cGen

Code for cGen: Contrastive pre-training for sequence based genomics models

Dependencies

cGen uses a custom fork of Selene available here -- please locally install the contrastive-training branch of this fork to run this framework.

Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
README.md		README.md
TrainChromProfiling.py		TrainChromProfiling.py
augmentations.py		augmentations.py
custom_callbacks.py		custom_callbacks.py
dataloader.py		dataloader.py
eval_pretrain.from_file.py		eval_pretrain.from_file.py
eval_pretrain.py		eval_pretrain.py
eval_pretrain_get_embeddings.py		eval_pretrain_get_embeddings.py
evaluate.py		evaluate.py
evaluate_expr.py		evaluate_expr.py
evaluate_gb.py		evaluate_gb.py
linear_probing_models.py		linear_probing_models.py
model.py		model.py
requirements.txt		requirements.txt
sei.py		sei.py
sei_body.py		sei_body.py
simCGen.py		simCGen.py
train.py		train.py
train_finetune.py		train_finetune.py
train_finetune_benchmarks.py		train_finetune_benchmarks.py
train_finetune_many_ckpt.py		train_finetune_many_ckpt.py
train_task.py		train_task.py