molcrawl-protein-sequence-proteingym-gpt2-small/README.md

---
license: apache-2.0
tags:
- pytorch
- gpt2
- protein
pipeline_tag: text-generation
---

# molcrawl-protein-sequence-proteingym-gpt2-small

## Model Description

GPT-2 small (124M parameters) fine-tuned on [ProteinGym](https://proteingym.org/) protein sequence data, starting from the `molcrawl-protein-sequence-gpt2-small` pre-trained model.

## Datasets

- **ProteinGym**: [https://proteingym.org/](https://proteingym.org/) (Fine-tuning dataset)

- **Model Type**: gpt2
- **Data Type**: Protein
- **Training Date**: 2026-04-24

## Usage

```python
from transformers import AutoModelForCausalLM, AutoTokenizer
import torch

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

# Generate protein sequence
prompt = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGT"
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))

```

## Source Code

Training pipeline, configuration files, and data preparation scripts are
available in the MolCrawl GitHub repository:
[https://github.com/mmai-framework-lab/MolCrawl](https://github.com/mmai-framework-lab/MolCrawl)

## License

This model is released under the APACHE-2.0 license.

## Citation

If you use this model, please cite:

```bibtex
@misc{molcrawl_protein_sequence_proteingym_gpt2_small,
  title={molcrawl-protein-sequence-proteingym-gpt2-small},
  author={{RIKEN}},
  year={2026},
  publisher={{Hugging Face}},
  url={{https://huggingface.co/kojima-lab/molcrawl-protein-sequence-proteingym-gpt2-small}}
}
```