train_teim

This directory contains files to train TEIM-Seq and TEIM-Res.

Requirements

Same as the environment for inference (requirement file is provided here in the parent directory).

Train TEIM-Seq

In this directory, run the following command to train TEIM-Seq using cross-validation:

python scripts/train_seqlevel.py --config configs/seqlevel_cv_shuffle.yml

Another configuration file configs/seqlevel_all.yml is provided for training TEIM-Seq with all sequence-level data.

Train TEIM-Res

In this directory, run the following command to train TEIM-Res using cross-validation:

python scripts/train_reslevel.py --config configs/<config_file>

where <config_file> is one of the following:

• reslevel_bothnew.yml: split with both-new setting (both CDR3 and epitope in the validation set are unseen in the training set)
• reslevel_newcdr3.yml: split with new-CDR3 setting
• reslevel_newepi.yml: split with new-epitope setting