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FastESMFold

Feature Extraction
Transformers
Safetensors
fast_esmfold
protein
structure-prediction
esmfold
test-time-training
custom_code
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lhallee commited on
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Upload config

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Files changed (2) hide show
  1. README.md +4 -4
  2. config.json +117 -117
README.md CHANGED
@@ -1,10 +1,10 @@
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  ---
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  library_name: transformers
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  tags:
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- - protein
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- - structure-prediction
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- - esmfold
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- - test-time-training
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  ---
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  # NOTE
 
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  ---
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  library_name: transformers
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  tags:
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+ - protein
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+ - structure-prediction
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+ - esmfold
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+ - test-time-training
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  ---
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  # NOTE
config.json CHANGED
@@ -1,117 +1,117 @@
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- {
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- "architectures": [
3
- "FastEsmForProteinFolding"
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- ],
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- "attention_probs_dropout_prob": 0.0,
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- "attn_backend": "sdpa",
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- "auto_map": {
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- "AutoConfig": "modeling_fast_esmfold.FastEsmFoldConfig",
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- "AutoModel": "modeling_fast_esmfold.FastEsmForProteinFolding"
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- },
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- "classifier_dropout": null,
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- "dtype": "float32",
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- "emb_layer_norm_before": false,
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- "esmfold_config": {
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- "bypass_lm": false,
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- "embed_aa": true,
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- "esm_ablate_pairwise": false,
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- "esm_ablate_sequence": false,
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- "esm_input_dropout": 0,
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- "esm_type": "esm2_3B",
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- "fp16_esm": false,
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- "lddt_head_hid_dim": 128,
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- "trunk": {
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- "chunk_size": null,
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- "cpu_grad_checkpoint": false,
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- "dropout": 0,
27
- "layer_drop": 0,
28
- "max_recycles": 4,
29
- "num_blocks": 48,
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- "pairwise_head_width": 32,
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- "pairwise_state_dim": 128,
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- "position_bins": 32,
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- "sequence_head_width": 32,
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- "sequence_state_dim": 1024,
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- "structure_module": {
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- "dropout_rate": 0.1,
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- "epsilon": 1e-08,
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- "inf": 100000.0,
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- "ipa_dim": 16,
40
- "num_angles": 7,
41
- "num_blocks": 8,
42
- "num_heads_ipa": 12,
43
- "num_qk_points": 4,
44
- "num_resnet_blocks": 2,
45
- "num_transition_layers": 1,
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- "num_v_points": 8,
47
- "pairwise_dim": 128,
48
- "resnet_dim": 128,
49
- "sequence_dim": 384,
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- "trans_scale_factor": 10
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- }
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- },
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- "use_esm_attn_map": false
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- },
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- "hidden_act": "gelu",
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- "hidden_dropout_prob": 0.0,
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- "hidden_size": 2560,
58
- "initializer_range": 0.02,
59
- "intermediate_size": 10240,
60
- "is_folding_model": true,
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- "layer_norm_eps": 1e-05,
62
- "mask_token_id": 32,
63
- "max_position_embeddings": 1026,
64
- "model_type": "fast_esmfold",
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- "num_attention_heads": 40,
66
- "num_hidden_layers": 36,
67
- "pad_token_id": 1,
68
- "position_embedding_type": "rotary",
69
- "token_dropout": true,
70
- "transformers_version": "4.57.0",
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- "ttt_config": {
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- "ags": 4,
73
- "batch_size": 4,
74
- "lora_alpha": 32.0,
75
- "lora_rank": 8,
76
- "lr": 0.0004,
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- "mask_ratio": 0.15,
78
- "steps": 30
79
- },
80
- "use_cache": true,
81
- "vocab_list": [
82
- "<cls>",
83
- "<pad>",
84
- "<eos>",
85
- "<unk>",
86
- "L",
87
- "A",
88
- "G",
89
- "V",
90
- "S",
91
- "E",
92
- "R",
93
- "T",
94
- "I",
95
- "D",
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- "P",
97
- "K",
98
- "Q",
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- "N",
100
- "F",
101
- "Y",
102
- "M",
103
- "H",
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- "W",
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- "C",
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- "X",
107
- "B",
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- "U",
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- "Z",
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- "O",
111
- ".",
112
- "-",
113
- "<null_1>",
114
- "<mask>"
115
- ],
116
- "vocab_size": 33
117
- }
 
1
+ {
2
+ "architectures": [
3
+ "FastEsmForProteinFolding"
4
+ ],
5
+ "attention_probs_dropout_prob": 0.0,
6
+ "attn_backend": "sdpa",
7
+ "auto_map": {
8
+ "AutoConfig": "modeling_fast_esmfold.FastEsmFoldConfig",
9
+ "AutoModel": "modeling_fast_esmfold.FastEsmForProteinFolding"
10
+ },
11
+ "classifier_dropout": null,
12
+ "dtype": "float32",
13
+ "emb_layer_norm_before": false,
14
+ "esmfold_config": {
15
+ "bypass_lm": false,
16
+ "embed_aa": true,
17
+ "esm_ablate_pairwise": false,
18
+ "esm_ablate_sequence": false,
19
+ "esm_input_dropout": 0,
20
+ "esm_type": "esm2_3B",
21
+ "fp16_esm": false,
22
+ "lddt_head_hid_dim": 128,
23
+ "trunk": {
24
+ "chunk_size": null,
25
+ "cpu_grad_checkpoint": false,
26
+ "dropout": 0,
27
+ "layer_drop": 0,
28
+ "max_recycles": 4,
29
+ "num_blocks": 48,
30
+ "pairwise_head_width": 32,
31
+ "pairwise_state_dim": 128,
32
+ "position_bins": 32,
33
+ "sequence_head_width": 32,
34
+ "sequence_state_dim": 1024,
35
+ "structure_module": {
36
+ "dropout_rate": 0.1,
37
+ "epsilon": 1e-08,
38
+ "inf": 100000.0,
39
+ "ipa_dim": 16,
40
+ "num_angles": 7,
41
+ "num_blocks": 8,
42
+ "num_heads_ipa": 12,
43
+ "num_qk_points": 4,
44
+ "num_resnet_blocks": 2,
45
+ "num_transition_layers": 1,
46
+ "num_v_points": 8,
47
+ "pairwise_dim": 128,
48
+ "resnet_dim": 128,
49
+ "sequence_dim": 384,
50
+ "trans_scale_factor": 10
51
+ }
52
+ },
53
+ "use_esm_attn_map": false
54
+ },
55
+ "hidden_act": "gelu",
56
+ "hidden_dropout_prob": 0.0,
57
+ "hidden_size": 2560,
58
+ "initializer_range": 0.02,
59
+ "intermediate_size": 10240,
60
+ "is_folding_model": true,
61
+ "layer_norm_eps": 1e-05,
62
+ "mask_token_id": 32,
63
+ "max_position_embeddings": 1026,
64
+ "model_type": "fast_esmfold",
65
+ "num_attention_heads": 40,
66
+ "num_hidden_layers": 36,
67
+ "pad_token_id": 1,
68
+ "position_embedding_type": "rotary",
69
+ "token_dropout": true,
70
+ "transformers_version": "4.57.6",
71
+ "ttt_config": {
72
+ "ags": 4,
73
+ "batch_size": 4,
74
+ "lora_alpha": 32.0,
75
+ "lora_rank": 8,
76
+ "lr": 0.0004,
77
+ "mask_ratio": 0.15,
78
+ "steps": 30
79
+ },
80
+ "use_cache": true,
81
+ "vocab_list": [
82
+ "<cls>",
83
+ "<pad>",
84
+ "<eos>",
85
+ "<unk>",
86
+ "L",
87
+ "A",
88
+ "G",
89
+ "V",
90
+ "S",
91
+ "E",
92
+ "R",
93
+ "T",
94
+ "I",
95
+ "D",
96
+ "P",
97
+ "K",
98
+ "Q",
99
+ "N",
100
+ "F",
101
+ "Y",
102
+ "M",
103
+ "H",
104
+ "W",
105
+ "C",
106
+ "X",
107
+ "B",
108
+ "U",
109
+ "Z",
110
+ "O",
111
+ ".",
112
+ "-",
113
+ "<null_1>",
114
+ "<mask>"
115
+ ],
116
+ "vocab_size": 33
117
+ }