dnagpt/OmniGene-4-MM-LoRA

OmniGene-4-MM (Stage 3 v3, LoRA + embedding)

Multi-modal extension of OmniGene-4 v5 that adds four vision modalities (chemical-structure images, medical / pathology imagery, charts) on top of the v5 sequence + language capability.

This repository hosts the LoRA adapter + extended embedding (~1.7 GB). You need to first load the base model dnagpt/OmniGene-4-SFT-v5-merged and then patch it with the artefacts here. A merged BF16 release is forthcoming as dnagpt/OmniGene-4-MM-merged.

Headline numbers

Capability	Stage 3 v3	v5 (text-only)
BioPAWS standard homology	85.0 %	99.4 %
BioPAWS remote homology	69.5 %	82.6 %
Vis-CheBI20 struct_recog	1.00	—
Vis-CheBI20 struct_cap	0.96	—
Cell-marker → cell-type ID (kw-overlap)	0.95	—
SMILES → physicochem descriptor (kw-overlap)	0.91	—
Protein-pair homology generation (kw-overlap)	1.00	—
Total compute	~1.5 GPU-days (single H20)	1.5 GPU-days

Files

File	Size	What it is
lora_weights.pt	160 MB	LoRA adapter state-dict (r=64, α=128, on q/k/v/o, gate/up/down, router.proj)
embedding_weights.pt	1.6 GB	Extended embedding table (290,172 × 2,816, BF16)
tokenizer.json + tokenizer_config.json	37 MB	Tokenizer with 28,028 biological tokens
processor_config.json	2 KB	Multimodal processor configuration
chat_template.jinja	16 KB	Chat template
meta.json	0.3 KB	Training hyperparameters

Loading

import torch
from transformers import AutoTokenizer, AutoProcessor, AutoModelForCausalLM
from peft import LoraConfig, inject_adapter_in_model
from huggingface_hub import hf_hub_download

# 1. Load base
BASE = "dnagpt/OmniGene-4-SFT-v5-merged"
ADAPTER = "dnagpt/OmniGene-4-MM-LoRA"

tok = AutoTokenizer.from_pretrained(ADAPTER)
proc = AutoProcessor.from_pretrained(ADAPTER)
model = AutoModelForCausalLM.from_pretrained(
    BASE, torch_dtype=torch.bfloat16, device_map="auto",
)

# 2. Inject empty LoRA at the same target modules used during training
lora_cfg = LoraConfig(
    r=64, lora_alpha=128, lora_dropout=0.05, bias="none",
    target_modules=['q_proj','k_proj','v_proj','o_proj',
                    'gate_proj','up_proj','down_proj','router.proj'],
)
inject_adapter_in_model(lora_cfg, model.model.language_model, adapter_name="stage2")

# 3. Patch in trained weights
sd = model.state_dict()
for k, v in torch.load(hf_hub_download(ADAPTER, "lora_weights.pt"), map_location="cpu").items():
    if k in sd: sd[k].copy_(v)
emb = torch.load(hf_hub_download(ADAPTER, "embedding_weights.pt"), map_location="cpu")
model.get_input_embeddings().weight.data.copy_(emb)
model.eval()

Multi-modal usage

from PIL import Image

img = Image.open("molecule.png").convert("RGB")
msgs = [{"role": "user", "content": [
    {"type": "image"},
    {"type": "text", "text": "Please list the functional groups of the molecule."},
]}]
text = proc.apply_chat_template(msgs, add_generation_prompt=True, tokenize=False)
inp = proc(text=text, images=[img], return_tensors="pt").to(model.device)

out = model.generate(**inp, max_new_tokens=160, do_sample=False)
print(tok.decode(out[0][inp.input_ids.shape[1]:], skip_special_tokens=True))

Training pipeline

Three-stage LoRA fine-tuning starting from the v5 merged checkpoint:

1. Stage 1 (~0.4 GPU-days): vision-only warmup, 10K steps, LR 5e-5
2. Stage 2 (~1.0 GPU-days): mixed text + vision, 6K steps, LR 5e-6
3. Stage 3 v3 (~0.5 GPU-days): heavy-homology with frozen embedding, 3K steps, LR 2e-5

See scripts in the GitHub repository for complete reproducibility.

Citation

@article{wang2026omnigene4,
  title  = {OmniGene-4: A Unified Bio-Language MoE Model with Router-Level
            Interpretability and Modality-Invariant Transfer},
  author = {Wang, Liang},
  year   = {2026},
  note   = {Manuscript at Patterns (Cell Press). Preprint:
            bioRxiv 10.1101/2026.01.03.697478. Code:
            https://github.com/maris205/omnigene4}
}

License

Code: MIT (see GitHub). Model weights: Apache 2.0 (inherited from Gemma-4 base).