This is the codes of ESM4SL, which performs synthetic lethality (SL) prediction based on ESM-2.
First, you can create the environment required for running our codes by
bash environment.sh
All the codes for data preprocessing is in data_preprocess/.
A simple example of running our program is
bash script/attn/train.sh
After the program finishes, you can see the outputs in output/attn/ by
tensorboard --logdir output/attn/<name_of_your_run>
If you would like to run multiple cell lines or scenes in one program, you can refer to script/attn/specific_all_in_one.py.
If you would like to run ESM-2+MLP instead of ESM4SL, you can refer to the same files in output/mlp/.
Our codes is based on coach-pl. We thank the authors for their great foundational work.
Some of our codes are credited to ESM.