config.yaml

data:
  data_dir: ../data
  download_dir: ${.data_dir}/ding_et_al
  multiclass:
    smiles: ${..data_dir}/full_iPhos_lipids.csv
    target: ${..data_dir}/iphos_targets.csv
    helper_lipids: ${..data_dir}/all_data.csv
    output: ${..data_dir}/iphos_multiclass.csv

tournament:
  data_path: ../data/iphos_multiclass.csv
  output_dir: ./results_multiclass
  fingerprints: [../data/mol2fp_CFP.json]
  train:
    seed: 42
    multiclass: true
    hyperparameters:
      batch_size: 64
      epochs: 5000
      patience: 500
      learning_rate: 0.005
      conv_width: 32
      conv_depth: 2
      conv_dropout: 0.3
      dense_width: 32
      dense_dropout: 0.3

embeddings:
  input_file:
  output_file:
  method: rdkit # or cfp

fingerprints:
  smiles_path: ../data/iphos_smiles.txt
  fingerprint_path: ../data/iphos_smiles.npz
  type: cfp # or expert, grover, gcn
  output_path: ../data/mol2fp_test.json

plotting:
  data_path: ../data/iphos_multiclass.csv
  binary_metrics: ../results_binary/metrics.pkl
  multiclass_metrics: ../results_multiclass/metrics.pkl
  save_path: ../colormesh_barplot.png