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model:
type: diffab
res_feat_dim: 128
pair_feat_dim: 64
diffusion:
num_steps: 100
eps_net_opt:
num_layers: 6
train_structure: true
train_sequence: true
train:
loss_weights:
rot: 1.0
pos: 1.0
seq: 1.0
max_iters: 450000
val_freq: 1000
batch_size: 1
seed: 2023
max_grad_norm: 100.0
optimizer:
type: adam
lr: 1.e-3
weight_decay: 0.0
beta1: 0.9
beta2: 0.999
scheduler:
type: plateau
factor: 0.8
patience: 10
min_lr: 5.e-6
dataset:
train:
type: sabdab
summary_path: ./data/sabdab_summary_all.tsv
chothia_dir: ./data/all_structures/chothia
processed_dir: ./data/processedHu
split: train
transform:
- type: mask_single_cdr
- type: merge_chains
- type: patch_around_anchor
val:
type: sabdab
summary_path: ./data/sabdab_summary_all.tsv
chothia_dir: ./data/all_structures/chothia
processed_dir: ./data/processedHu
split: val
transform:
- type: mask_single_cdr
selection: CDR3
- type: merge_chains
- type: patch_around_anchor
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