An updated version of the transformer model from https://www.biorxiv.org/content/10.1101/2022.07.07.499217v2.abstract
Now featuring:
- hyperparameter search
- faster transformer blocks
- optional hyena encoder
- gene encoding
- optional gene-gene interaction graph for gene encoding
train_classifier.py is the main entrypoint, train_encoder.py can be used to only pretrain the encoder.
See model_scripts/ for usage examples.
hyperparam_search.py runs a hyperparameter search.
Please cite our SNVformer paper if you find this useful: https://www.biorxiv.org/content/10.1101/2022.07.07.499217v2