Upload 15 files
Browse files- .gitattributes +1 -0
- checkpoints/100000.pt +3 -0
- checkpoints/200000.pt +3 -0
- checkpoints/300000.pt +3 -0
- checkpoints/400000.pt +3 -0
- checkpoints/500000.pt +3 -0
- checkpoints/600000.pt +3 -0
- checkpoints/codesign_single_yue100.yml +55 -0
- checkpoints/codesign_single_yue101.yml +55 -0
- checkpoints/codesign_single_yue102.yml +55 -0
- checkpoints/codesign_single_yue103.yml +55 -0
- checkpoints/events.out.tfevents.1693556914.vm-9020-c8935ef1e912.3867594.0 +3 -0
- checkpoints/events.out.tfevents.1694306202.vm-9020-c8935ef1e912.1803678.0 +3 -0
- checkpoints/events.out.tfevents.1695862364.vm-9020-c8935ef1e912.3954088.0 +3 -0
- checkpoints/events.out.tfevents.1697161536.vm-9020-c8935ef1e912.1153018.0 +3 -0
- checkpoints/log.txt +3 -0
.gitattributes
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@@ -56,3 +56,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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checkpoints/log.txt filter=lfs diff=lfs merge=lfs -text
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checkpoints/100000.pt
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version https://git-lfs.github.com/spec/v1
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checkpoints/200000.pt
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version https://git-lfs.github.com/spec/v1
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checkpoints/300000.pt
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version https://git-lfs.github.com/spec/v1
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checkpoints/400000.pt
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version https://git-lfs.github.com/spec/v1
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checkpoints/500000.pt
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version https://git-lfs.github.com/spec/v1
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checkpoints/600000.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:1012517b2b9b37afbec18dcde52842a0a3f49431556fafe408dd4af6c444d4d3
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size 179855139
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checkpoints/codesign_single_yue100.yml
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model:
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type: diffab
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res_feat_dim: 128
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pair_feat_dim: 64
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diffusion:
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num_steps: 100
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eps_net_opt:
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num_layers: 6
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train_structure: true
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train_sequence: true
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train:
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loss_weights:
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rot: 1.0
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pos: 1.0
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seq: 1.0
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max_iters: 100000
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val_freq: 1000
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batch_size: 1
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seed: 2023
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max_grad_norm: 100.0
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optimizer:
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type: adam
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lr: 1.e-3
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weight_decay: 0.0
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beta1: 0.9
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beta2: 0.999
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scheduler:
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type: plateau
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factor: 0.8
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patience: 10
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min_lr: 5.e-6
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dataset:
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train:
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type: sabdab
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summary_path: ./data/sabdab_summary_all.tsv
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chothia_dir: ./data/all_structures/chothia
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processed_dir: ./data/processedHu
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split: train
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transform:
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- type: mask_single_cdr
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- type: merge_chains
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+
- type: patch_around_anchor
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val:
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type: sabdab
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summary_path: ./data/sabdab_summary_all.tsv
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chothia_dir: ./data/all_structures/chothia
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processed_dir: ./data/processedHu
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split: val
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transform:
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- type: mask_single_cdr
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| 53 |
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selection: CDR3
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| 54 |
+
- type: merge_chains
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+
- type: patch_around_anchor
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checkpoints/codesign_single_yue101.yml
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@@ -0,0 +1,55 @@
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model:
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type: diffab
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res_feat_dim: 128
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+
pair_feat_dim: 64
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| 5 |
+
diffusion:
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+
num_steps: 100
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+
eps_net_opt:
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num_layers: 6
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train_structure: true
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train_sequence: true
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train:
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loss_weights:
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rot: 1.0
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pos: 1.0
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seq: 1.0
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| 17 |
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max_iters: 300000
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| 18 |
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val_freq: 1000
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| 19 |
+
batch_size: 1
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| 20 |
+
seed: 2023
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| 21 |
+
max_grad_norm: 100.0
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| 22 |
+
optimizer:
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| 23 |
+
type: adam
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| 24 |
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lr: 1.e-3
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| 25 |
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weight_decay: 0.0
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| 26 |
+
beta1: 0.9
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beta2: 0.999
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| 28 |
+
scheduler:
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type: plateau
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| 30 |
+
factor: 0.8
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| 31 |
+
patience: 10
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| 32 |
+
min_lr: 5.e-6
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| 33 |
+
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| 34 |
+
dataset:
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| 35 |
+
train:
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| 36 |
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type: sabdab
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| 37 |
+
summary_path: ./data/sabdab_summary_all.tsv
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| 38 |
+
chothia_dir: ./data/all_structures/chothia
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| 39 |
+
processed_dir: ./data/processedHu
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| 40 |
+
split: train
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| 41 |
+
transform:
|
| 42 |
+
- type: mask_single_cdr
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| 43 |
+
- type: merge_chains
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| 44 |
+
- type: patch_around_anchor
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| 45 |
+
val:
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| 46 |
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type: sabdab
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| 47 |
+
summary_path: ./data/sabdab_summary_all.tsv
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| 48 |
+
chothia_dir: ./data/all_structures/chothia
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| 49 |
+
processed_dir: ./data/processedHu
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| 50 |
+
split: val
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| 51 |
+
transform:
|
| 52 |
+
- type: mask_single_cdr
|
| 53 |
+
selection: CDR3
|
| 54 |
+
- type: merge_chains
|
| 55 |
+
- type: patch_around_anchor
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checkpoints/codesign_single_yue102.yml
ADDED
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@@ -0,0 +1,55 @@
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+
model:
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type: diffab
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| 3 |
+
res_feat_dim: 128
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| 4 |
+
pair_feat_dim: 64
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| 5 |
+
diffusion:
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| 6 |
+
num_steps: 100
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| 7 |
+
eps_net_opt:
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| 8 |
+
num_layers: 6
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| 9 |
+
train_structure: true
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| 10 |
+
train_sequence: true
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| 11 |
+
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+
train:
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+
loss_weights:
|
| 14 |
+
rot: 1.0
|
| 15 |
+
pos: 1.0
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| 16 |
+
seq: 1.0
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| 17 |
+
max_iters: 450000
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| 18 |
+
val_freq: 1000
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| 19 |
+
batch_size: 1
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| 20 |
+
seed: 2023
|
| 21 |
+
max_grad_norm: 100.0
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| 22 |
+
optimizer:
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| 23 |
+
type: adam
|
| 24 |
+
lr: 1.e-3
|
| 25 |
+
weight_decay: 0.0
|
| 26 |
+
beta1: 0.9
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| 27 |
+
beta2: 0.999
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| 28 |
+
scheduler:
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| 29 |
+
type: plateau
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| 30 |
+
factor: 0.8
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| 31 |
+
patience: 10
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| 32 |
+
min_lr: 5.e-6
|
| 33 |
+
|
| 34 |
+
dataset:
|
| 35 |
+
train:
|
| 36 |
+
type: sabdab
|
| 37 |
+
summary_path: ./data/sabdab_summary_all.tsv
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| 38 |
+
chothia_dir: ./data/all_structures/chothia
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| 39 |
+
processed_dir: ./data/processedHu
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| 40 |
+
split: train
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| 41 |
+
transform:
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| 42 |
+
- type: mask_single_cdr
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| 43 |
+
- type: merge_chains
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| 44 |
+
- type: patch_around_anchor
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| 45 |
+
val:
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| 46 |
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type: sabdab
|
| 47 |
+
summary_path: ./data/sabdab_summary_all.tsv
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| 48 |
+
chothia_dir: ./data/all_structures/chothia
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| 49 |
+
processed_dir: ./data/processedHu
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| 50 |
+
split: val
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| 51 |
+
transform:
|
| 52 |
+
- type: mask_single_cdr
|
| 53 |
+
selection: CDR3
|
| 54 |
+
- type: merge_chains
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| 55 |
+
- type: patch_around_anchor
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checkpoints/codesign_single_yue103.yml
ADDED
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model:
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type: diffab
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res_feat_dim: 128
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| 4 |
+
pair_feat_dim: 64
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| 5 |
+
diffusion:
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| 6 |
+
num_steps: 100
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| 7 |
+
eps_net_opt:
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+
num_layers: 6
|
| 9 |
+
train_structure: true
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| 10 |
+
train_sequence: true
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| 11 |
+
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train:
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+
loss_weights:
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| 14 |
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rot: 1.0
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| 15 |
+
pos: 1.0
|
| 16 |
+
seq: 1.0
|
| 17 |
+
max_iters: 600000
|
| 18 |
+
val_freq: 1000
|
| 19 |
+
batch_size: 1
|
| 20 |
+
seed: 2023
|
| 21 |
+
max_grad_norm: 100.0
|
| 22 |
+
optimizer:
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| 23 |
+
type: adam
|
| 24 |
+
lr: 1.e-3
|
| 25 |
+
weight_decay: 0.0
|
| 26 |
+
beta1: 0.9
|
| 27 |
+
beta2: 0.999
|
| 28 |
+
scheduler:
|
| 29 |
+
type: plateau
|
| 30 |
+
factor: 0.8
|
| 31 |
+
patience: 10
|
| 32 |
+
min_lr: 5.e-6
|
| 33 |
+
|
| 34 |
+
dataset:
|
| 35 |
+
train:
|
| 36 |
+
type: sabdab
|
| 37 |
+
summary_path: ./data/sabdab_summary_all.tsv
|
| 38 |
+
chothia_dir: ./data/all_structures/chothia
|
| 39 |
+
processed_dir: ./data/processedHu
|
| 40 |
+
split: train
|
| 41 |
+
transform:
|
| 42 |
+
- type: mask_single_cdr
|
| 43 |
+
- type: merge_chains
|
| 44 |
+
- type: patch_around_anchor
|
| 45 |
+
val:
|
| 46 |
+
type: sabdab
|
| 47 |
+
summary_path: ./data/sabdab_summary_all.tsv
|
| 48 |
+
chothia_dir: ./data/all_structures/chothia
|
| 49 |
+
processed_dir: ./data/processedHu
|
| 50 |
+
split: val
|
| 51 |
+
transform:
|
| 52 |
+
- type: mask_single_cdr
|
| 53 |
+
selection: CDR3
|
| 54 |
+
- type: merge_chains
|
| 55 |
+
- type: patch_around_anchor
|
checkpoints/events.out.tfevents.1693556914.vm-9020-c8935ef1e912.3867594.0
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:0e926897fb17b85a74be6657c97ccd8a6ae4a61c78954a6d7fe16c39df251805
|
| 3 |
+
size 42588344
|
checkpoints/events.out.tfevents.1694306202.vm-9020-c8935ef1e912.1803678.0
ADDED
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@@ -0,0 +1,3 @@
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|
|
| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:9a2396abe28f1bdcb355c3e72cc6ef4fc773618eb9e44ee87d7f3ecb45c22a12
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| 3 |
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size 85441519
|
checkpoints/events.out.tfevents.1695862364.vm-9020-c8935ef1e912.3954088.0
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:b5840ca2b89df349f927305422ef153748d8ae961f485d71482e77d286a40788
|
| 3 |
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size 64081319
|
checkpoints/events.out.tfevents.1697161536.vm-9020-c8935ef1e912.1153018.0
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
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|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:bab4e8537ace501b98eed858e3c078bc9b4f5286582a148233948893667c6c04
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| 3 |
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size 64081319
|
checkpoints/log.txt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:5816fa20a7328c40bb7f706069c05a8316fd2ce01b94c3e01b070a43324f1e40
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| 3 |
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size 120658186
|