Nhoodie/omni-dna-sad-mutation-dataset

Omni-DNA SAD Mutation Dataset

Synthetic and real DNA mutation pairs for training cross-domain HGT mutation prediction models.

Files

File	Pairs	Source
synthetic_expanded.jsonl	8,112	ICI dual-model generation (Omni + HyenaDNA consensus)
train.jsonl	3,317	Real NCBI sequences
test.jsonl	826	Real NCBI sequences (held-out)

Format

Each line is a JSON object:

{"parent": "ATGGCT...", "child": "ATAGCT..."}

Generation Method (Synthetic Data)

1. Source: 1,014 real DNA sequences from diverse species
2. FDI (Focus-Doped Interleaving): Every 3 codons (9 bp), a 1-codon (3 bp) gap is introduced
3. Dual-model consensus: Omni-DNA-20M and HyenaDNA tiny-1k independently predict gap nucleotides
4. Consensus tagging: Agreement = consensus, disagreement = contested
5. 8 generation passes with different gap intervals (3-6) and seeds, then deduplicated

Key Statistics

Metric	Synthetic	Real (Train)	Real (Test)
Mean mutation rate	17.8%	4.2%	3.9%
Mean sequence length	~450 bp	~350 bp	~350 bp
Consensus rate	2.0%	N/A	N/A

Domains

Sequences sourced from NCBI across diverse prokaryotic and archaeal species for cross-domain HGT analysis.

SAD Coefficient

The synthetic-to-real exposure ratio used in training:

• SAD Coefficient = 4.89 (81,120 synthetic exposures / 16,585 real exposures)
• This is noted as too high — a coefficient of ~1.5 is recommended for future runs

Citation

If using this dataset, please also cite:

• Omni-DNA
• HyenaDNA