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Model: kojima-lab/molcrawl-protein-sequence-gpt2-small Source: Original Platform
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README.md
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---
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license: apache-2.0
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tags:
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- pytorch
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- gpt2
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- protein
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pipeline_tag: text-generation
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---
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# molcrawl-protein-sequence-gpt2-small
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## Model Description
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GPT-2 small (124M parameters) foundation model pre-trained on protein amino acid sequences from the MolCrawl dataset.
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- **Model Type**: gpt2
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- **Data Type**: Protein
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- **Training Date**: 2026-04-24
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## Usage
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```python
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from transformers import AutoModelForCausalLM, AutoTokenizer
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import torch
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model = AutoModelForCausalLM.from_pretrained("kojima-lab/molcrawl-protein-sequence-gpt2-small")
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tokenizer = AutoTokenizer.from_pretrained("kojima-lab/molcrawl-protein-sequence-gpt2-small")
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# Generate protein sequence
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prompt = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGT"
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inputs = tokenizer(prompt, return_tensors="pt")
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with torch.no_grad():
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output_ids = model.generate(
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**inputs,
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max_new_tokens=50,
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do_sample=True,
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temperature=0.8,
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eos_token_id=None, # HF config.json has legacy eos_token_id=0; disable early stop
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pad_token_id=0,
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)
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print(tokenizer.decode(output_ids[0], skip_special_tokens=True))
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```
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## Source Code
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Training pipeline, configuration files, and data preparation scripts are
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available in the MolCrawl GitHub repository:
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[https://github.com/mmai-framework-lab/MolCrawl](https://github.com/mmai-framework-lab/MolCrawl)
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## License
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This model is released under the APACHE-2.0 license.
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## Citation
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If you use this model, please cite:
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```bibtex
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@misc{molcrawl_protein_sequence_gpt2_small,
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title={molcrawl-protein-sequence-gpt2-small},
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author={{RIKEN}},
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year={2026},
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publisher={{Hugging Face}},
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url={{https://huggingface.co/kojima-lab/molcrawl-protein-sequence-gpt2-small}}
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}
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```
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config.json
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config.json
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{
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"architectures": [
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"GPT2LMHeadModel"
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],
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"model_type": "gpt2",
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"vocab_size": 33,
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"n_positions": 1024,
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"n_ctx": 1024,
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"n_embd": 768,
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"n_layer": 12,
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"n_head": 12,
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"n_inner": 3072,
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"activation_function": "gelu_new",
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"resid_pdrop": 0.1,
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"embd_pdrop": 0.1,
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"attn_pdrop": 0.1,
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"layer_norm_epsilon": 1e-05,
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"initializer_range": 0.02,
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"use_cache": true,
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"bos_token_id": 0,
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"eos_token_id": 2,
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"transformers_version": "4.0.0",
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"_name_or_path": "riken-gpt2",
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"_riken_model_args": {
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"n_layer": 12,
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"n_head": 12,
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"n_embd": 768,
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"block_size": 1024,
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"bias": false,
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"vocab_size": 33,
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"dropout": 0.1
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},
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"_riken_bias": false,
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"pad_token_id": 1
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}
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model.safetensors
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special_tokens_map.json
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special_tokens_map.json
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{
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"additional_special_tokens": [
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],
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"cls_token": "<cls>",
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"pad_token": "<pad>",
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"unk_token": "<unk>"
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}
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tokenizer.json
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"single_word": false,
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"lstrip": false,
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"rstrip": false,
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"normalized": false,
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tokenizer_config.json
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}
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training_args.json
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training_args.json
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{
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"bias": false,
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"vocab_size": 33,
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"dropout": 0.1
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}
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}
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