I am currently using the enzymeNER package for a project and have encountered some confusion regarding the expected folder structure and file handling during model training and inference.
In particular, I noticed that the script attempts to save model data in directories such as BioBertModels or SciBertModels along with a run_id. However, these directories do not seem to exist by default in the package, and I am unsure if they are supposed to be created automatically, if I need to create them manually, or if I am possibly misunderstanding the intended workflow.
Could you please clarify:
Are the BioBertModels and SciBertModels directories supposed to be created manually by the user, or are they generated by the script during the training process?
Is there a specific folder structure that needs to be in place before running the training or inference scripts?
Am I missing any critical setup steps that might explain the errors related to missing folders or files?
Is there any more in depth tutorial to use enzymeNER as I am relatively new to using programming and wanted to integrate this to my dissertation in bioinformatics.
I am currently using the enzymeNER package for a project and have encountered some confusion regarding the expected folder structure and file handling during model training and inference.
In particular, I noticed that the script attempts to save model data in directories such as BioBertModels or SciBertModels along with a run_id. However, these directories do not seem to exist by default in the package, and I am unsure if they are supposed to be created automatically, if I need to create them manually, or if I am possibly misunderstanding the intended workflow.
Could you please clarify:
Are the BioBertModels and SciBertModels directories supposed to be created manually by the user, or are they generated by the script during the training process?
Is there a specific folder structure that needs to be in place before running the training or inference scripts?
Am I missing any critical setup steps that might explain the errors related to missing folders or files?
Is there any more in depth tutorial to use enzymeNER as I am relatively new to using programming and wanted to integrate this to my dissertation in bioinformatics.