mtDNA-FM Haplogroup Adapter (LoRA r=8)
LoRA adapter for haplogroup classification (26 major haplogroups) on top of
vthawfeek/mtdna-foundation-model.
Usage
1from mtdna_fm.model.model import MtDNAForHaplogroupClassification, MtDNAModel
2from peft import PeftModel
3
4base = MtDNAModel.from_pretrained("vthawfeek/mtdna-foundation-model")
5model = MtDNAForHaplogroupClassification(base, num_labels=26)
6model = PeftModel.from_pretrained(model, "vthawfeek/mtdna-fm-haplogroup")
7model.eval()
LoRA Configuration
- r = 8, lora_alpha = 16
- target_modules: query, key, value, dense
- lora_dropout = 0.1
Task
26-class haplogroup classification: A, B, C, D, E, F, G, H, HV, I, J, K,
L0, L1, L2, L3, L4, L5, M, N, R, T, U, V, W, X.
Input: full 16,569-bp mtDNA genome sequence. Mean-pooled CLS embeddings across
overlapping windows (size=512, stride=256) fed into a Linear(256, 26) head.
Limitations
HmtDB training data has a European population bias (haplogroup H is overrepresented).
Performance on underrepresented African L sub-haplogroups may be lower.
