configs/preset/transformer_cpi_2.yaml

# @package _global_
defaults:
  - override /data/drug_featurizer: mol_features
  - override /data/protein_featurizer: tokenizer

model:
  optimizer:
    lr: 0.00001

  predictor:

    _target_: deepscreen.models.predictors.transformer_cpi_2.TransformerCPI2

    encoder:
      _target_: deepscreen.models.predictors.transformer_cpi_2.Encoder
      # /model/protein_encoder@pretrain: tape_bert
      n_layers: 3
      pretrain:
        _target_: tape.ProteinBertModel.from_pretrained
        pretrained_model_name_or_path: resources/models/tape/bert-base/ # bert-base

    decoder:
      _target_: deepscreen.models.predictors.transformer_cpi_2.Decoder
      n_layers: 3
      dropout: 0.1

data:
  batch_size: 16
  collator:
    automatic_padding: True

  protein_featurizer:
    tokenizer:
      _target_: tape.TAPETokenizer.from_pretrained
      vocab: iupac

#  collator:
#    _target_: deepscreen.models.predictors.transformer_cpi_2.pack
#    _partial_: true