AmelieSchreiber
commited on
Commit
•
35b297d
1
Parent(s):
a912e2f
Upload 11 files
Browse files- adapter_config.json +29 -0
- adapter_model.bin +3 -0
- added_tokens.json +7 -0
- optimizer.pt +3 -0
- rng_state.pth +3 -0
- scheduler.pt +3 -0
- special_tokens_map.json +7 -0
- tokenizer_config.json +54 -0
- trainer_state.json +147 -0
- training_args.bin +3 -0
- vocab.txt +33 -0
adapter_config.json
ADDED
@@ -0,0 +1,29 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"alpha_pattern": {},
|
3 |
+
"auto_mapping": null,
|
4 |
+
"base_model_name_or_path": "facebook/esm2_t6_8M_UR50D",
|
5 |
+
"bias": "none",
|
6 |
+
"fan_in_fan_out": false,
|
7 |
+
"inference_mode": true,
|
8 |
+
"init_lora_weights": true,
|
9 |
+
"layers_pattern": null,
|
10 |
+
"layers_to_transform": null,
|
11 |
+
"lora_alpha": 1,
|
12 |
+
"lora_dropout": 0.5,
|
13 |
+
"modules_to_save": null,
|
14 |
+
"peft_type": "LORA",
|
15 |
+
"r": 2,
|
16 |
+
"rank_pattern": {},
|
17 |
+
"revision": null,
|
18 |
+
"target_modules": [
|
19 |
+
"query",
|
20 |
+
"key",
|
21 |
+
"value",
|
22 |
+
"EsmSelfOutput.dense",
|
23 |
+
"EsmIntermediate.dense",
|
24 |
+
"EsmOutput.dense",
|
25 |
+
"EsmContactPredictionHead.regression",
|
26 |
+
"classifier"
|
27 |
+
],
|
28 |
+
"task_type": "TOKEN_CLS"
|
29 |
+
}
|
adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:44501128da965af2da76593044b359220b9cbd2c5b399bc9de7aac4197d83273
|
3 |
+
size 114991
|
added_tokens.json
ADDED
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"<cls>": 0,
|
3 |
+
"<eos>": 2,
|
4 |
+
"<mask>": 32,
|
5 |
+
"<pad>": 1,
|
6 |
+
"<unk>": 3
|
7 |
+
}
|
optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:550477f400ea5edc292478c534a1dae4e96fbbd3c25f393b7ce864fbce100b69
|
3 |
+
size 218073
|
rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:f4867cc190d63a633b96f2672fb906a1c6c53f31c353db36e79d6433f4038473
|
3 |
+
size 14575
|
scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:4bc87ecdf29595d0187df2e3c0721fbf08cc9aa799fab4c51aafa53363300bd1
|
3 |
+
size 627
|
special_tokens_map.json
ADDED
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"cls_token": "<cls>",
|
3 |
+
"eos_token": "<eos>",
|
4 |
+
"mask_token": "<mask>",
|
5 |
+
"pad_token": "<pad>",
|
6 |
+
"unk_token": "<unk>"
|
7 |
+
}
|
tokenizer_config.json
ADDED
@@ -0,0 +1,54 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"added_tokens_decoder": {
|
3 |
+
"0": {
|
4 |
+
"content": "<cls>",
|
5 |
+
"lstrip": false,
|
6 |
+
"normalized": false,
|
7 |
+
"rstrip": false,
|
8 |
+
"single_word": false,
|
9 |
+
"special": true
|
10 |
+
},
|
11 |
+
"1": {
|
12 |
+
"content": "<pad>",
|
13 |
+
"lstrip": false,
|
14 |
+
"normalized": false,
|
15 |
+
"rstrip": false,
|
16 |
+
"single_word": false,
|
17 |
+
"special": true
|
18 |
+
},
|
19 |
+
"2": {
|
20 |
+
"content": "<eos>",
|
21 |
+
"lstrip": false,
|
22 |
+
"normalized": false,
|
23 |
+
"rstrip": false,
|
24 |
+
"single_word": false,
|
25 |
+
"special": true
|
26 |
+
},
|
27 |
+
"3": {
|
28 |
+
"content": "<unk>",
|
29 |
+
"lstrip": false,
|
30 |
+
"normalized": false,
|
31 |
+
"rstrip": false,
|
32 |
+
"single_word": false,
|
33 |
+
"special": true
|
34 |
+
},
|
35 |
+
"32": {
|
36 |
+
"content": "<mask>",
|
37 |
+
"lstrip": false,
|
38 |
+
"normalized": false,
|
39 |
+
"rstrip": false,
|
40 |
+
"single_word": false,
|
41 |
+
"special": true
|
42 |
+
}
|
43 |
+
},
|
44 |
+
"additional_special_tokens": [],
|
45 |
+
"clean_up_tokenization_spaces": true,
|
46 |
+
"cls_token": "<cls>",
|
47 |
+
"eos_token": "<eos>",
|
48 |
+
"mask_token": "<mask>",
|
49 |
+
"model_max_length": 1024,
|
50 |
+
"pad_token": "<pad>",
|
51 |
+
"tokenizer_class": "EsmTokenizer",
|
52 |
+
"tokenizer_file": null,
|
53 |
+
"unk_token": "<unk>"
|
54 |
+
}
|
trainer_state.json
ADDED
@@ -0,0 +1,147 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.19848246486644372,
|
3 |
+
"best_model_checkpoint": "esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939",
|
4 |
+
"epoch": 1.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 3939,
|
7 |
+
"is_hyper_param_search": false,
|
8 |
+
"is_local_process_zero": true,
|
9 |
+
"is_world_process_zero": true,
|
10 |
+
"log_history": [
|
11 |
+
{
|
12 |
+
"epoch": 0.05,
|
13 |
+
"learning_rate": 0.0003700096638060586,
|
14 |
+
"loss": 0.5009,
|
15 |
+
"step": 200
|
16 |
+
},
|
17 |
+
{
|
18 |
+
"epoch": 0.1,
|
19 |
+
"learning_rate": 0.0003695684724487918,
|
20 |
+
"loss": 0.3725,
|
21 |
+
"step": 400
|
22 |
+
},
|
23 |
+
{
|
24 |
+
"epoch": 0.15,
|
25 |
+
"learning_rate": 0.00036883393302294926,
|
26 |
+
"loss": 0.3363,
|
27 |
+
"step": 600
|
28 |
+
},
|
29 |
+
{
|
30 |
+
"epoch": 0.2,
|
31 |
+
"learning_rate": 0.0003678072134814851,
|
32 |
+
"loss": 0.3171,
|
33 |
+
"step": 800
|
34 |
+
},
|
35 |
+
{
|
36 |
+
"epoch": 0.25,
|
37 |
+
"learning_rate": 0.0003664899463577655,
|
38 |
+
"loss": 0.3041,
|
39 |
+
"step": 1000
|
40 |
+
},
|
41 |
+
{
|
42 |
+
"epoch": 0.3,
|
43 |
+
"learning_rate": 0.00036488422616976233,
|
44 |
+
"loss": 0.2954,
|
45 |
+
"step": 1200
|
46 |
+
},
|
47 |
+
{
|
48 |
+
"epoch": 0.36,
|
49 |
+
"learning_rate": 0.0003629926060896693,
|
50 |
+
"loss": 0.2872,
|
51 |
+
"step": 1400
|
52 |
+
},
|
53 |
+
{
|
54 |
+
"epoch": 0.41,
|
55 |
+
"learning_rate": 0.00036081809388423475,
|
56 |
+
"loss": 0.2804,
|
57 |
+
"step": 1600
|
58 |
+
},
|
59 |
+
{
|
60 |
+
"epoch": 0.46,
|
61 |
+
"learning_rate": 0.0003583641471322691,
|
62 |
+
"loss": 0.2754,
|
63 |
+
"step": 1800
|
64 |
+
},
|
65 |
+
{
|
66 |
+
"epoch": 0.51,
|
67 |
+
"learning_rate": 0.00035563466772692797,
|
68 |
+
"loss": 0.2696,
|
69 |
+
"step": 2000
|
70 |
+
},
|
71 |
+
{
|
72 |
+
"epoch": 0.56,
|
73 |
+
"learning_rate": 0.0003526339956715147,
|
74 |
+
"loss": 0.2675,
|
75 |
+
"step": 2200
|
76 |
+
},
|
77 |
+
{
|
78 |
+
"epoch": 0.61,
|
79 |
+
"learning_rate": 0.00034936690217866705,
|
80 |
+
"loss": 0.2642,
|
81 |
+
"step": 2400
|
82 |
+
},
|
83 |
+
{
|
84 |
+
"epoch": 0.66,
|
85 |
+
"learning_rate": 0.00034583858208389975,
|
86 |
+
"loss": 0.262,
|
87 |
+
"step": 2600
|
88 |
+
},
|
89 |
+
{
|
90 |
+
"epoch": 0.71,
|
91 |
+
"learning_rate": 0.0003420546455855667,
|
92 |
+
"loss": 0.2592,
|
93 |
+
"step": 2800
|
94 |
+
},
|
95 |
+
{
|
96 |
+
"epoch": 0.76,
|
97 |
+
"learning_rate": 0.00033802110932437625,
|
98 |
+
"loss": 0.2565,
|
99 |
+
"step": 3000
|
100 |
+
},
|
101 |
+
{
|
102 |
+
"epoch": 0.81,
|
103 |
+
"learning_rate": 0.0003337443868166437,
|
104 |
+
"loss": 0.2542,
|
105 |
+
"step": 3200
|
106 |
+
},
|
107 |
+
{
|
108 |
+
"epoch": 0.86,
|
109 |
+
"learning_rate": 0.00032923127825649205,
|
110 |
+
"loss": 0.2509,
|
111 |
+
"step": 3400
|
112 |
+
},
|
113 |
+
{
|
114 |
+
"epoch": 0.91,
|
115 |
+
"learning_rate": 0.00032448895970321745,
|
116 |
+
"loss": 0.2509,
|
117 |
+
"step": 3600
|
118 |
+
},
|
119 |
+
{
|
120 |
+
"epoch": 0.96,
|
121 |
+
"learning_rate": 0.0003195249716710097,
|
122 |
+
"loss": 0.2464,
|
123 |
+
"step": 3800
|
124 |
+
},
|
125 |
+
{
|
126 |
+
"epoch": 1.0,
|
127 |
+
"eval_accuracy": 0.8625347674451358,
|
128 |
+
"eval_auc": 0.8222331548742136,
|
129 |
+
"eval_f1": 0.19848246486644372,
|
130 |
+
"eval_loss": 0.41490185260772705,
|
131 |
+
"eval_mcc": 0.2639007297474409,
|
132 |
+
"eval_precision": 0.11370668247419904,
|
133 |
+
"eval_recall": 0.7800926533683039,
|
134 |
+
"eval_runtime": 1163.712,
|
135 |
+
"eval_samples_per_second": 109.693,
|
136 |
+
"eval_steps_per_second": 1.714,
|
137 |
+
"step": 3939
|
138 |
+
}
|
139 |
+
],
|
140 |
+
"logging_steps": 200,
|
141 |
+
"max_steps": 15756,
|
142 |
+
"num_train_epochs": 4,
|
143 |
+
"save_steps": 500,
|
144 |
+
"total_flos": 2.0257292207917116e+16,
|
145 |
+
"trial_name": null,
|
146 |
+
"trial_params": null
|
147 |
+
}
|
training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:19560f827f37de980ef9907eb4a996feaadf6e4f6a723cacbef99fc7a0ba1b25
|
3 |
+
size 4155
|
vocab.txt
ADDED
@@ -0,0 +1,33 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
<cls>
|
2 |
+
<pad>
|
3 |
+
<eos>
|
4 |
+
<unk>
|
5 |
+
L
|
6 |
+
A
|
7 |
+
G
|
8 |
+
V
|
9 |
+
S
|
10 |
+
E
|
11 |
+
R
|
12 |
+
T
|
13 |
+
I
|
14 |
+
D
|
15 |
+
P
|
16 |
+
K
|
17 |
+
Q
|
18 |
+
N
|
19 |
+
F
|
20 |
+
Y
|
21 |
+
M
|
22 |
+
H
|
23 |
+
W
|
24 |
+
C
|
25 |
+
X
|
26 |
+
B
|
27 |
+
U
|
28 |
+
Z
|
29 |
+
O
|
30 |
+
.
|
31 |
+
-
|
32 |
+
<null_1>
|
33 |
+
<mask>
|