/PeptideBERT

Transformer Based Language Model for Peptide Property Prediction

Primary LanguagePythonMIT LicenseMIT

PeptideBERT

Transformer Based Language Model for Peptide Property Prediction.
Corresponding paper. PeptideBERT


Getting Started

  • Clone this repository
  • cd PeptideBERT
  • Install the required packages (pip install -r requirements.txt)
  • Download the datasets by running python data/download_data.py
  • Run python data/split_augment.py to convert the data into the required format

How to Use

  • Update the config.py file with the desired parameters
  • Optionally, to augment the data, use data/split_augment.py (uncomment the line that calls augment_data)
  • Run python main.py to train the model

Note: For a detailed walkthrough of the codebase, please refer to tutorial.ipynb.