PeptideBERT

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

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 train.py to train the model

Note: For a detailed walkthrough of the codebase (including how to run inference using a trained model), please refer to tutorial.ipynb.