dna-origin-atlas

The learned weights of dna-origin-classifier as an interpretable table: one row for each of the 65,536 8-mers, with the weight that 8-mer carries in each classifier head. It is the model's parameters presented as readable data, the genomic signature of DNA origin written out 8-mer by 8-mer.

Schema

field	description
kmer	the 8-mer (ACGT)
gc	number of G or C bases (0-8)
cpg	number of CpG dinucleotides in the 8-mer
host_weight	weight in the host head: positive pushes toward human, negative toward non-host
engineered_weight	weight in the engineered head: positive pushes toward engineered, negative toward natural
origin_human, origin_eukaryote, origin_bacteria, origin_virus, origin_engineered	weight of the 8-mer in each class of the 5-way origin head

Weights are the effective weight on each 8-mer's within-sequence frequency (the model's stored weight divided by its per-feature scale), so a sequence's head score is the frequency-weighted sum of these values. Larger magnitude means a more decisive 8-mer.

What it shows

The dominant axis of human-vs-non-host discrimination is the methylation signature. CpG-bearing 8-mers carry a mean host_weight of -6.47, pushing toward non-host, against +0.27 for 8-mers without CpG. This is the vertebrate CpG-depletion left by cytosine methylation and deamination, recovered as a number from a model that was only ever shown labeled sequence. The most human-pushing 8-mers are GC-rich and CpG-free; the most bacterial-pushing are CpG-rich.

Usage

import pandas as pd
df = pd.read_parquet("data.parquet")
df.sort_values("host_weight", ascending=False).head(20)   # most human-characteristic 8-mers
df.sort_values("engineered_weight", ascending=False).head(20)  # synthetic-biology signature
df.groupby(df.cpg > 0)["host_weight"].mean()              # the CpG effect

Provenance

Derived directly from the weights of phanerozoic/dna-origin-classifier (MIT), which is fit on phanerozoic/dna-origin-benchmark. The chain is reproducible: the benchmark builds the model, the model's weights are this atlas.

License

MIT.