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Adibvafa / CodonTransformer

CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.
https://adibvafa.github.io/CodonTransformer
Apache License 2.0
82 stars 2 forks source link

Add support for expanding the list of organisms #2

Closed JackKay404 closed 6 days ago

JackKay404 commented 1 week ago

Hi, Love the package, great work! It would be nice to enable expansion of the model to organisms not on the list. Or maybe this can be done via the fine-tuning script? Thanks!

Adibvafa commented 6 days ago

Hello! Thank you for opening an issue.

You can use the finetuning guide on readme and finetune.py to finetune the model on any new datasets. To add new organisms, you need to use both pretrain.py and finetune.py to train the model from scratch.

Adibvafa commented 6 days ago

Please reopen the issue if you get into any problems during training!