default.yaml

pos_prec: ['[M+H]+', '[M+H-H2O]+', '[M+H-2H2O]+', '[M+2H]2+', '[M+H-NH3]+']
neg_prec: ['[M-H]-', '[M-H-H2O]-']
element_list: ['H', 'C',  'O', 'N', 'P', 'S', 'Cl', 'F', 'Br', 'I']
debug_flag: False

data_dir: "data/KIBA/"
train_data: "data/KIBA/train_fold0.fa"
valid_data: "data/KIBA/valid_fold0.fa"
test_data: "data/KIBA/test_fold0.fa"
mode: 'positive'
atom_feature: 'medium'
bond_feature: 'full'
self_loop: True
num_virtual_nodes: 0
batch_size_train: 8
batch_size_val: 128
cpu_workers: 4
logfile: "logs/KIBA_train_log.txt"
sanity_check: True

prot_model: 'cnn'

prot_min_len: -1
prot_max_len: -1
prot_truncate: -1

mle_sigma: 0.08
early_stopping_patience: 5

prot_num_layers: 3
prot_hidden_dim: 512
prot_embedding_dim: 100

cnn_prot_length: 1000
cnn_out_channels: 32
cnn_kernel_size: 8

#pretrained_model: "saved_models/PLUS-RNN_BASE.pt"
pretrained_model: "early_stopping/prot_1611267202557"
pretrained_mol_model: "early_stopping/mol_1611267202557"
num_classes: 1
gnn_type: "gcn"
num_gnn_layers: 3
gnn_hidden_dim: 512
gnn_out_feat: 196
global_pooling: "max"
num_mlp_layers: 3
gnn_channels: [64,64,64,64,64,64,64,64,64,64]
attn_heads: [12,12,12,12,12,12,12,12,12,12]
mlp_out_feat: 1000
glu: True
gat_num_heads: 4
gin_agg: 'max'
gnn_dropout: 0.15
activation: 'relu'
attn_type: 0

l2: 0.1
prot_lr: 0.5e-3
mol_lr: 0.5e-3
num_epoch: 20

cand_size: 50
cand_iterations: 3