marin-dna/gpn-star-p-uniform-v1-enhancer-arm-a

marin-dna/gpn-star-p-uniform-v1-enhancer-arm-a

Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment. This draft covers the enhancer region cohort with all species scope and preserves source FASTA/2bit letter case.

Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.

Anchor eligibility uses calibrated entropy from the primate gpn-star-hg38-p243-200m score set. A human window is eligible when at least 51 of 255 positions satisfy the strict rule entropy_calibrated < 0.081001. Sequence case is independent of that filter: lowercase bases preserve source repeat masking, uppercase bases preserve source non-repeat-masked sequence, and conservation scores never rewrite emitted characters or case.

Produced by the commit-pinned vertebrate projection pipeline.

Human anchor provenance

The authoritative projection table was produced by source commit 65b7806ea56a270124c9973af0366f5ab412c665 with source config SHA-256 28cb7786197945ef1798c3581873e4b3d68b7bf91189a59585b0dcabcad7a5e4. Human anchors use the uniform GRCh38 255 bp grid at 128 bp stride and require at least 51 positions with entropy_calibrated < 0.081001 from the pinned primate GPN-Star-P score set. The six labels are the issue #232 v4 CDS, 3-prime UTR, protein-coding TSS/5-prime UTR, and ncRNA-exon assignments; issue #326 Arm A enhancer; and the exhaustive GPN-constrained remainder background.

Coordinates and sequence semantics

Human source coordinates use GRCh38/hg38 primary chromosomes. All human and target coordinates are 0-based and half-open. Every emitted sequence is exactly 255 bases, preserves its source FASTA/2bit letter case, and is oriented to the human anchor.

The published format is zstd-compressed JSON Lines under data/train/ and data/validation/. The release is validated before upload against a producer-keyed manifest of file sizes and SHA-256 checksums, and the immutable Hub revision exposes each large-file SHA-256 identifier.

license: other preserves the source-specific terms of the public genome assemblies, annotations, and alignments rather than relicensing those inputs.

Splits

• —train: 131,467,840 rows after removing the validation sample and applying the configured reverse-complement augmentation.
• —validation: 16,384 original-orientation rows sampled uniformly without replacement with seed 517 before augmentation (4,194,304 tokens including BOS).

The split is row-level and does not stratify by chromosome, species, or human anchor. Different species projections from one human anchor may occur on opposite sides of the split. The reverse complement of a selected validation row is excluded from training.

The selected target manifest contains 135 family-deduplicated projection targets; human reference rows are added separately once per anchor.

Schema

• —query_name: String
• —source_chrom: String
• —source_start: Int64
• —source_end: Int64
• —region_label: String
• —species: String
• —alignment_name: String
• —assembly: String
• —taxonomy_id: Int64
• —family: String
• —clade: String
• —phylogenetic_rank: Int64
• —alignment_source: String
• —t_chrom: String
• —t_start: Int64
• —t_end: Int64
• —t_strand: String
• —t_src_size: Int64
• —pre_resize_t_start: Int64
• —pre_resize_t_end: Int64
• —fragment_count: Int64
• —aligned_bases: Int64
• —sequence: String
• —augmentation: String

Intended use and limitations

This dataset is intended for genomic language-model research and is not a clinical resource. Assembly quality, alignment gaps, repeat masking, family-deduplicated species selection, human conservation selection, and the center-nucleotide acceptance contract affect the observed sequence distribution. Projecting the center nucleotide does not establish that both 127 bp target flanks are homologous to the full human anchor.