UNet 1024-embedding

UNet 1024-embedding on SegmentNT human genome annotation 3UTR auPRC: 3UTR: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation 3UTR MCC: 3UTR: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation 5UTR auPRC: 5UTR: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation 5UTR MCC: 5UTR: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation CTCF-bound auPRC: CTCF-bound: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation CTCF-bound MCC: CTCF-bound: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation enhancer tissue-invariant auPRC: enhancer tissue-invariant: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation enhancer tissue-invariant MCC: enhancer tissue-invariant: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation enhancer tissue-specific auPRC: enhancer tissue-specific: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation enhancer tissue-specific MCC: enhancer tissue-specific: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation exon auPRC: exon: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation exon MCC: exon: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation intron auPRC: intron: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation intron MCC: intron: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation lncRNA auPRC: lncRNA: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation lncRNA MCC: lncRNA: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation polyA signal auPRC: polyA signal: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation polyA signal MCC: polyA signal: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation promoter tissue-invariant auPRC: promoter tissue-invariant: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation promoter tissue-invariant MCC: promoter tissue-invariant: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation promoter tissue-specific auPRC: promoter tissue-specific: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation promoter tissue-specific MCC: promoter tissue-specific: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation protein coding gene auPRC: protein coding gene: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation protein coding gene MCC: protein coding gene: per-nucleotide annotation (MCC)

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.

Aggregation: Not reported

UNet 1024-embedding on SegmentNT human genome annotation splice acceptor auPRC: splice acceptor: per-nucleotide annotation (auPRC)

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.

Aggregation: Not reported