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UCL-CSSB/PlasmidGPT

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PlasmidGPT

A HuggingFace-compatible repackaging of PlasmidGPT (Shao, 2024) — a GPT-2-style decoder pretrained on 153k engineered plasmid sequences from Addgene. Loadable with standard AutoModelForCausalLM and AutoTokenizer. Used as the base for PlasmidGPT-SFT and PlasmidGPT-GRPO.

Quick start

python

from transformers import AutoModelForCausalLM, AutoTokenizer

model = AutoModelForCausalLM.from_pretrained("UCL-CSSB/PlasmidGPT")
tokenizer = AutoTokenizer.from_pretrained("UCL-CSSB/PlasmidGPT")

input_ids = tokenizer("ATG", return_tensors="pt").input_ids
outputs = model.generate(input_ids, max_new_tokens=512, do_sample=True, temperature=1.0)
print(tokenizer.decode(outputs[0], skip_special_tokens=True))

Citation

bibtex

@article{shao2024plasmidgpt,
  title   = {{PlasmidGPT}: a generative framework for plasmid design and annotation},
  author  = {Shao, Bin},
  journal = {bioRxiv},
  year    = {2024},
  doi     = {10.1101/2024.09.30.615762}
}