molcrawl-rna-gpt2-small

Model Description

GPT-2 small (124M parameters) foundation model pre-trained on RNA gene expression sequences from the MolCrawl dataset.

Datasets

• MolCrawl RNA gene expression sequence dataset: https://github.com/mmai-framework-lab/MolCrawl-HFuploader/blob/main/workflows/hugging_face/run_upload_hf.sh (Pre-training corpus)

• Model Type: gpt2

• Data Type: RNA

• Training Date: 2026-04-14

Usage

from transformers import AutoModelForCausalLM, AutoTokenizer
import torch

model = AutoModelForCausalLM.from_pretrained("kojima-lab/molcrawl-rna-gpt2-small")
tokenizer = AutoTokenizer.from_pretrained("kojima-lab/molcrawl-rna-gpt2-small")

# Generate next gene-id tokens (RNA gene-list model)
prompt = "ENSG00000000003 ENSG00000000005 ENSG00000000419"
inputs = tokenizer(prompt, return_tensors="pt")
with torch.no_grad():
    output_ids = model.generate(
        **inputs,
        max_new_tokens=50,
        do_sample=True,
        temperature=0.8,
        eos_token_id=None,  # HF config.json has legacy eos_token_id=0; disable early stop
        pad_token_id=0,
    )
print(tokenizer.decode(output_ids[0], skip_special_tokens=True))

Training

This model was trained with the RIKEN Foundation Model pipeline. For more details, please refer to the training configuration files included in this repository.

License

This model is released under the APACHE-2.0 license.

Citation

If you use this model, please cite:

@misc{molcrawl_rna_gpt2_small,
  title={molcrawl-rna-gpt2-small},
  author={{RIKEN}},
  year={2026},
  publisher={{Hugging Face}},
  url={{https://huggingface.co/kojima-lab/molcrawl-rna-gpt2-small}}
}