Hugging Face's logo

AngxiaoYue
/
ReQFlow

Other
PyTorch
flow-matching
diffusion
generative-ai
biology
chemistry
Model card Files Community
1
ReQFlow
File size: 3,571 Bytes 
8d11573
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
 
data:
  task: hallucination
  dataset: scope
  loader:
    num_workers: 4
    prefetch_factor: 10
  sampler:
    max_batch_size: 128
    max_num_res_squared: 500000
interpolant:
  min_t: 0.01
  twisting:
    use: false
  rots:
    corrupt: true
    sample_schedule: exp
    exp_rate: 10
  trans:
    corrupt: true
    batch_ot: true
    sample_schedule: linear
    sample_temp: 1.0
    vpsde_bmin: 0.1
    vpsde_bmax: 20.0
    potential: null
    potential_t_scaling: false
    rog:
      weight: 10.0
      cutoff: 5.0
  sampling:
    num_timesteps: 100
    do_sde: false
  self_condition: ${model.edge_features.self_condition}
experiment:
  debug: false
  seed: 123
  num_devices: 4
  warm_start: null
  warm_start_cfg_override: true
  resume_cfg_path: null
  resume_ckpt_path: null
  resume: true
  training:
    mask_plddt: true
    bb_atom_scale: 0.1
    trans_scale: 0.1
    translation_loss_weight: 2.0
    t_normalize_clip: 0.9
    rotation_loss_weights: 1.0
    aux_loss_weight: 1.0
    aux_loss_use_bb_loss: true
    aux_loss_use_pair_loss: true
    aux_loss_t_pass: 0.25
  wandb:
    name: null
    project: null
  optimizer:
    lr: 0.0001
  trainer:
    overfit_batches: 0
    min_epochs: 1
    max_epochs: 1000
    accelerator: gpu
    log_every_n_steps: 1
    deterministic: false
    strategy: ddp
    check_val_every_n_epoch: 2
    accumulate_grad_batches: 2
  checkpointer:
    save_last: false
    save_top_k: -1
    dirpath: null
  inference_dir: null
  batch_ot:
    enabled: true
    cost: kabsch
    noise_per_sample: 1
    permute: false
shared:
  seed: 123
  max_cache_size: 100000
  samples_per_eval_length: 5
  num_eval_lengths: 8
  max_eval_length: 256
  min_motif_percent: 0.05
  max_motif_percent: 0.5
scope_dataset:
  seed: ${shared.seed}
  csv_path: ./metadata/scope_metadata.csv
  max_cache_size: ${shared.max_cache_size}
  cache_num_res: 0
  add_plddt_mask: false
  max_eval_length: ${shared.max_eval_length}
  inpainting_percent: 1.0
  samples_per_eval_length: ${shared.samples_per_eval_length}
  num_eval_lengths: ${shared.num_eval_lengths}
  filter:
    max_num_res: 128
    min_num_res: 60
  min_motif_percent: ${shared.min_motif_percent}
  max_motif_percent: ${shared.max_motif_percent}
pdb_dataset:
  seed: ${shared.seed}
  csv_path: null
  cluster_path: ./metadata/pdb.clusters
  max_cache_size: ${shared.max_cache_size}
  cache_num_res: 0
  inpainting_percent: 1.0
  add_plddt_mask: false
  max_eval_length: ${shared.max_eval_length}
  samples_per_eval_length: ${shared.samples_per_eval_length}
  num_eval_lengths: ${shared.num_eval_lengths}
  filter:
    max_num_res: 512
    min_num_res: 60
    max_coil_percent: 0.5
    rog_quantile: 0.96
    oligomeric:
    - monomeric
    num_chains:
    - 1
  min_motif_percent: ${shared.min_motif_percent}
  max_motif_percent: ${shared.max_motif_percent}
model:
  node_embed_size: 256
  edge_embed_size: 128
  symmetric: false
  node_features:
    c_s: ${model.node_embed_size}
    c_pos_emb: 128
    c_timestep_emb: 128
    max_num_res: 2000
    timestep_int: 1000
    embed_chain: false
  edge_features:
    single_bias_transition_n: 2
    c_s: ${model.node_embed_size}
    c_p: ${model.edge_embed_size}
    relpos_k: 64
    feat_dim: 64
    num_bins: 22
    self_condition: true
    embed_chain: false
    embed_diffuse_mask: true
    use_rbf: true
    num_rbf: 32
  ipa:
    c_s: ${model.node_embed_size}
    c_z: ${model.edge_embed_size}
    c_hidden: 128
    no_heads: 8
    no_qk_points: 8
    no_v_points: 12
    seq_tfmr_num_heads: 4
    seq_tfmr_num_layers: 2
    num_blocks: 6