FungiDNA-FM model weights

Inference checkpoints for the five downstream tasks of FungiDNA-FM, organised as they should appear in the Hugging Face repository <user>/FungiDNA-FM.

Contents

Path	Task	Size	Notes
backbone_final.pt	shared pretrained backbone	217 MB	bare state dict, bfloat16
tokenizer/bpe_fungi.model	SentencePiece model	296 KB	vocab 4096
tokenizer/bpe_fungi.vocab	SentencePiece vocab	64 KB	4096 entries
coding_potential/best_model.pt	CDS vs intergenic	217 MB	FungiDNAForSequenceClassification(2), ours fine-tuned
splice_site/best_model.pt	donor/acceptor/non-site	434 MB	FungiDNAForSequenceClassification(3) + UnifiedHead, float32
taxonomy/{rank}/mlp_best.pt	5-rank taxonomy heads	~0.8–1.1 MB each	bare MLP net.* state dict; requires backbone_final.pt
bgc_boundary/best_model.pt	BGC boundary regression	217 MB	FungiDNAForBGCBoundary(2), ours fine-tuned

Taxonomy rank class counts

phylum 6, subphylum 11, class 26, order 98, family 281.

Usage

These are the files the fungidna.invoke handlers load. Configure the handler to find them (after downloading to your machine) via ~/.config/fungidna/weights.yaml:

backbone: /path/to/backbone_final.pt
tokenizer: /path/to/tokenizer/bpe_fungi.model
coding_potential: /path/to/coding_potential/best_model.pt
splice_site: /path/to/splice_site/best_model.pt
taxonomy: /path/to/taxonomy/phylum/mlp_best.pt
bgc_boundary: /path/to/bgc_boundary/best_model.pt

Or set the FUNGIDNA_BACKBONE_WEIGHTS, FUNGIDNA_TOKENIZER_WEIGHTS, etc. environment variables.