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gearnet.yaml
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gearnet.yaml
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output_dir: ~/scratch/protein_output
dataset:
class: Fold3D
path: ~/scratch/protein-datasets/
test_split: test_fold
transform:
class: ProteinView
view: residue
task:
class: PropertyPrediction
num_mlp_layer: 3
mlp_batch_norm: True
mlp_dropout: 0.5
model:
class: GearNetIEConv
input_dim: 21
embedding_dim: 512
hidden_dims: [512, 512, 512, 512, 512, 512]
batch_norm: True
concat_hidden: True
short_cut: True
readout: 'sum'
num_relation: 7
# edge_input_dim: 59
# num_angle_bin: 8
layer_norm: True
dropout: 0.2
# use_ieconv: True
graph_construction_model:
class: GraphConstruction
node_layers:
- class: AlphaCarbonNode
edge_layers:
- class: SequentialEdge
max_distance: 2
- class: SpatialEdge
radius: 10.0
min_distance: 5
- class: KNNEdge
k: 10
min_distance: 5
edge_feature: gearnet
criterion: ce
metric: ['acc']
num_class: 1195
optimizer:
class: SGD
lr: 1.0e-3
weight_decay: 5.0e-4
momentum: 0.98
scheduler:
class: StepLR
step_size: 50
gamma: 0.5
engine:
gpus: {{ gpus }}
batch_size: 2
log_interval: 1000
model_checkpoint: {{ ckpt }}
metric: accuracy [fold_label]
train:
num_epoch: 300