configs/preset/mol_trans.yaml

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

data:
  batch_size: 16
  drug_featurizer:
    max_sequence_length: 205
  protein_featurizer:
    max_sequence_length: 545

model:
  predictor:
    _target_: deepscreen.models.predictors.mol_trans.MolTrans

    input_dim_drug: 23532
    input_dim_target: 16693
    max_drug_seq: ${data.drug_featurizer.max_sequence_length}
    max_protein_seq: ${data.protein_featurizer.max_sequence_length}
    emb_size: 384
    dropout_rate: 0.1

    # DenseNet
    scale_down_ratio: 0.25
    growth_rate: 20
    transition_rate: 0.5
    num_dense_blocks: 4
    kernal_dense_size: 3

    # Encoder
    intermediate_size: 1536
    num_attention_heads: 12
    attention_probs_dropout_prob: 0.1
    hidden_dropout_prob: 0.1
    #flatten_dim: 293412

  optimizer:
    lr: 1e-6