AmelieSchreiber
commited on
Commit
•
85c9414
1
Parent(s):
28bad80
Upload 36 files
Browse files- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/README.md +21 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/adapter_config.json +29 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/adapter_model.bin +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/added_tokens.json +7 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/optimizer.pt +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/rng_state.pth +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/scheduler.pt +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/special_tokens_map.json +7 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/tokenizer_config.json +54 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/trainer_state.json +359 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/training_args.bin +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/vocab.txt +33 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/README.md +21 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/adapter_config.json +29 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/adapter_model.bin +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/added_tokens.json +7 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/optimizer.pt +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/rng_state.pth +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/scheduler.pt +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/special_tokens_map.json +7 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/tokenizer_config.json +54 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/trainer_state.json +535 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/training_args.bin +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/vocab.txt +33 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/README.md +21 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/adapter_config.json +29 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/adapter_model.bin +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/added_tokens.json +7 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/optimizer.pt +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/rng_state.pth +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/scheduler.pt +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/special_tokens_map.json +7 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/tokenizer_config.json +54 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/trainer_state.json +189 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/training_args.bin +3 -0
- esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/vocab.txt +33 -0
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/README.md
ADDED
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
---
|
2 |
+
library_name: peft
|
3 |
+
---
|
4 |
+
## Training procedure
|
5 |
+
|
6 |
+
|
7 |
+
The following `bitsandbytes` quantization config was used during training:
|
8 |
+
- quant_method: bitsandbytes
|
9 |
+
- load_in_8bit: False
|
10 |
+
- load_in_4bit: True
|
11 |
+
- llm_int8_threshold: 6.0
|
12 |
+
- llm_int8_skip_modules: None
|
13 |
+
- llm_int8_enable_fp32_cpu_offload: False
|
14 |
+
- llm_int8_has_fp16_weight: False
|
15 |
+
- bnb_4bit_quant_type: nf4
|
16 |
+
- bnb_4bit_use_double_quant: True
|
17 |
+
- bnb_4bit_compute_dtype: bfloat16
|
18 |
+
### Framework versions
|
19 |
+
|
20 |
+
|
21 |
+
- PEFT 0.6.0.dev0
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/adapter_config.json
ADDED
@@ -0,0 +1,29 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"alpha_pattern": {},
|
3 |
+
"auto_mapping": null,
|
4 |
+
"base_model_name_or_path": "facebook/esm2_t12_35M_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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:61603f9daa3bc5426da6a9e63b9cd87357286d668b7e1bea44d3fbadd044ffa1
|
3 |
+
size 316315
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:66dd295f17f17a981b2542eb96066ea1cb61b5570e9d4878e71c30f67f72db63
|
3 |
+
size 613061
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:3825cc7bd56dd7de04ff391db0d3fba19f0e08a47cdd6ec62f6ae3d21bfe4519
|
3 |
+
size 14575
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:d8a7e486b2eaac07274ab77c32387d286c9a5d11eab8cd4b9575bcc5d00c2535
|
3 |
+
size 627
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/trainer_state.json
ADDED
@@ -0,0 +1,359 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.3534505903118732,
|
3 |
+
"best_model_checkpoint": "esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578",
|
4 |
+
"epoch": 2.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 10578,
|
7 |
+
"is_hyper_param_search": false,
|
8 |
+
"is_local_process_zero": true,
|
9 |
+
"is_world_process_zero": true,
|
10 |
+
"log_history": [
|
11 |
+
{
|
12 |
+
"epoch": 0.04,
|
13 |
+
"learning_rate": 0.0003700117150420716,
|
14 |
+
"loss": 0.4265,
|
15 |
+
"step": 200
|
16 |
+
},
|
17 |
+
{
|
18 |
+
"epoch": 0.08,
|
19 |
+
"learning_rate": 0.0003695766709151845,
|
20 |
+
"loss": 0.2446,
|
21 |
+
"step": 400
|
22 |
+
},
|
23 |
+
{
|
24 |
+
"epoch": 0.11,
|
25 |
+
"learning_rate": 0.00036885235529645174,
|
26 |
+
"loss": 0.1964,
|
27 |
+
"step": 600
|
28 |
+
},
|
29 |
+
{
|
30 |
+
"epoch": 0.15,
|
31 |
+
"learning_rate": 0.00036783990382720894,
|
32 |
+
"loss": 0.1714,
|
33 |
+
"step": 800
|
34 |
+
},
|
35 |
+
{
|
36 |
+
"epoch": 0.19,
|
37 |
+
"learning_rate": 0.000366540903911771,
|
38 |
+
"loss": 0.1556,
|
39 |
+
"step": 1000
|
40 |
+
},
|
41 |
+
{
|
42 |
+
"epoch": 0.23,
|
43 |
+
"learning_rate": 0.00036495739222857005,
|
44 |
+
"loss": 0.1454,
|
45 |
+
"step": 1200
|
46 |
+
},
|
47 |
+
{
|
48 |
+
"epoch": 0.26,
|
49 |
+
"learning_rate": 0.00036309185153688393,
|
50 |
+
"loss": 0.1387,
|
51 |
+
"step": 1400
|
52 |
+
},
|
53 |
+
{
|
54 |
+
"epoch": 0.3,
|
55 |
+
"learning_rate": 0.0003609472067841633,
|
56 |
+
"loss": 0.133,
|
57 |
+
"step": 1600
|
58 |
+
},
|
59 |
+
{
|
60 |
+
"epoch": 0.34,
|
61 |
+
"learning_rate": 0.0003585268205200591,
|
62 |
+
"loss": 0.1289,
|
63 |
+
"step": 1800
|
64 |
+
},
|
65 |
+
{
|
66 |
+
"epoch": 0.38,
|
67 |
+
"learning_rate": 0.0003558344876243421,
|
68 |
+
"loss": 0.1228,
|
69 |
+
"step": 2000
|
70 |
+
},
|
71 |
+
{
|
72 |
+
"epoch": 0.42,
|
73 |
+
"learning_rate": 0.0003528744293569798,
|
74 |
+
"loss": 0.1208,
|
75 |
+
"step": 2200
|
76 |
+
},
|
77 |
+
{
|
78 |
+
"epoch": 0.45,
|
79 |
+
"learning_rate": 0.00034965128673969907,
|
80 |
+
"loss": 0.1167,
|
81 |
+
"step": 2400
|
82 |
+
},
|
83 |
+
{
|
84 |
+
"epoch": 0.49,
|
85 |
+
"learning_rate": 0.0003461701132794125,
|
86 |
+
"loss": 0.1131,
|
87 |
+
"step": 2600
|
88 |
+
},
|
89 |
+
{
|
90 |
+
"epoch": 0.53,
|
91 |
+
"learning_rate": 0.0003424363670449164,
|
92 |
+
"loss": 0.1113,
|
93 |
+
"step": 2800
|
94 |
+
},
|
95 |
+
{
|
96 |
+
"epoch": 0.57,
|
97 |
+
"learning_rate": 0.00033845590210928363,
|
98 |
+
"loss": 0.1088,
|
99 |
+
"step": 3000
|
100 |
+
},
|
101 |
+
{
|
102 |
+
"epoch": 0.61,
|
103 |
+
"learning_rate": 0.00033423495937136847,
|
104 |
+
"loss": 0.1081,
|
105 |
+
"step": 3200
|
106 |
+
},
|
107 |
+
{
|
108 |
+
"epoch": 0.64,
|
109 |
+
"learning_rate": 0.00032978015677081454,
|
110 |
+
"loss": 0.1054,
|
111 |
+
"step": 3400
|
112 |
+
},
|
113 |
+
{
|
114 |
+
"epoch": 0.68,
|
115 |
+
"learning_rate": 0.00032509847891190683,
|
116 |
+
"loss": 0.1029,
|
117 |
+
"step": 3600
|
118 |
+
},
|
119 |
+
{
|
120 |
+
"epoch": 0.72,
|
121 |
+
"learning_rate": 0.0003201972661125376,
|
122 |
+
"loss": 0.102,
|
123 |
+
"step": 3800
|
124 |
+
},
|
125 |
+
{
|
126 |
+
"epoch": 0.76,
|
127 |
+
"learning_rate": 0.0003150842028954544,
|
128 |
+
"loss": 0.0999,
|
129 |
+
"step": 4000
|
130 |
+
},
|
131 |
+
{
|
132 |
+
"epoch": 0.79,
|
133 |
+
"learning_rate": 0.0003097673059398367,
|
134 |
+
"loss": 0.098,
|
135 |
+
"step": 4200
|
136 |
+
},
|
137 |
+
{
|
138 |
+
"epoch": 0.83,
|
139 |
+
"learning_rate": 0.00030425491151208934,
|
140 |
+
"loss": 0.0972,
|
141 |
+
"step": 4400
|
142 |
+
},
|
143 |
+
{
|
144 |
+
"epoch": 0.87,
|
145 |
+
"learning_rate": 0.00029855566239556173,
|
146 |
+
"loss": 0.0968,
|
147 |
+
"step": 4600
|
148 |
+
},
|
149 |
+
{
|
150 |
+
"epoch": 0.91,
|
151 |
+
"learning_rate": 0.0002926784943396845,
|
152 |
+
"loss": 0.0947,
|
153 |
+
"step": 4800
|
154 |
+
},
|
155 |
+
{
|
156 |
+
"epoch": 0.95,
|
157 |
+
"learning_rate": 0.00028663262204976965,
|
158 |
+
"loss": 0.0933,
|
159 |
+
"step": 5000
|
160 |
+
},
|
161 |
+
{
|
162 |
+
"epoch": 0.98,
|
163 |
+
"learning_rate": 0.00028042752473944106,
|
164 |
+
"loss": 0.094,
|
165 |
+
"step": 5200
|
166 |
+
},
|
167 |
+
{
|
168 |
+
"epoch": 1.0,
|
169 |
+
"eval_accuracy": 0.9297529150299436,
|
170 |
+
"eval_auc": 0.8167222019799886,
|
171 |
+
"eval_f1": 0.3440490710592986,
|
172 |
+
"eval_loss": 0.6011912822723389,
|
173 |
+
"eval_mcc": 0.3730152153022164,
|
174 |
+
"eval_precision": 0.22835223718675476,
|
175 |
+
"eval_recall": 0.697386656717114,
|
176 |
+
"eval_runtime": 3756.1015,
|
177 |
+
"eval_samples_per_second": 144.201,
|
178 |
+
"eval_steps_per_second": 0.687,
|
179 |
+
"step": 5289
|
180 |
+
},
|
181 |
+
{
|
182 |
+
"epoch": 1.02,
|
183 |
+
"learning_rate": 0.00027407293126834736,
|
184 |
+
"loss": 0.0924,
|
185 |
+
"step": 5400
|
186 |
+
},
|
187 |
+
{
|
188 |
+
"epoch": 1.06,
|
189 |
+
"learning_rate": 0.00026757880488845914,
|
190 |
+
"loss": 0.0912,
|
191 |
+
"step": 5600
|
192 |
+
},
|
193 |
+
{
|
194 |
+
"epoch": 1.1,
|
195 |
+
"learning_rate": 0.00026095532762286633,
|
196 |
+
"loss": 0.0902,
|
197 |
+
"step": 5800
|
198 |
+
},
|
199 |
+
{
|
200 |
+
"epoch": 1.13,
|
201 |
+
"learning_rate": 0.0002542128843015694,
|
202 |
+
"loss": 0.09,
|
203 |
+
"step": 6000
|
204 |
+
},
|
205 |
+
{
|
206 |
+
"epoch": 1.17,
|
207 |
+
"learning_rate": 0.00024739655239955165,
|
208 |
+
"loss": 0.0901,
|
209 |
+
"step": 6200
|
210 |
+
},
|
211 |
+
{
|
212 |
+
"epoch": 1.21,
|
213 |
+
"learning_rate": 0.00024048348750604134,
|
214 |
+
"loss": 0.0889,
|
215 |
+
"step": 6400
|
216 |
+
},
|
217 |
+
{
|
218 |
+
"epoch": 1.25,
|
219 |
+
"learning_rate": 0.00023344905030678293,
|
220 |
+
"loss": 0.0872,
|
221 |
+
"step": 6600
|
222 |
+
},
|
223 |
+
{
|
224 |
+
"epoch": 1.29,
|
225 |
+
"learning_rate": 0.00022633877364566408,
|
226 |
+
"loss": 0.0873,
|
227 |
+
"step": 6800
|
228 |
+
},
|
229 |
+
{
|
230 |
+
"epoch": 1.32,
|
231 |
+
"learning_rate": 0.0002191638055966375,
|
232 |
+
"loss": 0.0866,
|
233 |
+
"step": 7000
|
234 |
+
},
|
235 |
+
{
|
236 |
+
"epoch": 1.36,
|
237 |
+
"learning_rate": 0.00021193539566211078,
|
238 |
+
"loss": 0.0864,
|
239 |
+
"step": 7200
|
240 |
+
},
|
241 |
+
{
|
242 |
+
"epoch": 1.4,
|
243 |
+
"learning_rate": 0.00020466487713505563,
|
244 |
+
"loss": 0.085,
|
245 |
+
"step": 7400
|
246 |
+
},
|
247 |
+
{
|
248 |
+
"epoch": 1.44,
|
249 |
+
"learning_rate": 0.000197363649329743,
|
250 |
+
"loss": 0.086,
|
251 |
+
"step": 7600
|
252 |
+
},
|
253 |
+
{
|
254 |
+
"epoch": 1.47,
|
255 |
+
"learning_rate": 0.00019004315970896487,
|
256 |
+
"loss": 0.0847,
|
257 |
+
"step": 7800
|
258 |
+
},
|
259 |
+
{
|
260 |
+
"epoch": 1.51,
|
261 |
+
"learning_rate": 0.00018271488593576474,
|
262 |
+
"loss": 0.0836,
|
263 |
+
"step": 8000
|
264 |
+
},
|
265 |
+
{
|
266 |
+
"epoch": 1.55,
|
267 |
+
"learning_rate": 0.0001753903178778174,
|
268 |
+
"loss": 0.0844,
|
269 |
+
"step": 8200
|
270 |
+
},
|
271 |
+
{
|
272 |
+
"epoch": 1.59,
|
273 |
+
"learning_rate": 0.00016808093959267418,
|
274 |
+
"loss": 0.0828,
|
275 |
+
"step": 8400
|
276 |
+
},
|
277 |
+
{
|
278 |
+
"epoch": 1.63,
|
279 |
+
"learning_rate": 0.00016079821132211663,
|
280 |
+
"loss": 0.0848,
|
281 |
+
"step": 8600
|
282 |
+
},
|
283 |
+
{
|
284 |
+
"epoch": 1.66,
|
285 |
+
"learning_rate": 0.00015355355152385142,
|
286 |
+
"loss": 0.0826,
|
287 |
+
"step": 8800
|
288 |
+
},
|
289 |
+
{
|
290 |
+
"epoch": 1.7,
|
291 |
+
"learning_rate": 0.00014635831896871702,
|
292 |
+
"loss": 0.0826,
|
293 |
+
"step": 9000
|
294 |
+
},
|
295 |
+
{
|
296 |
+
"epoch": 1.74,
|
297 |
+
"learning_rate": 0.00013922379493147316,
|
298 |
+
"loss": 0.0833,
|
299 |
+
"step": 9200
|
300 |
+
},
|
301 |
+
{
|
302 |
+
"epoch": 1.78,
|
303 |
+
"learning_rate": 0.0001321611655030941,
|
304 |
+
"loss": 0.0816,
|
305 |
+
"step": 9400
|
306 |
+
},
|
307 |
+
{
|
308 |
+
"epoch": 1.82,
|
309 |
+
"learning_rate": 0.00012518150405229972,
|
310 |
+
"loss": 0.0817,
|
311 |
+
"step": 9600
|
312 |
+
},
|
313 |
+
{
|
314 |
+
"epoch": 1.85,
|
315 |
+
"learning_rate": 0.0001182957538638206,
|
316 |
+
"loss": 0.0827,
|
317 |
+
"step": 9800
|
318 |
+
},
|
319 |
+
{
|
320 |
+
"epoch": 1.89,
|
321 |
+
"learning_rate": 0.00011151471098062111,
|
322 |
+
"loss": 0.0807,
|
323 |
+
"step": 10000
|
324 |
+
},
|
325 |
+
{
|
326 |
+
"epoch": 1.93,
|
327 |
+
"learning_rate": 0.00010484900727697857,
|
328 |
+
"loss": 0.0818,
|
329 |
+
"step": 10200
|
330 |
+
},
|
331 |
+
{
|
332 |
+
"epoch": 1.97,
|
333 |
+
"learning_rate": 9.830909378896018e-05,
|
334 |
+
"loss": 0.0811,
|
335 |
+
"step": 10400
|
336 |
+
},
|
337 |
+
{
|
338 |
+
"epoch": 2.0,
|
339 |
+
"eval_accuracy": 0.9345128329975654,
|
340 |
+
"eval_auc": 0.8095464647248594,
|
341 |
+
"eval_f1": 0.3534505903118732,
|
342 |
+
"eval_loss": 0.646632730960846,
|
343 |
+
"eval_mcc": 0.37724366807619925,
|
344 |
+
"eval_precision": 0.23907868925380343,
|
345 |
+
"eval_recall": 0.6776094956043187,
|
346 |
+
"eval_runtime": 3741.5855,
|
347 |
+
"eval_samples_per_second": 144.761,
|
348 |
+
"eval_steps_per_second": 0.69,
|
349 |
+
"step": 10578
|
350 |
+
}
|
351 |
+
],
|
352 |
+
"logging_steps": 200,
|
353 |
+
"max_steps": 15867,
|
354 |
+
"num_train_epochs": 3,
|
355 |
+
"save_steps": 500,
|
356 |
+
"total_flos": 8.013035409672134e+17,
|
357 |
+
"trial_name": null,
|
358 |
+
"trial_params": null
|
359 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:b915c4deb5ba56cacb3593b78264a7c9bd0e44e5e5af7a361d94ad20b8ca1c89
|
3 |
+
size 4155
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-10578/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>
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/README.md
ADDED
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
---
|
2 |
+
library_name: peft
|
3 |
+
---
|
4 |
+
## Training procedure
|
5 |
+
|
6 |
+
|
7 |
+
The following `bitsandbytes` quantization config was used during training:
|
8 |
+
- quant_method: bitsandbytes
|
9 |
+
- load_in_8bit: False
|
10 |
+
- load_in_4bit: True
|
11 |
+
- llm_int8_threshold: 6.0
|
12 |
+
- llm_int8_skip_modules: None
|
13 |
+
- llm_int8_enable_fp32_cpu_offload: False
|
14 |
+
- llm_int8_has_fp16_weight: False
|
15 |
+
- bnb_4bit_quant_type: nf4
|
16 |
+
- bnb_4bit_use_double_quant: True
|
17 |
+
- bnb_4bit_compute_dtype: bfloat16
|
18 |
+
### Framework versions
|
19 |
+
|
20 |
+
|
21 |
+
- PEFT 0.6.0.dev0
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/adapter_config.json
ADDED
@@ -0,0 +1,29 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"alpha_pattern": {},
|
3 |
+
"auto_mapping": null,
|
4 |
+
"base_model_name_or_path": "facebook/esm2_t12_35M_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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:ba4edd057f3a0bc2a442f8477de0e0ea8035db2595747ba855e70bd963307e3b
|
3 |
+
size 316315
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:ac484a31bf2f2adfd47adeae9e731c1edd93bc3a1a02bc0f0c4da3c2e52addee
|
3 |
+
size 613061
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:e15e4908e305ead99c37b0c73cda396d47059d09d3389e311282bf02b9b21f8d
|
3 |
+
size 14575
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:55939009af75a35b0d684fd3fd80e9b6bc79f81fc341707729eb4dbfe06fb08c
|
3 |
+
size 627
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/trainer_state.json
ADDED
@@ -0,0 +1,535 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.35447033515145,
|
3 |
+
"best_model_checkpoint": "esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867",
|
4 |
+
"epoch": 3.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 15867,
|
7 |
+
"is_hyper_param_search": false,
|
8 |
+
"is_local_process_zero": true,
|
9 |
+
"is_world_process_zero": true,
|
10 |
+
"log_history": [
|
11 |
+
{
|
12 |
+
"epoch": 0.04,
|
13 |
+
"learning_rate": 0.0003700117150420716,
|
14 |
+
"loss": 0.4265,
|
15 |
+
"step": 200
|
16 |
+
},
|
17 |
+
{
|
18 |
+
"epoch": 0.08,
|
19 |
+
"learning_rate": 0.0003695766709151845,
|
20 |
+
"loss": 0.2446,
|
21 |
+
"step": 400
|
22 |
+
},
|
23 |
+
{
|
24 |
+
"epoch": 0.11,
|
25 |
+
"learning_rate": 0.00036885235529645174,
|
26 |
+
"loss": 0.1964,
|
27 |
+
"step": 600
|
28 |
+
},
|
29 |
+
{
|
30 |
+
"epoch": 0.15,
|
31 |
+
"learning_rate": 0.00036783990382720894,
|
32 |
+
"loss": 0.1714,
|
33 |
+
"step": 800
|
34 |
+
},
|
35 |
+
{
|
36 |
+
"epoch": 0.19,
|
37 |
+
"learning_rate": 0.000366540903911771,
|
38 |
+
"loss": 0.1556,
|
39 |
+
"step": 1000
|
40 |
+
},
|
41 |
+
{
|
42 |
+
"epoch": 0.23,
|
43 |
+
"learning_rate": 0.00036495739222857005,
|
44 |
+
"loss": 0.1454,
|
45 |
+
"step": 1200
|
46 |
+
},
|
47 |
+
{
|
48 |
+
"epoch": 0.26,
|
49 |
+
"learning_rate": 0.00036309185153688393,
|
50 |
+
"loss": 0.1387,
|
51 |
+
"step": 1400
|
52 |
+
},
|
53 |
+
{
|
54 |
+
"epoch": 0.3,
|
55 |
+
"learning_rate": 0.0003609472067841633,
|
56 |
+
"loss": 0.133,
|
57 |
+
"step": 1600
|
58 |
+
},
|
59 |
+
{
|
60 |
+
"epoch": 0.34,
|
61 |
+
"learning_rate": 0.0003585268205200591,
|
62 |
+
"loss": 0.1289,
|
63 |
+
"step": 1800
|
64 |
+
},
|
65 |
+
{
|
66 |
+
"epoch": 0.38,
|
67 |
+
"learning_rate": 0.0003558344876243421,
|
68 |
+
"loss": 0.1228,
|
69 |
+
"step": 2000
|
70 |
+
},
|
71 |
+
{
|
72 |
+
"epoch": 0.42,
|
73 |
+
"learning_rate": 0.0003528744293569798,
|
74 |
+
"loss": 0.1208,
|
75 |
+
"step": 2200
|
76 |
+
},
|
77 |
+
{
|
78 |
+
"epoch": 0.45,
|
79 |
+
"learning_rate": 0.00034965128673969907,
|
80 |
+
"loss": 0.1167,
|
81 |
+
"step": 2400
|
82 |
+
},
|
83 |
+
{
|
84 |
+
"epoch": 0.49,
|
85 |
+
"learning_rate": 0.0003461701132794125,
|
86 |
+
"loss": 0.1131,
|
87 |
+
"step": 2600
|
88 |
+
},
|
89 |
+
{
|
90 |
+
"epoch": 0.53,
|
91 |
+
"learning_rate": 0.0003424363670449164,
|
92 |
+
"loss": 0.1113,
|
93 |
+
"step": 2800
|
94 |
+
},
|
95 |
+
{
|
96 |
+
"epoch": 0.57,
|
97 |
+
"learning_rate": 0.00033845590210928363,
|
98 |
+
"loss": 0.1088,
|
99 |
+
"step": 3000
|
100 |
+
},
|
101 |
+
{
|
102 |
+
"epoch": 0.61,
|
103 |
+
"learning_rate": 0.00033423495937136847,
|
104 |
+
"loss": 0.1081,
|
105 |
+
"step": 3200
|
106 |
+
},
|
107 |
+
{
|
108 |
+
"epoch": 0.64,
|
109 |
+
"learning_rate": 0.00032978015677081454,
|
110 |
+
"loss": 0.1054,
|
111 |
+
"step": 3400
|
112 |
+
},
|
113 |
+
{
|
114 |
+
"epoch": 0.68,
|
115 |
+
"learning_rate": 0.00032509847891190683,
|
116 |
+
"loss": 0.1029,
|
117 |
+
"step": 3600
|
118 |
+
},
|
119 |
+
{
|
120 |
+
"epoch": 0.72,
|
121 |
+
"learning_rate": 0.0003201972661125376,
|
122 |
+
"loss": 0.102,
|
123 |
+
"step": 3800
|
124 |
+
},
|
125 |
+
{
|
126 |
+
"epoch": 0.76,
|
127 |
+
"learning_rate": 0.0003150842028954544,
|
128 |
+
"loss": 0.0999,
|
129 |
+
"step": 4000
|
130 |
+
},
|
131 |
+
{
|
132 |
+
"epoch": 0.79,
|
133 |
+
"learning_rate": 0.0003097673059398367,
|
134 |
+
"loss": 0.098,
|
135 |
+
"step": 4200
|
136 |
+
},
|
137 |
+
{
|
138 |
+
"epoch": 0.83,
|
139 |
+
"learning_rate": 0.00030425491151208934,
|
140 |
+
"loss": 0.0972,
|
141 |
+
"step": 4400
|
142 |
+
},
|
143 |
+
{
|
144 |
+
"epoch": 0.87,
|
145 |
+
"learning_rate": 0.00029855566239556173,
|
146 |
+
"loss": 0.0968,
|
147 |
+
"step": 4600
|
148 |
+
},
|
149 |
+
{
|
150 |
+
"epoch": 0.91,
|
151 |
+
"learning_rate": 0.0002926784943396845,
|
152 |
+
"loss": 0.0947,
|
153 |
+
"step": 4800
|
154 |
+
},
|
155 |
+
{
|
156 |
+
"epoch": 0.95,
|
157 |
+
"learning_rate": 0.00028663262204976965,
|
158 |
+
"loss": 0.0933,
|
159 |
+
"step": 5000
|
160 |
+
},
|
161 |
+
{
|
162 |
+
"epoch": 0.98,
|
163 |
+
"learning_rate": 0.00028042752473944106,
|
164 |
+
"loss": 0.094,
|
165 |
+
"step": 5200
|
166 |
+
},
|
167 |
+
{
|
168 |
+
"epoch": 1.0,
|
169 |
+
"eval_accuracy": 0.9297529150299436,
|
170 |
+
"eval_auc": 0.8167222019799886,
|
171 |
+
"eval_f1": 0.3440490710592986,
|
172 |
+
"eval_loss": 0.6011912822723389,
|
173 |
+
"eval_mcc": 0.3730152153022164,
|
174 |
+
"eval_precision": 0.22835223718675476,
|
175 |
+
"eval_recall": 0.697386656717114,
|
176 |
+
"eval_runtime": 3756.1015,
|
177 |
+
"eval_samples_per_second": 144.201,
|
178 |
+
"eval_steps_per_second": 0.687,
|
179 |
+
"step": 5289
|
180 |
+
},
|
181 |
+
{
|
182 |
+
"epoch": 1.02,
|
183 |
+
"learning_rate": 0.00027407293126834736,
|
184 |
+
"loss": 0.0924,
|
185 |
+
"step": 5400
|
186 |
+
},
|
187 |
+
{
|
188 |
+
"epoch": 1.06,
|
189 |
+
"learning_rate": 0.00026757880488845914,
|
190 |
+
"loss": 0.0912,
|
191 |
+
"step": 5600
|
192 |
+
},
|
193 |
+
{
|
194 |
+
"epoch": 1.1,
|
195 |
+
"learning_rate": 0.00026095532762286633,
|
196 |
+
"loss": 0.0902,
|
197 |
+
"step": 5800
|
198 |
+
},
|
199 |
+
{
|
200 |
+
"epoch": 1.13,
|
201 |
+
"learning_rate": 0.0002542128843015694,
|
202 |
+
"loss": 0.09,
|
203 |
+
"step": 6000
|
204 |
+
},
|
205 |
+
{
|
206 |
+
"epoch": 1.17,
|
207 |
+
"learning_rate": 0.00024739655239955165,
|
208 |
+
"loss": 0.0901,
|
209 |
+
"step": 6200
|
210 |
+
},
|
211 |
+
{
|
212 |
+
"epoch": 1.21,
|
213 |
+
"learning_rate": 0.00024048348750604134,
|
214 |
+
"loss": 0.0889,
|
215 |
+
"step": 6400
|
216 |
+
},
|
217 |
+
{
|
218 |
+
"epoch": 1.25,
|
219 |
+
"learning_rate": 0.00023344905030678293,
|
220 |
+
"loss": 0.0872,
|
221 |
+
"step": 6600
|
222 |
+
},
|
223 |
+
{
|
224 |
+
"epoch": 1.29,
|
225 |
+
"learning_rate": 0.00022633877364566408,
|
226 |
+
"loss": 0.0873,
|
227 |
+
"step": 6800
|
228 |
+
},
|
229 |
+
{
|
230 |
+
"epoch": 1.32,
|
231 |
+
"learning_rate": 0.0002191638055966375,
|
232 |
+
"loss": 0.0866,
|
233 |
+
"step": 7000
|
234 |
+
},
|
235 |
+
{
|
236 |
+
"epoch": 1.36,
|
237 |
+
"learning_rate": 0.00021193539566211078,
|
238 |
+
"loss": 0.0864,
|
239 |
+
"step": 7200
|
240 |
+
},
|
241 |
+
{
|
242 |
+
"epoch": 1.4,
|
243 |
+
"learning_rate": 0.00020466487713505563,
|
244 |
+
"loss": 0.085,
|
245 |
+
"step": 7400
|
246 |
+
},
|
247 |
+
{
|
248 |
+
"epoch": 1.44,
|
249 |
+
"learning_rate": 0.000197363649329743,
|
250 |
+
"loss": 0.086,
|
251 |
+
"step": 7600
|
252 |
+
},
|
253 |
+
{
|
254 |
+
"epoch": 1.47,
|
255 |
+
"learning_rate": 0.00019004315970896487,
|
256 |
+
"loss": 0.0847,
|
257 |
+
"step": 7800
|
258 |
+
},
|
259 |
+
{
|
260 |
+
"epoch": 1.51,
|
261 |
+
"learning_rate": 0.00018271488593576474,
|
262 |
+
"loss": 0.0836,
|
263 |
+
"step": 8000
|
264 |
+
},
|
265 |
+
{
|
266 |
+
"epoch": 1.55,
|
267 |
+
"learning_rate": 0.0001753903178778174,
|
268 |
+
"loss": 0.0844,
|
269 |
+
"step": 8200
|
270 |
+
},
|
271 |
+
{
|
272 |
+
"epoch": 1.59,
|
273 |
+
"learning_rate": 0.00016808093959267418,
|
274 |
+
"loss": 0.0828,
|
275 |
+
"step": 8400
|
276 |
+
},
|
277 |
+
{
|
278 |
+
"epoch": 1.63,
|
279 |
+
"learning_rate": 0.00016079821132211663,
|
280 |
+
"loss": 0.0848,
|
281 |
+
"step": 8600
|
282 |
+
},
|
283 |
+
{
|
284 |
+
"epoch": 1.66,
|
285 |
+
"learning_rate": 0.00015355355152385142,
|
286 |
+
"loss": 0.0826,
|
287 |
+
"step": 8800
|
288 |
+
},
|
289 |
+
{
|
290 |
+
"epoch": 1.7,
|
291 |
+
"learning_rate": 0.00014635831896871702,
|
292 |
+
"loss": 0.0826,
|
293 |
+
"step": 9000
|
294 |
+
},
|
295 |
+
{
|
296 |
+
"epoch": 1.74,
|
297 |
+
"learning_rate": 0.00013922379493147316,
|
298 |
+
"loss": 0.0833,
|
299 |
+
"step": 9200
|
300 |
+
},
|
301 |
+
{
|
302 |
+
"epoch": 1.78,
|
303 |
+
"learning_rate": 0.0001321611655030941,
|
304 |
+
"loss": 0.0816,
|
305 |
+
"step": 9400
|
306 |
+
},
|
307 |
+
{
|
308 |
+
"epoch": 1.82,
|
309 |
+
"learning_rate": 0.00012518150405229972,
|
310 |
+
"loss": 0.0817,
|
311 |
+
"step": 9600
|
312 |
+
},
|
313 |
+
{
|
314 |
+
"epoch": 1.85,
|
315 |
+
"learning_rate": 0.0001182957538638206,
|
316 |
+
"loss": 0.0827,
|
317 |
+
"step": 9800
|
318 |
+
},
|
319 |
+
{
|
320 |
+
"epoch": 1.89,
|
321 |
+
"learning_rate": 0.00011151471098062111,
|
322 |
+
"loss": 0.0807,
|
323 |
+
"step": 10000
|
324 |
+
},
|
325 |
+
{
|
326 |
+
"epoch": 1.93,
|
327 |
+
"learning_rate": 0.00010484900727697857,
|
328 |
+
"loss": 0.0818,
|
329 |
+
"step": 10200
|
330 |
+
},
|
331 |
+
{
|
332 |
+
"epoch": 1.97,
|
333 |
+
"learning_rate": 9.830909378896018e-05,
|
334 |
+
"loss": 0.0811,
|
335 |
+
"step": 10400
|
336 |
+
},
|
337 |
+
{
|
338 |
+
"epoch": 2.0,
|
339 |
+
"eval_accuracy": 0.9345128329975654,
|
340 |
+
"eval_auc": 0.8095464647248594,
|
341 |
+
"eval_f1": 0.3534505903118732,
|
342 |
+
"eval_loss": 0.646632730960846,
|
343 |
+
"eval_mcc": 0.37724366807619925,
|
344 |
+
"eval_precision": 0.23907868925380343,
|
345 |
+
"eval_recall": 0.6776094956043187,
|
346 |
+
"eval_runtime": 3741.5855,
|
347 |
+
"eval_samples_per_second": 144.761,
|
348 |
+
"eval_steps_per_second": 0.69,
|
349 |
+
"step": 10578
|
350 |
+
},
|
351 |
+
{
|
352 |
+
"epoch": 2.0,
|
353 |
+
"learning_rate": 9.19368885647311e-05,
|
354 |
+
"loss": 0.0811,
|
355 |
+
"step": 10600
|
356 |
+
},
|
357 |
+
{
|
358 |
+
"epoch": 2.04,
|
359 |
+
"learning_rate": 8.567834861656006e-05,
|
360 |
+
"loss": 0.0807,
|
361 |
+
"step": 10800
|
362 |
+
},
|
363 |
+
{
|
364 |
+
"epoch": 2.08,
|
365 |
+
"learning_rate": 7.960576607056005e-05,
|
366 |
+
"loss": 0.0804,
|
367 |
+
"step": 11000
|
368 |
+
},
|
369 |
+
{
|
370 |
+
"epoch": 2.12,
|
371 |
+
"learning_rate": 7.3667639053756e-05,
|
372 |
+
"loss": 0.0814,
|
373 |
+
"step": 11200
|
374 |
+
},
|
375 |
+
{
|
376 |
+
"epoch": 2.16,
|
377 |
+
"learning_rate": 6.790419095486784e-05,
|
378 |
+
"loss": 0.0806,
|
379 |
+
"step": 11400
|
380 |
+
},
|
381 |
+
{
|
382 |
+
"epoch": 2.19,
|
383 |
+
"learning_rate": 6.232445817974756e-05,
|
384 |
+
"loss": 0.0801,
|
385 |
+
"step": 11600
|
386 |
+
},
|
387 |
+
{
|
388 |
+
"epoch": 2.23,
|
389 |
+
"learning_rate": 5.6937189090319155e-05,
|
390 |
+
"loss": 0.0791,
|
391 |
+
"step": 11800
|
392 |
+
},
|
393 |
+
{
|
394 |
+
"epoch": 2.27,
|
395 |
+
"learning_rate": 5.1750830288181386e-05,
|
396 |
+
"loss": 0.0803,
|
397 |
+
"step": 12000
|
398 |
+
},
|
399 |
+
{
|
400 |
+
"epoch": 2.31,
|
401 |
+
"learning_rate": 4.677351337133321e-05,
|
402 |
+
"loss": 0.0802,
|
403 |
+
"step": 12200
|
404 |
+
},
|
405 |
+
{
|
406 |
+
"epoch": 2.34,
|
407 |
+
"learning_rate": 4.2013042184789433e-05,
|
408 |
+
"loss": 0.0786,
|
409 |
+
"step": 12400
|
410 |
+
},
|
411 |
+
{
|
412 |
+
"epoch": 2.38,
|
413 |
+
"learning_rate": 3.7476880585072944e-05,
|
414 |
+
"loss": 0.0792,
|
415 |
+
"step": 12600
|
416 |
+
},
|
417 |
+
{
|
418 |
+
"epoch": 2.42,
|
419 |
+
"learning_rate": 3.317214073776957e-05,
|
420 |
+
"loss": 0.0798,
|
421 |
+
"step": 12800
|
422 |
+
},
|
423 |
+
{
|
424 |
+
"epoch": 2.46,
|
425 |
+
"learning_rate": 2.9105571966492357e-05,
|
426 |
+
"loss": 0.0784,
|
427 |
+
"step": 13000
|
428 |
+
},
|
429 |
+
{
|
430 |
+
"epoch": 2.5,
|
431 |
+
"learning_rate": 2.5302041894688252e-05,
|
432 |
+
"loss": 0.079,
|
433 |
+
"step": 13200
|
434 |
+
},
|
435 |
+
{
|
436 |
+
"epoch": 2.53,
|
437 |
+
"learning_rate": 2.172929259566275e-05,
|
438 |
+
"loss": 0.0787,
|
439 |
+
"step": 13400
|
440 |
+
},
|
441 |
+
{
|
442 |
+
"epoch": 2.57,
|
443 |
+
"learning_rate": 1.8412655406943377e-05,
|
444 |
+
"loss": 0.0791,
|
445 |
+
"step": 13600
|
446 |
+
},
|
447 |
+
{
|
448 |
+
"epoch": 2.61,
|
449 |
+
"learning_rate": 1.5357330423887333e-05,
|
450 |
+
"loss": 0.0795,
|
451 |
+
"step": 13800
|
452 |
+
},
|
453 |
+
{
|
454 |
+
"epoch": 2.65,
|
455 |
+
"learning_rate": 1.2568108035179009e-05,
|
456 |
+
"loss": 0.0785,
|
457 |
+
"step": 14000
|
458 |
+
},
|
459 |
+
{
|
460 |
+
"epoch": 2.68,
|
461 |
+
"learning_rate": 1.0049361412066457e-05,
|
462 |
+
"loss": 0.0777,
|
463 |
+
"step": 14200
|
464 |
+
},
|
465 |
+
{
|
466 |
+
"epoch": 2.72,
|
467 |
+
"learning_rate": 7.805039651745196e-06,
|
468 |
+
"loss": 0.0781,
|
469 |
+
"step": 14400
|
470 |
+
},
|
471 |
+
{
|
472 |
+
"epoch": 2.76,
|
473 |
+
"learning_rate": 5.838661585640596e-06,
|
474 |
+
"loss": 0.0801,
|
475 |
+
"step": 14600
|
476 |
+
},
|
477 |
+
{
|
478 |
+
"epoch": 2.8,
|
479 |
+
"learning_rate": 4.153310262295508e-06,
|
480 |
+
"loss": 0.0782,
|
481 |
+
"step": 14800
|
482 |
+
},
|
483 |
+
{
|
484 |
+
"epoch": 2.84,
|
485 |
+
"learning_rate": 2.7516281135145465e-06,
|
486 |
+
"loss": 0.0782,
|
487 |
+
"step": 15000
|
488 |
+
},
|
489 |
+
{
|
490 |
+
"epoch": 2.87,
|
491 |
+
"learning_rate": 1.6358128113430393e-06,
|
492 |
+
"loss": 0.0775,
|
493 |
+
"step": 15200
|
494 |
+
},
|
495 |
+
{
|
496 |
+
"epoch": 2.91,
|
497 |
+
"learning_rate": 8.076138223768694e-07,
|
498 |
+
"loss": 0.0786,
|
499 |
+
"step": 15400
|
500 |
+
},
|
501 |
+
{
|
502 |
+
"epoch": 2.95,
|
503 |
+
"learning_rate": 2.6832966480547197e-07,
|
504 |
+
"loss": 0.0776,
|
505 |
+
"step": 15600
|
506 |
+
},
|
507 |
+
{
|
508 |
+
"epoch": 2.99,
|
509 |
+
"learning_rate": 1.8805872488762563e-08,
|
510 |
+
"loss": 0.0785,
|
511 |
+
"step": 15800
|
512 |
+
},
|
513 |
+
{
|
514 |
+
"epoch": 3.0,
|
515 |
+
"eval_accuracy": 0.9350567264686818,
|
516 |
+
"eval_auc": 0.8085491733369476,
|
517 |
+
"eval_f1": 0.35447033515145,
|
518 |
+
"eval_loss": 0.6618000268936157,
|
519 |
+
"eval_mcc": 0.3776148132284474,
|
520 |
+
"eval_precision": 0.24034378012664542,
|
521 |
+
"eval_recall": 0.6749850523517478,
|
522 |
+
"eval_runtime": 3760.204,
|
523 |
+
"eval_samples_per_second": 144.044,
|
524 |
+
"eval_steps_per_second": 0.686,
|
525 |
+
"step": 15867
|
526 |
+
}
|
527 |
+
],
|
528 |
+
"logging_steps": 200,
|
529 |
+
"max_steps": 15867,
|
530 |
+
"num_train_epochs": 3,
|
531 |
+
"save_steps": 500,
|
532 |
+
"total_flos": 1.20195531145082e+18,
|
533 |
+
"trial_name": null,
|
534 |
+
"trial_params": null
|
535 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:b915c4deb5ba56cacb3593b78264a7c9bd0e44e5e5af7a361d94ad20b8ca1c89
|
3 |
+
size 4155
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-15867/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>
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/README.md
ADDED
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
---
|
2 |
+
library_name: peft
|
3 |
+
---
|
4 |
+
## Training procedure
|
5 |
+
|
6 |
+
|
7 |
+
The following `bitsandbytes` quantization config was used during training:
|
8 |
+
- quant_method: bitsandbytes
|
9 |
+
- load_in_8bit: False
|
10 |
+
- load_in_4bit: True
|
11 |
+
- llm_int8_threshold: 6.0
|
12 |
+
- llm_int8_skip_modules: None
|
13 |
+
- llm_int8_enable_fp32_cpu_offload: False
|
14 |
+
- llm_int8_has_fp16_weight: False
|
15 |
+
- bnb_4bit_quant_type: nf4
|
16 |
+
- bnb_4bit_use_double_quant: True
|
17 |
+
- bnb_4bit_compute_dtype: bfloat16
|
18 |
+
### Framework versions
|
19 |
+
|
20 |
+
|
21 |
+
- PEFT 0.6.0.dev0
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/adapter_config.json
ADDED
@@ -0,0 +1,29 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"alpha_pattern": {},
|
3 |
+
"auto_mapping": null,
|
4 |
+
"base_model_name_or_path": "facebook/esm2_t12_35M_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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:43b452dd060767dd70f47cedeaf44542b697374130a372bf310a1f45bd6c156f
|
3 |
+
size 316315
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:0246b16ad2a4ff5346cc7cd436d9865710a83f218ce64578c913184989a1485a
|
3 |
+
size 613061
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:cd9c5833a930482059798aab998f33fa3d0167a6fcf4b32dba0ae0b19178c0c2
|
3 |
+
size 14575
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:081e2d3bd93b47a1a918240d8077826ebb0b43206a9f65cc14d171889238fc62
|
3 |
+
size 627
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/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 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/trainer_state.json
ADDED
@@ -0,0 +1,189 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.3440490710592986,
|
3 |
+
"best_model_checkpoint": "esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289",
|
4 |
+
"epoch": 1.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 5289,
|
7 |
+
"is_hyper_param_search": false,
|
8 |
+
"is_local_process_zero": true,
|
9 |
+
"is_world_process_zero": true,
|
10 |
+
"log_history": [
|
11 |
+
{
|
12 |
+
"epoch": 0.04,
|
13 |
+
"learning_rate": 0.0003700117150420716,
|
14 |
+
"loss": 0.4265,
|
15 |
+
"step": 200
|
16 |
+
},
|
17 |
+
{
|
18 |
+
"epoch": 0.08,
|
19 |
+
"learning_rate": 0.0003695766709151845,
|
20 |
+
"loss": 0.2446,
|
21 |
+
"step": 400
|
22 |
+
},
|
23 |
+
{
|
24 |
+
"epoch": 0.11,
|
25 |
+
"learning_rate": 0.00036885235529645174,
|
26 |
+
"loss": 0.1964,
|
27 |
+
"step": 600
|
28 |
+
},
|
29 |
+
{
|
30 |
+
"epoch": 0.15,
|
31 |
+
"learning_rate": 0.00036783990382720894,
|
32 |
+
"loss": 0.1714,
|
33 |
+
"step": 800
|
34 |
+
},
|
35 |
+
{
|
36 |
+
"epoch": 0.19,
|
37 |
+
"learning_rate": 0.000366540903911771,
|
38 |
+
"loss": 0.1556,
|
39 |
+
"step": 1000
|
40 |
+
},
|
41 |
+
{
|
42 |
+
"epoch": 0.23,
|
43 |
+
"learning_rate": 0.00036495739222857005,
|
44 |
+
"loss": 0.1454,
|
45 |
+
"step": 1200
|
46 |
+
},
|
47 |
+
{
|
48 |
+
"epoch": 0.26,
|
49 |
+
"learning_rate": 0.00036309185153688393,
|
50 |
+
"loss": 0.1387,
|
51 |
+
"step": 1400
|
52 |
+
},
|
53 |
+
{
|
54 |
+
"epoch": 0.3,
|
55 |
+
"learning_rate": 0.0003609472067841633,
|
56 |
+
"loss": 0.133,
|
57 |
+
"step": 1600
|
58 |
+
},
|
59 |
+
{
|
60 |
+
"epoch": 0.34,
|
61 |
+
"learning_rate": 0.0003585268205200591,
|
62 |
+
"loss": 0.1289,
|
63 |
+
"step": 1800
|
64 |
+
},
|
65 |
+
{
|
66 |
+
"epoch": 0.38,
|
67 |
+
"learning_rate": 0.0003558344876243421,
|
68 |
+
"loss": 0.1228,
|
69 |
+
"step": 2000
|
70 |
+
},
|
71 |
+
{
|
72 |
+
"epoch": 0.42,
|
73 |
+
"learning_rate": 0.0003528744293569798,
|
74 |
+
"loss": 0.1208,
|
75 |
+
"step": 2200
|
76 |
+
},
|
77 |
+
{
|
78 |
+
"epoch": 0.45,
|
79 |
+
"learning_rate": 0.00034965128673969907,
|
80 |
+
"loss": 0.1167,
|
81 |
+
"step": 2400
|
82 |
+
},
|
83 |
+
{
|
84 |
+
"epoch": 0.49,
|
85 |
+
"learning_rate": 0.0003461701132794125,
|
86 |
+
"loss": 0.1131,
|
87 |
+
"step": 2600
|
88 |
+
},
|
89 |
+
{
|
90 |
+
"epoch": 0.53,
|
91 |
+
"learning_rate": 0.0003424363670449164,
|
92 |
+
"loss": 0.1113,
|
93 |
+
"step": 2800
|
94 |
+
},
|
95 |
+
{
|
96 |
+
"epoch": 0.57,
|
97 |
+
"learning_rate": 0.00033845590210928363,
|
98 |
+
"loss": 0.1088,
|
99 |
+
"step": 3000
|
100 |
+
},
|
101 |
+
{
|
102 |
+
"epoch": 0.61,
|
103 |
+
"learning_rate": 0.00033423495937136847,
|
104 |
+
"loss": 0.1081,
|
105 |
+
"step": 3200
|
106 |
+
},
|
107 |
+
{
|
108 |
+
"epoch": 0.64,
|
109 |
+
"learning_rate": 0.00032978015677081454,
|
110 |
+
"loss": 0.1054,
|
111 |
+
"step": 3400
|
112 |
+
},
|
113 |
+
{
|
114 |
+
"epoch": 0.68,
|
115 |
+
"learning_rate": 0.00032509847891190683,
|
116 |
+
"loss": 0.1029,
|
117 |
+
"step": 3600
|
118 |
+
},
|
119 |
+
{
|
120 |
+
"epoch": 0.72,
|
121 |
+
"learning_rate": 0.0003201972661125376,
|
122 |
+
"loss": 0.102,
|
123 |
+
"step": 3800
|
124 |
+
},
|
125 |
+
{
|
126 |
+
"epoch": 0.76,
|
127 |
+
"learning_rate": 0.0003150842028954544,
|
128 |
+
"loss": 0.0999,
|
129 |
+
"step": 4000
|
130 |
+
},
|
131 |
+
{
|
132 |
+
"epoch": 0.79,
|
133 |
+
"learning_rate": 0.0003097673059398367,
|
134 |
+
"loss": 0.098,
|
135 |
+
"step": 4200
|
136 |
+
},
|
137 |
+
{
|
138 |
+
"epoch": 0.83,
|
139 |
+
"learning_rate": 0.00030425491151208934,
|
140 |
+
"loss": 0.0972,
|
141 |
+
"step": 4400
|
142 |
+
},
|
143 |
+
{
|
144 |
+
"epoch": 0.87,
|
145 |
+
"learning_rate": 0.00029855566239556173,
|
146 |
+
"loss": 0.0968,
|
147 |
+
"step": 4600
|
148 |
+
},
|
149 |
+
{
|
150 |
+
"epoch": 0.91,
|
151 |
+
"learning_rate": 0.0002926784943396845,
|
152 |
+
"loss": 0.0947,
|
153 |
+
"step": 4800
|
154 |
+
},
|
155 |
+
{
|
156 |
+
"epoch": 0.95,
|
157 |
+
"learning_rate": 0.00028663262204976965,
|
158 |
+
"loss": 0.0933,
|
159 |
+
"step": 5000
|
160 |
+
},
|
161 |
+
{
|
162 |
+
"epoch": 0.98,
|
163 |
+
"learning_rate": 0.00028042752473944106,
|
164 |
+
"loss": 0.094,
|
165 |
+
"step": 5200
|
166 |
+
},
|
167 |
+
{
|
168 |
+
"epoch": 1.0,
|
169 |
+
"eval_accuracy": 0.9297529150299436,
|
170 |
+
"eval_auc": 0.8167222019799886,
|
171 |
+
"eval_f1": 0.3440490710592986,
|
172 |
+
"eval_loss": 0.6011912822723389,
|
173 |
+
"eval_mcc": 0.3730152153022164,
|
174 |
+
"eval_precision": 0.22835223718675476,
|
175 |
+
"eval_recall": 0.697386656717114,
|
176 |
+
"eval_runtime": 3756.1015,
|
177 |
+
"eval_samples_per_second": 144.201,
|
178 |
+
"eval_steps_per_second": 0.687,
|
179 |
+
"step": 5289
|
180 |
+
}
|
181 |
+
],
|
182 |
+
"logging_steps": 200,
|
183 |
+
"max_steps": 15867,
|
184 |
+
"num_train_epochs": 3,
|
185 |
+
"save_steps": 500,
|
186 |
+
"total_flos": 4.006517704836067e+17,
|
187 |
+
"trial_name": null,
|
188 |
+
"trial_params": null
|
189 |
+
}
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:b915c4deb5ba56cacb3593b78264a7c9bd0e44e5e5af7a361d94ad20b8ca1c89
|
3 |
+
size 4155
|
esm2_t12_35M_qlora_binding_sites_2023-09-30_06-27-21/checkpoint-5289/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>
|