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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… See the full description on the dataset page: https://huggingface.co/datasets/Nhoodie/omni-dna-sad-mutation-dataset.

sourceHugging Faceapache-2.0updated 6mo agoView on Hugging Face
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Omni-DNA SAD Mutation Dataset

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

Files

FilePairsSource
synthetic_expanded.jsonl8,112ICI dual-model generation (Omni + HyenaDNA consensus)
train.jsonl3,317Real NCBI sequences
test.jsonl826Real NCBI sequences (held-out)

Format

Each line is a JSON object:

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

Generation Method (Synthetic Data)

  1. 1.Source: 1,014 real DNA sequences from diverse species
  2. 2.FDI (Focus-Doped Interleaving): Every 3 codons (9 bp), a 1-codon (3 bp) gap is introduced
  3. 3.Dual-model consensus: Omni-DNA-20M and HyenaDNA tiny-1k independently predict gap nucleotides
  4. 4.Consensus tagging: Agreement = consensus, disagreement = contested
  5. 5.8 generation passes with different gap intervals (3-6) and seeds, then deduplicated

Key Statistics

MetricSyntheticReal (Train)Real (Test)
Mean mutation rate17.8%4.2%3.9%
Mean sequence length~450 bp~350 bp~350 bp
Consensus rate2.0%N/AN/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

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