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
CHANGED
@@ -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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checkpoints/200000.pt
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checkpoints/300000.pt
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checkpoints/400000.pt
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checkpoints/500000.pt
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checkpoints/600000.pt
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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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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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scheduler:
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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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selection: CDR3
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- type: merge_chains
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- type: patch_around_anchor
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checkpoints/codesign_single_yue101.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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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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selection: CDR3
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- type: merge_chains
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+
- type: patch_around_anchor
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checkpoints/codesign_single_yue102.yml
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model:
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type: diffab
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res_feat_dim: 128
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eps_net_opt:
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patience: 10
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|
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dataset:
|
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train:
|
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type: sabdab
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37 |
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summary_path: ./data/sabdab_summary_all.tsv
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38 |
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chothia_dir: ./data/all_structures/chothia
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39 |
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processed_dir: ./data/processedHu
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40 |
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split: train
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transform:
|
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- type: mask_single_cdr
|
43 |
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- type: merge_chains
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44 |
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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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50 |
+
split: val
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transform:
|
52 |
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- type: mask_single_cdr
|
53 |
+
selection: CDR3
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54 |
+
- type: merge_chains
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55 |
+
- type: patch_around_anchor
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checkpoints/codesign_single_yue103.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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seed: 2023
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type: adam
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patience: 10
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min_lr: 5.e-6
|
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|
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dataset:
|
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train:
|
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type: sabdab
|
37 |
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summary_path: ./data/sabdab_summary_all.tsv
|
38 |
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chothia_dir: ./data/all_structures/chothia
|
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processed_dir: ./data/processedHu
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40 |
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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
|
47 |
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summary_path: ./data/sabdab_summary_all.tsv
|
48 |
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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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selection: CDR3
|
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- type: merge_chains
|
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checkpoints/events.out.tfevents.1693556914.vm-9020-c8935ef1e912.3867594.0
ADDED
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version https://git-lfs.github.com/spec/v1
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checkpoints/events.out.tfevents.1694306202.vm-9020-c8935ef1e912.1803678.0
ADDED
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version https://git-lfs.github.com/spec/v1
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checkpoints/events.out.tfevents.1695862364.vm-9020-c8935ef1e912.3954088.0
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checkpoints/events.out.tfevents.1697161536.vm-9020-c8935ef1e912.1153018.0
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version https://git-lfs.github.com/spec/v1
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checkpoints/log.txt
ADDED
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version https://git-lfs.github.com/spec/v1
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