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README.md

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+---
+license: apache-2.0
+tags:
+- pytorch
+- bert
+- protein
+pipeline_tag: fill-mask
+---
+
+# molcrawl-protein-sequence-bert-medium
+
+## Model Description
+
+GPT-2 medium (345M parameters) foundation model pre-trained on protein amino acid sequences from the MolCrawl dataset.
+
+- **Model Type**: bert
+- **Data Type**: Protein
+- **Training Date**: 2026-05-11
+
+## Usage
+
+```python
+from transformers import AutoModelForMaskedLM, AutoTokenizer
+import torch
+
+model = AutoModelForMaskedLM.from_pretrained("kojima-lab/molcrawl-protein-sequence-bert-medium")
+tokenizer = AutoTokenizer.from_pretrained("kojima-lab/molcrawl-protein-sequence-bert-medium")
+
+# Predict masked amino acid
+# Use tokenizer.mask_token instead of hardcoded "[MASK]":
+# BERT-style tokenizers vary ("[MASK]", "<mask>", etc.)
+if tokenizer.mask_token is None:
+    raise ValueError("This tokenizer has no mask_token; masked LM inference is not supported.")
+prompt = "MKTAYIAK{MASK}RQISFVKSHFSRQ".replace("{MASK}", tokenizer.mask_token)
+inputs = tokenizer(prompt, return_tensors="pt")
+mask_index = (inputs["input_ids"] == tokenizer.mask_token_id).nonzero(as_tuple=True)[1]
+
+with torch.no_grad():
+    outputs = model(**inputs)
+logits = outputs.logits
+
+predicted_token_id = logits[0, mask_index].argmax(dim=-1)
+predicted_token = tokenizer.decode(predicted_token_id)
+result = prompt.replace(tokenizer.mask_token, predicted_token)
+print(f"Predicted: {result}")
+
+```
+
+## 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_bert_medium,
+  title={molcrawl-protein-sequence-bert-medium},
+  author={{RIKEN}},
+  year={2026},
+  publisher={{Hugging Face}},
+  url={{https://huggingface.co/kojima-lab/molcrawl-protein-sequence-bert-medium}}
+}
+```