25 (± 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 1; data row 13; model SegmentNT-3kb; column enhancer tissue-specific |
| Configuration: SegmentNT-3kb (NTv1 human; 2.5B) | Protocol: SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC) Dataset subset: Human genome enhancer tissue-specific test chromosomes 20 and 21 (SegmentNT human genome annotation split) | 0.30 (± 0.002) auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.002 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 1; data row 12; model SegmentNT-3kb (NTv1 human; 2.5B); column enhancer tissue-specific |
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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 enhancer tissue-specific 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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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: segmentnt-supplement-2025-dataset-human-genome-enhancer-tissue-specific-test-chromosomes-20-and-21