AmelieSchreiber
commited on
Commit
·
692f69c
1
Parent(s):
32ec1db
Upload 48 files
Browse files- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/README.md +21 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/adapter_config.json +29 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/adapter_model.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/added_tokens.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/optimizer.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/rng_state.pth +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/scheduler.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/special_tokens_map.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/tokenizer_config.json +54 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/trainer_state.json +415 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/training_args.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/vocab.txt +33 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/README.md +21 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/adapter_config.json +29 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/adapter_model.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/added_tokens.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/optimizer.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/rng_state.pth +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/scheduler.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/special_tokens_map.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/tokenizer_config.json +54 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/trainer_state.json +543 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/training_args.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/vocab.txt +33 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/README.md +21 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/adapter_config.json +29 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/adapter_model.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/added_tokens.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/optimizer.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/rng_state.pth +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/scheduler.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/special_tokens_map.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/tokenizer_config.json +54 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/trainer_state.json +147 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/training_args.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/vocab.txt +33 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/README.md +21 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/adapter_config.json +29 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/adapter_model.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/added_tokens.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/optimizer.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/rng_state.pth +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/scheduler.pt +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/special_tokens_map.json +7 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/tokenizer_config.json +54 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/trainer_state.json +281 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/training_args.bin +3 -0
- esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/vocab.txt +33 -0
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/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 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:a3e861c1a99b016ce76e69794f42346cccbdc6bf95658b3c3bc4d3cf0b8b999c
|
3 |
+
size 114991
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:84927c18255420a7ed70e70a5f7bf68e48b1a0b356f64c733677a7eeb9ad36c5
|
3 |
+
size 218073
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:baa211bb85c9638f95b353de5eefb72e14175247f5be85ccfed47b88c3f91a13
|
3 |
+
size 14575
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:d3676a61e287c72a94f887301dbd12aad47cd3033c71e16308c1190c5c28aecd
|
3 |
+
size 627
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/trainer_state.json
ADDED
@@ -0,0 +1,415 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.21386215966220054,
|
3 |
+
"best_model_checkpoint": "esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878",
|
4 |
+
"epoch": 3.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 11817,
|
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 |
+
"epoch": 1.02,
|
141 |
+
"learning_rate": 0.00031434720713917336,
|
142 |
+
"loss": 0.2484,
|
143 |
+
"step": 4000
|
144 |
+
},
|
145 |
+
{
|
146 |
+
"epoch": 1.07,
|
147 |
+
"learning_rate": 0.0003089913128054233,
|
148 |
+
"loss": 0.2437,
|
149 |
+
"step": 4200
|
150 |
+
},
|
151 |
+
{
|
152 |
+
"epoch": 1.12,
|
153 |
+
"learning_rate": 0.0003034119838843777,
|
154 |
+
"loss": 0.242,
|
155 |
+
"step": 4400
|
156 |
+
},
|
157 |
+
{
|
158 |
+
"epoch": 1.17,
|
159 |
+
"learning_rate": 0.00029764449888790783,
|
160 |
+
"loss": 0.2423,
|
161 |
+
"step": 4600
|
162 |
+
},
|
163 |
+
{
|
164 |
+
"epoch": 1.22,
|
165 |
+
"learning_rate": 0.0002916980283940693,
|
166 |
+
"loss": 0.2387,
|
167 |
+
"step": 4800
|
168 |
+
},
|
169 |
+
{
|
170 |
+
"epoch": 1.27,
|
171 |
+
"learning_rate": 0.00028558202757645164,
|
172 |
+
"loss": 0.239,
|
173 |
+
"step": 5000
|
174 |
+
},
|
175 |
+
{
|
176 |
+
"epoch": 1.32,
|
177 |
+
"learning_rate": 0.0002793062211699992,
|
178 |
+
"loss": 0.2376,
|
179 |
+
"step": 5200
|
180 |
+
},
|
181 |
+
{
|
182 |
+
"epoch": 1.37,
|
183 |
+
"learning_rate": 0.0002728805880082148,
|
184 |
+
"loss": 0.2384,
|
185 |
+
"step": 5400
|
186 |
+
},
|
187 |
+
{
|
188 |
+
"epoch": 1.42,
|
189 |
+
"learning_rate": 0.00026631534515633606,
|
190 |
+
"loss": 0.2355,
|
191 |
+
"step": 5600
|
192 |
+
},
|
193 |
+
{
|
194 |
+
"epoch": 1.47,
|
195 |
+
"learning_rate": 0.0002596209316657108,
|
196 |
+
"loss": 0.2352,
|
197 |
+
"step": 5800
|
198 |
+
},
|
199 |
+
{
|
200 |
+
"epoch": 1.52,
|
201 |
+
"learning_rate": 0.00025280799197520415,
|
202 |
+
"loss": 0.2343,
|
203 |
+
"step": 6000
|
204 |
+
},
|
205 |
+
{
|
206 |
+
"epoch": 1.57,
|
207 |
+
"learning_rate": 0.0002458873589860299,
|
208 |
+
"loss": 0.231,
|
209 |
+
"step": 6200
|
210 |
+
},
|
211 |
+
{
|
212 |
+
"epoch": 1.62,
|
213 |
+
"learning_rate": 0.00023890534556422294,
|
214 |
+
"loss": 0.2339,
|
215 |
+
"step": 6400
|
216 |
+
},
|
217 |
+
{
|
218 |
+
"epoch": 1.68,
|
219 |
+
"learning_rate": 0.00023180289180308998,
|
220 |
+
"loss": 0.2332,
|
221 |
+
"step": 6600
|
222 |
+
},
|
223 |
+
{
|
224 |
+
"epoch": 1.73,
|
225 |
+
"learning_rate": 0.00022462614386106907,
|
226 |
+
"loss": 0.232,
|
227 |
+
"step": 6800
|
228 |
+
},
|
229 |
+
{
|
230 |
+
"epoch": 1.78,
|
231 |
+
"learning_rate": 0.00021738651311196128,
|
232 |
+
"loss": 0.231,
|
233 |
+
"step": 7000
|
234 |
+
},
|
235 |
+
{
|
236 |
+
"epoch": 1.83,
|
237 |
+
"learning_rate": 0.00021013207456600314,
|
238 |
+
"loss": 0.2305,
|
239 |
+
"step": 7200
|
240 |
+
},
|
241 |
+
{
|
242 |
+
"epoch": 1.88,
|
243 |
+
"learning_rate": 0.00020280146390924225,
|
244 |
+
"loss": 0.2298,
|
245 |
+
"step": 7400
|
246 |
+
},
|
247 |
+
{
|
248 |
+
"epoch": 1.93,
|
249 |
+
"learning_rate": 0.00019544267273437384,
|
250 |
+
"loss": 0.2302,
|
251 |
+
"step": 7600
|
252 |
+
},
|
253 |
+
{
|
254 |
+
"epoch": 1.98,
|
255 |
+
"learning_rate": 0.0001880674018726795,
|
256 |
+
"loss": 0.2295,
|
257 |
+
"step": 7800
|
258 |
+
},
|
259 |
+
{
|
260 |
+
"epoch": 2.0,
|
261 |
+
"eval_accuracy": 0.8789903474277315,
|
262 |
+
"eval_auc": 0.8180827968848764,
|
263 |
+
"eval_f1": 0.21386215966220054,
|
264 |
+
"eval_loss": 0.4392629563808441,
|
265 |
+
"eval_mcc": 0.27446788968929925,
|
266 |
+
"eval_precision": 0.12459111498869992,
|
267 |
+
"eval_recall": 0.7543961461123881,
|
268 |
+
"eval_runtime": 1167.9434,
|
269 |
+
"eval_samples_per_second": 109.296,
|
270 |
+
"eval_steps_per_second": 1.708,
|
271 |
+
"step": 7878
|
272 |
+
},
|
273 |
+
{
|
274 |
+
"epoch": 2.03,
|
275 |
+
"learning_rate": 0.00018068737835893393,
|
276 |
+
"loss": 0.2261,
|
277 |
+
"step": 8000
|
278 |
+
},
|
279 |
+
{
|
280 |
+
"epoch": 2.08,
|
281 |
+
"learning_rate": 0.00017331433678485712,
|
282 |
+
"loss": 0.2277,
|
283 |
+
"step": 8200
|
284 |
+
},
|
285 |
+
{
|
286 |
+
"epoch": 2.13,
|
287 |
+
"learning_rate": 0.00016596000064054934,
|
288 |
+
"loss": 0.2275,
|
289 |
+
"step": 8400
|
290 |
+
},
|
291 |
+
{
|
292 |
+
"epoch": 2.18,
|
293 |
+
"learning_rate": 0.0001586360636735797,
|
294 |
+
"loss": 0.2267,
|
295 |
+
"step": 8600
|
296 |
+
},
|
297 |
+
{
|
298 |
+
"epoch": 2.23,
|
299 |
+
"learning_rate": 0.0001513541712953658,
|
300 |
+
"loss": 0.2243,
|
301 |
+
"step": 8800
|
302 |
+
},
|
303 |
+
{
|
304 |
+
"epoch": 2.28,
|
305 |
+
"learning_rate": 0.00014412590206441025,
|
306 |
+
"loss": 0.2266,
|
307 |
+
"step": 9000
|
308 |
+
},
|
309 |
+
{
|
310 |
+
"epoch": 2.34,
|
311 |
+
"learning_rate": 0.00013696274927583722,
|
312 |
+
"loss": 0.2243,
|
313 |
+
"step": 9200
|
314 |
+
},
|
315 |
+
{
|
316 |
+
"epoch": 2.39,
|
317 |
+
"learning_rate": 0.00012987610268650092,
|
318 |
+
"loss": 0.2253,
|
319 |
+
"step": 9400
|
320 |
+
},
|
321 |
+
{
|
322 |
+
"epoch": 2.44,
|
323 |
+
"learning_rate": 0.00012287723040472557,
|
324 |
+
"loss": 0.2255,
|
325 |
+
"step": 9600
|
326 |
+
},
|
327 |
+
{
|
328 |
+
"epoch": 2.49,
|
329 |
+
"learning_rate": 0.00011597726097347204,
|
330 |
+
"loss": 0.2254,
|
331 |
+
"step": 9800
|
332 |
+
},
|
333 |
+
{
|
334 |
+
"epoch": 2.54,
|
335 |
+
"learning_rate": 0.00010918716567542043,
|
336 |
+
"loss": 0.2241,
|
337 |
+
"step": 10000
|
338 |
+
},
|
339 |
+
{
|
340 |
+
"epoch": 2.59,
|
341 |
+
"learning_rate": 0.0001025177410881037,
|
342 |
+
"loss": 0.223,
|
343 |
+
"step": 10200
|
344 |
+
},
|
345 |
+
{
|
346 |
+
"epoch": 2.64,
|
347 |
+
"learning_rate": 9.597959191683088e-05,
|
348 |
+
"loss": 0.2217,
|
349 |
+
"step": 10400
|
350 |
+
},
|
351 |
+
{
|
352 |
+
"epoch": 2.69,
|
353 |
+
"learning_rate": 8.958311413269684e-05,
|
354 |
+
"loss": 0.222,
|
355 |
+
"step": 10600
|
356 |
+
},
|
357 |
+
{
|
358 |
+
"epoch": 2.74,
|
359 |
+
"learning_rate": 8.333847844248891e-05,
|
360 |
+
"loss": 0.2219,
|
361 |
+
"step": 10800
|
362 |
+
},
|
363 |
+
{
|
364 |
+
"epoch": 2.79,
|
365 |
+
"learning_rate": 7.725561411677462e-05,
|
366 |
+
"loss": 0.2218,
|
367 |
+
"step": 11000
|
368 |
+
},
|
369 |
+
{
|
370 |
+
"epoch": 2.84,
|
371 |
+
"learning_rate": 7.134419320188491e-05,
|
372 |
+
"loss": 0.2233,
|
373 |
+
"step": 11200
|
374 |
+
},
|
375 |
+
{
|
376 |
+
"epoch": 2.89,
|
377 |
+
"learning_rate": 6.564180298866504e-05,
|
378 |
+
"loss": 0.2261,
|
379 |
+
"step": 11400
|
380 |
+
},
|
381 |
+
{
|
382 |
+
"epoch": 2.94,
|
383 |
+
"learning_rate": 6.010020772997792e-05,
|
384 |
+
"loss": 0.2225,
|
385 |
+
"step": 11600
|
386 |
+
},
|
387 |
+
{
|
388 |
+
"epoch": 3.0,
|
389 |
+
"learning_rate": 5.475733380194338e-05,
|
390 |
+
"loss": 0.2176,
|
391 |
+
"step": 11800
|
392 |
+
},
|
393 |
+
{
|
394 |
+
"epoch": 3.0,
|
395 |
+
"eval_accuracy": 0.8735072413749101,
|
396 |
+
"eval_auc": 0.8195797310899098,
|
397 |
+
"eval_f1": 0.20841207680022153,
|
398 |
+
"eval_loss": 0.4386225640773773,
|
399 |
+
"eval_mcc": 0.2707498152735772,
|
400 |
+
"eval_precision": 0.12068424210520438,
|
401 |
+
"eval_recall": 0.7631916070570107,
|
402 |
+
"eval_runtime": 1165.7733,
|
403 |
+
"eval_samples_per_second": 109.499,
|
404 |
+
"eval_steps_per_second": 1.711,
|
405 |
+
"step": 11817
|
406 |
+
}
|
407 |
+
],
|
408 |
+
"logging_steps": 200,
|
409 |
+
"max_steps": 15756,
|
410 |
+
"num_train_epochs": 4,
|
411 |
+
"save_steps": 500,
|
412 |
+
"total_flos": 6.077187662375136e+16,
|
413 |
+
"trial_name": null,
|
414 |
+
"trial_params": null
|
415 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:19560f827f37de980ef9907eb4a996feaadf6e4f6a723cacbef99fc7a0ba1b25
|
3 |
+
size 4155
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-11817/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/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 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:f3075ce6140607858becdd4528bfbba621d0fe5981ed48db8ecdfdd6ed1679e3
|
3 |
+
size 114991
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:a02b58d7f2080fec37a419183d7fefebe47ae919ad6368dd61a35b4e860a40c0
|
3 |
+
size 218073
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:f8a9a8ddf2bef1b580758f72457a9be5be71f4dc25e234839bea7418a3d9bc67
|
3 |
+
size 14575
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:86ab8ca8d941f7a9dc0e1bfb3c414eb3afc0b3e1513ea8a7ce0db94586cd403d
|
3 |
+
size 627
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/trainer_state.json
ADDED
@@ -0,0 +1,543 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.21386215966220054,
|
3 |
+
"best_model_checkpoint": "esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878",
|
4 |
+
"epoch": 4.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 15756,
|
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 |
+
"epoch": 1.02,
|
141 |
+
"learning_rate": 0.00031434720713917336,
|
142 |
+
"loss": 0.2484,
|
143 |
+
"step": 4000
|
144 |
+
},
|
145 |
+
{
|
146 |
+
"epoch": 1.07,
|
147 |
+
"learning_rate": 0.0003089913128054233,
|
148 |
+
"loss": 0.2437,
|
149 |
+
"step": 4200
|
150 |
+
},
|
151 |
+
{
|
152 |
+
"epoch": 1.12,
|
153 |
+
"learning_rate": 0.0003034119838843777,
|
154 |
+
"loss": 0.242,
|
155 |
+
"step": 4400
|
156 |
+
},
|
157 |
+
{
|
158 |
+
"epoch": 1.17,
|
159 |
+
"learning_rate": 0.00029764449888790783,
|
160 |
+
"loss": 0.2423,
|
161 |
+
"step": 4600
|
162 |
+
},
|
163 |
+
{
|
164 |
+
"epoch": 1.22,
|
165 |
+
"learning_rate": 0.0002916980283940693,
|
166 |
+
"loss": 0.2387,
|
167 |
+
"step": 4800
|
168 |
+
},
|
169 |
+
{
|
170 |
+
"epoch": 1.27,
|
171 |
+
"learning_rate": 0.00028558202757645164,
|
172 |
+
"loss": 0.239,
|
173 |
+
"step": 5000
|
174 |
+
},
|
175 |
+
{
|
176 |
+
"epoch": 1.32,
|
177 |
+
"learning_rate": 0.0002793062211699992,
|
178 |
+
"loss": 0.2376,
|
179 |
+
"step": 5200
|
180 |
+
},
|
181 |
+
{
|
182 |
+
"epoch": 1.37,
|
183 |
+
"learning_rate": 0.0002728805880082148,
|
184 |
+
"loss": 0.2384,
|
185 |
+
"step": 5400
|
186 |
+
},
|
187 |
+
{
|
188 |
+
"epoch": 1.42,
|
189 |
+
"learning_rate": 0.00026631534515633606,
|
190 |
+
"loss": 0.2355,
|
191 |
+
"step": 5600
|
192 |
+
},
|
193 |
+
{
|
194 |
+
"epoch": 1.47,
|
195 |
+
"learning_rate": 0.0002596209316657108,
|
196 |
+
"loss": 0.2352,
|
197 |
+
"step": 5800
|
198 |
+
},
|
199 |
+
{
|
200 |
+
"epoch": 1.52,
|
201 |
+
"learning_rate": 0.00025280799197520415,
|
202 |
+
"loss": 0.2343,
|
203 |
+
"step": 6000
|
204 |
+
},
|
205 |
+
{
|
206 |
+
"epoch": 1.57,
|
207 |
+
"learning_rate": 0.0002458873589860299,
|
208 |
+
"loss": 0.231,
|
209 |
+
"step": 6200
|
210 |
+
},
|
211 |
+
{
|
212 |
+
"epoch": 1.62,
|
213 |
+
"learning_rate": 0.00023890534556422294,
|
214 |
+
"loss": 0.2339,
|
215 |
+
"step": 6400
|
216 |
+
},
|
217 |
+
{
|
218 |
+
"epoch": 1.68,
|
219 |
+
"learning_rate": 0.00023180289180308998,
|
220 |
+
"loss": 0.2332,
|
221 |
+
"step": 6600
|
222 |
+
},
|
223 |
+
{
|
224 |
+
"epoch": 1.73,
|
225 |
+
"learning_rate": 0.00022462614386106907,
|
226 |
+
"loss": 0.232,
|
227 |
+
"step": 6800
|
228 |
+
},
|
229 |
+
{
|
230 |
+
"epoch": 1.78,
|
231 |
+
"learning_rate": 0.00021738651311196128,
|
232 |
+
"loss": 0.231,
|
233 |
+
"step": 7000
|
234 |
+
},
|
235 |
+
{
|
236 |
+
"epoch": 1.83,
|
237 |
+
"learning_rate": 0.00021013207456600314,
|
238 |
+
"loss": 0.2305,
|
239 |
+
"step": 7200
|
240 |
+
},
|
241 |
+
{
|
242 |
+
"epoch": 1.88,
|
243 |
+
"learning_rate": 0.00020280146390924225,
|
244 |
+
"loss": 0.2298,
|
245 |
+
"step": 7400
|
246 |
+
},
|
247 |
+
{
|
248 |
+
"epoch": 1.93,
|
249 |
+
"learning_rate": 0.00019544267273437384,
|
250 |
+
"loss": 0.2302,
|
251 |
+
"step": 7600
|
252 |
+
},
|
253 |
+
{
|
254 |
+
"epoch": 1.98,
|
255 |
+
"learning_rate": 0.0001880674018726795,
|
256 |
+
"loss": 0.2295,
|
257 |
+
"step": 7800
|
258 |
+
},
|
259 |
+
{
|
260 |
+
"epoch": 2.0,
|
261 |
+
"eval_accuracy": 0.8789903474277315,
|
262 |
+
"eval_auc": 0.8180827968848764,
|
263 |
+
"eval_f1": 0.21386215966220054,
|
264 |
+
"eval_loss": 0.4392629563808441,
|
265 |
+
"eval_mcc": 0.27446788968929925,
|
266 |
+
"eval_precision": 0.12459111498869992,
|
267 |
+
"eval_recall": 0.7543961461123881,
|
268 |
+
"eval_runtime": 1167.9434,
|
269 |
+
"eval_samples_per_second": 109.296,
|
270 |
+
"eval_steps_per_second": 1.708,
|
271 |
+
"step": 7878
|
272 |
+
},
|
273 |
+
{
|
274 |
+
"epoch": 2.03,
|
275 |
+
"learning_rate": 0.00018068737835893393,
|
276 |
+
"loss": 0.2261,
|
277 |
+
"step": 8000
|
278 |
+
},
|
279 |
+
{
|
280 |
+
"epoch": 2.08,
|
281 |
+
"learning_rate": 0.00017331433678485712,
|
282 |
+
"loss": 0.2277,
|
283 |
+
"step": 8200
|
284 |
+
},
|
285 |
+
{
|
286 |
+
"epoch": 2.13,
|
287 |
+
"learning_rate": 0.00016596000064054934,
|
288 |
+
"loss": 0.2275,
|
289 |
+
"step": 8400
|
290 |
+
},
|
291 |
+
{
|
292 |
+
"epoch": 2.18,
|
293 |
+
"learning_rate": 0.0001586360636735797,
|
294 |
+
"loss": 0.2267,
|
295 |
+
"step": 8600
|
296 |
+
},
|
297 |
+
{
|
298 |
+
"epoch": 2.23,
|
299 |
+
"learning_rate": 0.0001513541712953658,
|
300 |
+
"loss": 0.2243,
|
301 |
+
"step": 8800
|
302 |
+
},
|
303 |
+
{
|
304 |
+
"epoch": 2.28,
|
305 |
+
"learning_rate": 0.00014412590206441025,
|
306 |
+
"loss": 0.2266,
|
307 |
+
"step": 9000
|
308 |
+
},
|
309 |
+
{
|
310 |
+
"epoch": 2.34,
|
311 |
+
"learning_rate": 0.00013696274927583722,
|
312 |
+
"loss": 0.2243,
|
313 |
+
"step": 9200
|
314 |
+
},
|
315 |
+
{
|
316 |
+
"epoch": 2.39,
|
317 |
+
"learning_rate": 0.00012987610268650092,
|
318 |
+
"loss": 0.2253,
|
319 |
+
"step": 9400
|
320 |
+
},
|
321 |
+
{
|
322 |
+
"epoch": 2.44,
|
323 |
+
"learning_rate": 0.00012287723040472557,
|
324 |
+
"loss": 0.2255,
|
325 |
+
"step": 9600
|
326 |
+
},
|
327 |
+
{
|
328 |
+
"epoch": 2.49,
|
329 |
+
"learning_rate": 0.00011597726097347204,
|
330 |
+
"loss": 0.2254,
|
331 |
+
"step": 9800
|
332 |
+
},
|
333 |
+
{
|
334 |
+
"epoch": 2.54,
|
335 |
+
"learning_rate": 0.00010918716567542043,
|
336 |
+
"loss": 0.2241,
|
337 |
+
"step": 10000
|
338 |
+
},
|
339 |
+
{
|
340 |
+
"epoch": 2.59,
|
341 |
+
"learning_rate": 0.0001025177410881037,
|
342 |
+
"loss": 0.223,
|
343 |
+
"step": 10200
|
344 |
+
},
|
345 |
+
{
|
346 |
+
"epoch": 2.64,
|
347 |
+
"learning_rate": 9.597959191683088e-05,
|
348 |
+
"loss": 0.2217,
|
349 |
+
"step": 10400
|
350 |
+
},
|
351 |
+
{
|
352 |
+
"epoch": 2.69,
|
353 |
+
"learning_rate": 8.958311413269684e-05,
|
354 |
+
"loss": 0.222,
|
355 |
+
"step": 10600
|
356 |
+
},
|
357 |
+
{
|
358 |
+
"epoch": 2.74,
|
359 |
+
"learning_rate": 8.333847844248891e-05,
|
360 |
+
"loss": 0.2219,
|
361 |
+
"step": 10800
|
362 |
+
},
|
363 |
+
{
|
364 |
+
"epoch": 2.79,
|
365 |
+
"learning_rate": 7.725561411677462e-05,
|
366 |
+
"loss": 0.2218,
|
367 |
+
"step": 11000
|
368 |
+
},
|
369 |
+
{
|
370 |
+
"epoch": 2.84,
|
371 |
+
"learning_rate": 7.134419320188491e-05,
|
372 |
+
"loss": 0.2233,
|
373 |
+
"step": 11200
|
374 |
+
},
|
375 |
+
{
|
376 |
+
"epoch": 2.89,
|
377 |
+
"learning_rate": 6.564180298866504e-05,
|
378 |
+
"loss": 0.2261,
|
379 |
+
"step": 11400
|
380 |
+
},
|
381 |
+
{
|
382 |
+
"epoch": 2.94,
|
383 |
+
"learning_rate": 6.010020772997792e-05,
|
384 |
+
"loss": 0.2225,
|
385 |
+
"step": 11600
|
386 |
+
},
|
387 |
+
{
|
388 |
+
"epoch": 3.0,
|
389 |
+
"learning_rate": 5.475733380194338e-05,
|
390 |
+
"loss": 0.2176,
|
391 |
+
"step": 11800
|
392 |
+
},
|
393 |
+
{
|
394 |
+
"epoch": 3.0,
|
395 |
+
"eval_accuracy": 0.8735072413749101,
|
396 |
+
"eval_auc": 0.8195797310899098,
|
397 |
+
"eval_f1": 0.20841207680022153,
|
398 |
+
"eval_loss": 0.4386225640773773,
|
399 |
+
"eval_mcc": 0.2707498152735772,
|
400 |
+
"eval_precision": 0.12068424210520438,
|
401 |
+
"eval_recall": 0.7631916070570107,
|
402 |
+
"eval_runtime": 1165.7733,
|
403 |
+
"eval_samples_per_second": 109.499,
|
404 |
+
"eval_steps_per_second": 1.711,
|
405 |
+
"step": 11817
|
406 |
+
},
|
407 |
+
{
|
408 |
+
"epoch": 3.05,
|
409 |
+
"learning_rate": 4.962167663063128e-05,
|
410 |
+
"loss": 0.2223,
|
411 |
+
"step": 12000
|
412 |
+
},
|
413 |
+
{
|
414 |
+
"epoch": 3.1,
|
415 |
+
"learning_rate": 4.4701402157519476e-05,
|
416 |
+
"loss": 0.2204,
|
417 |
+
"step": 12200
|
418 |
+
},
|
419 |
+
{
|
420 |
+
"epoch": 3.15,
|
421 |
+
"learning_rate": 4.000433385525458e-05,
|
422 |
+
"loss": 0.2224,
|
423 |
+
"step": 12400
|
424 |
+
},
|
425 |
+
{
|
426 |
+
"epoch": 3.2,
|
427 |
+
"learning_rate": 3.553794028795492e-05,
|
428 |
+
"loss": 0.2239,
|
429 |
+
"step": 12600
|
430 |
+
},
|
431 |
+
{
|
432 |
+
"epoch": 3.25,
|
433 |
+
"learning_rate": 3.130932323583492e-05,
|
434 |
+
"loss": 0.2188,
|
435 |
+
"step": 12800
|
436 |
+
},
|
437 |
+
{
|
438 |
+
"epoch": 3.3,
|
439 |
+
"learning_rate": 2.7325206403033605e-05,
|
440 |
+
"loss": 0.2214,
|
441 |
+
"step": 13000
|
442 |
+
},
|
443 |
+
{
|
444 |
+
"epoch": 3.35,
|
445 |
+
"learning_rate": 2.359192472660235e-05,
|
446 |
+
"loss": 0.2216,
|
447 |
+
"step": 13200
|
448 |
+
},
|
449 |
+
{
|
450 |
+
"epoch": 3.4,
|
451 |
+
"learning_rate": 2.0132148821294626e-05,
|
452 |
+
"loss": 0.2207,
|
453 |
+
"step": 13400
|
454 |
+
},
|
455 |
+
{
|
456 |
+
"epoch": 3.45,
|
457 |
+
"learning_rate": 1.691661291092208e-05,
|
458 |
+
"loss": 0.2199,
|
459 |
+
"step": 13600
|
460 |
+
},
|
461 |
+
{
|
462 |
+
"epoch": 3.5,
|
463 |
+
"learning_rate": 1.3968462320313953e-05,
|
464 |
+
"loss": 0.219,
|
465 |
+
"step": 13800
|
466 |
+
},
|
467 |
+
{
|
468 |
+
"epoch": 3.55,
|
469 |
+
"learning_rate": 1.1292384750457188e-05,
|
470 |
+
"loss": 0.2219,
|
471 |
+
"step": 14000
|
472 |
+
},
|
473 |
+
{
|
474 |
+
"epoch": 3.6,
|
475 |
+
"learning_rate": 8.892635293172929e-06,
|
476 |
+
"loss": 0.2202,
|
477 |
+
"step": 14200
|
478 |
+
},
|
479 |
+
{
|
480 |
+
"epoch": 3.66,
|
481 |
+
"learning_rate": 6.773029665315992e-06,
|
482 |
+
"loss": 0.2202,
|
483 |
+
"step": 14400
|
484 |
+
},
|
485 |
+
{
|
486 |
+
"epoch": 3.71,
|
487 |
+
"learning_rate": 4.936938141602164e-06,
|
488 |
+
"loss": 0.2168,
|
489 |
+
"step": 14600
|
490 |
+
},
|
491 |
+
{
|
492 |
+
"epoch": 3.76,
|
493 |
+
"learning_rate": 3.387280195709328e-06,
|
494 |
+
"loss": 0.221,
|
495 |
+
"step": 14800
|
496 |
+
},
|
497 |
+
{
|
498 |
+
"epoch": 3.81,
|
499 |
+
"learning_rate": 2.1321015191903147e-06,
|
500 |
+
"loss": 0.2195,
|
501 |
+
"step": 15000
|
502 |
+
},
|
503 |
+
{
|
504 |
+
"epoch": 3.86,
|
505 |
+
"learning_rate": 1.1607847254776198e-06,
|
506 |
+
"loss": 0.2214,
|
507 |
+
"step": 15200
|
508 |
+
},
|
509 |
+
{
|
510 |
+
"epoch": 3.91,
|
511 |
+
"learning_rate": 4.819057748199279e-07,
|
512 |
+
"loss": 0.2202,
|
513 |
+
"step": 15400
|
514 |
+
},
|
515 |
+
{
|
516 |
+
"epoch": 3.96,
|
517 |
+
"learning_rate": 9.654411734337413e-08,
|
518 |
+
"loss": 0.2222,
|
519 |
+
"step": 15600
|
520 |
+
},
|
521 |
+
{
|
522 |
+
"epoch": 4.0,
|
523 |
+
"eval_accuracy": 0.8741850393920096,
|
524 |
+
"eval_auc": 0.819488037818028,
|
525 |
+
"eval_f1": 0.20910544751589633,
|
526 |
+
"eval_loss": 0.43909892439842224,
|
527 |
+
"eval_mcc": 0.27126529185336096,
|
528 |
+
"eval_precision": 0.12117210076100346,
|
529 |
+
"eval_recall": 0.7622953120147897,
|
530 |
+
"eval_runtime": 1162.7299,
|
531 |
+
"eval_samples_per_second": 109.786,
|
532 |
+
"eval_steps_per_second": 1.716,
|
533 |
+
"step": 15756
|
534 |
+
}
|
535 |
+
],
|
536 |
+
"logging_steps": 200,
|
537 |
+
"max_steps": 15756,
|
538 |
+
"num_train_epochs": 4,
|
539 |
+
"save_steps": 500,
|
540 |
+
"total_flos": 8.102916883166848e+16,
|
541 |
+
"trial_name": null,
|
542 |
+
"trial_params": null
|
543 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:19560f827f37de980ef9907eb4a996feaadf6e4f6a723cacbef99fc7a0ba1b25
|
3 |
+
size 4155
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-15756/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/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 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:44501128da965af2da76593044b359220b9cbd2c5b399bc9de7aac4197d83273
|
3 |
+
size 114991
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:550477f400ea5edc292478c534a1dae4e96fbbd3c25f393b7ce864fbce100b69
|
3 |
+
size 218073
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:f4867cc190d63a633b96f2672fb906a1c6c53f31c353db36e79d6433f4038473
|
3 |
+
size 14575
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:4bc87ecdf29595d0187df2e3c0721fbf08cc9aa799fab4c51aafa53363300bd1
|
3 |
+
size 627
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/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 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:19560f827f37de980ef9907eb4a996feaadf6e4f6a723cacbef99fc7a0ba1b25
|
3 |
+
size 4155
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-3939/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/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 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/adapter_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:9d6bae6aa0fe5623cd84eb369c0e9e8027fbbc24839cc196e742de63964ef886
|
3 |
+
size 114991
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:3b24037eda5de7e73c7d7b3ffec29293e2178a5511cb51b0d27fca0ff899fabe
|
3 |
+
size 218073
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:370252d5d09ed129e985231b3e21fc550a6f7a7c660b7c74edd054a4e7ae94ed
|
3 |
+
size 14575
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:b402c76a39b9f4986855645efcbcac8cfd51de5b448f17a8868056e810e6bdf0
|
3 |
+
size 627
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/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_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/trainer_state.json
ADDED
@@ -0,0 +1,281 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.21386215966220054,
|
3 |
+
"best_model_checkpoint": "esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878",
|
4 |
+
"epoch": 2.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 7878,
|
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 |
+
"epoch": 1.02,
|
141 |
+
"learning_rate": 0.00031434720713917336,
|
142 |
+
"loss": 0.2484,
|
143 |
+
"step": 4000
|
144 |
+
},
|
145 |
+
{
|
146 |
+
"epoch": 1.07,
|
147 |
+
"learning_rate": 0.0003089913128054233,
|
148 |
+
"loss": 0.2437,
|
149 |
+
"step": 4200
|
150 |
+
},
|
151 |
+
{
|
152 |
+
"epoch": 1.12,
|
153 |
+
"learning_rate": 0.0003034119838843777,
|
154 |
+
"loss": 0.242,
|
155 |
+
"step": 4400
|
156 |
+
},
|
157 |
+
{
|
158 |
+
"epoch": 1.17,
|
159 |
+
"learning_rate": 0.00029764449888790783,
|
160 |
+
"loss": 0.2423,
|
161 |
+
"step": 4600
|
162 |
+
},
|
163 |
+
{
|
164 |
+
"epoch": 1.22,
|
165 |
+
"learning_rate": 0.0002916980283940693,
|
166 |
+
"loss": 0.2387,
|
167 |
+
"step": 4800
|
168 |
+
},
|
169 |
+
{
|
170 |
+
"epoch": 1.27,
|
171 |
+
"learning_rate": 0.00028558202757645164,
|
172 |
+
"loss": 0.239,
|
173 |
+
"step": 5000
|
174 |
+
},
|
175 |
+
{
|
176 |
+
"epoch": 1.32,
|
177 |
+
"learning_rate": 0.0002793062211699992,
|
178 |
+
"loss": 0.2376,
|
179 |
+
"step": 5200
|
180 |
+
},
|
181 |
+
{
|
182 |
+
"epoch": 1.37,
|
183 |
+
"learning_rate": 0.0002728805880082148,
|
184 |
+
"loss": 0.2384,
|
185 |
+
"step": 5400
|
186 |
+
},
|
187 |
+
{
|
188 |
+
"epoch": 1.42,
|
189 |
+
"learning_rate": 0.00026631534515633606,
|
190 |
+
"loss": 0.2355,
|
191 |
+
"step": 5600
|
192 |
+
},
|
193 |
+
{
|
194 |
+
"epoch": 1.47,
|
195 |
+
"learning_rate": 0.0002596209316657108,
|
196 |
+
"loss": 0.2352,
|
197 |
+
"step": 5800
|
198 |
+
},
|
199 |
+
{
|
200 |
+
"epoch": 1.52,
|
201 |
+
"learning_rate": 0.00025280799197520415,
|
202 |
+
"loss": 0.2343,
|
203 |
+
"step": 6000
|
204 |
+
},
|
205 |
+
{
|
206 |
+
"epoch": 1.57,
|
207 |
+
"learning_rate": 0.0002458873589860299,
|
208 |
+
"loss": 0.231,
|
209 |
+
"step": 6200
|
210 |
+
},
|
211 |
+
{
|
212 |
+
"epoch": 1.62,
|
213 |
+
"learning_rate": 0.00023890534556422294,
|
214 |
+
"loss": 0.2339,
|
215 |
+
"step": 6400
|
216 |
+
},
|
217 |
+
{
|
218 |
+
"epoch": 1.68,
|
219 |
+
"learning_rate": 0.00023180289180308998,
|
220 |
+
"loss": 0.2332,
|
221 |
+
"step": 6600
|
222 |
+
},
|
223 |
+
{
|
224 |
+
"epoch": 1.73,
|
225 |
+
"learning_rate": 0.00022462614386106907,
|
226 |
+
"loss": 0.232,
|
227 |
+
"step": 6800
|
228 |
+
},
|
229 |
+
{
|
230 |
+
"epoch": 1.78,
|
231 |
+
"learning_rate": 0.00021738651311196128,
|
232 |
+
"loss": 0.231,
|
233 |
+
"step": 7000
|
234 |
+
},
|
235 |
+
{
|
236 |
+
"epoch": 1.83,
|
237 |
+
"learning_rate": 0.00021013207456600314,
|
238 |
+
"loss": 0.2305,
|
239 |
+
"step": 7200
|
240 |
+
},
|
241 |
+
{
|
242 |
+
"epoch": 1.88,
|
243 |
+
"learning_rate": 0.00020280146390924225,
|
244 |
+
"loss": 0.2298,
|
245 |
+
"step": 7400
|
246 |
+
},
|
247 |
+
{
|
248 |
+
"epoch": 1.93,
|
249 |
+
"learning_rate": 0.00019544267273437384,
|
250 |
+
"loss": 0.2302,
|
251 |
+
"step": 7600
|
252 |
+
},
|
253 |
+
{
|
254 |
+
"epoch": 1.98,
|
255 |
+
"learning_rate": 0.0001880674018726795,
|
256 |
+
"loss": 0.2295,
|
257 |
+
"step": 7800
|
258 |
+
},
|
259 |
+
{
|
260 |
+
"epoch": 2.0,
|
261 |
+
"eval_accuracy": 0.8789903474277315,
|
262 |
+
"eval_auc": 0.8180827968848764,
|
263 |
+
"eval_f1": 0.21386215966220054,
|
264 |
+
"eval_loss": 0.4392629563808441,
|
265 |
+
"eval_mcc": 0.27446788968929925,
|
266 |
+
"eval_precision": 0.12459111498869992,
|
267 |
+
"eval_recall": 0.7543961461123881,
|
268 |
+
"eval_runtime": 1167.9434,
|
269 |
+
"eval_samples_per_second": 109.296,
|
270 |
+
"eval_steps_per_second": 1.708,
|
271 |
+
"step": 7878
|
272 |
+
}
|
273 |
+
],
|
274 |
+
"logging_steps": 200,
|
275 |
+
"max_steps": 15756,
|
276 |
+
"num_train_epochs": 4,
|
277 |
+
"save_steps": 500,
|
278 |
+
"total_flos": 4.051458441583424e+16,
|
279 |
+
"trial_name": null,
|
280 |
+
"trial_params": null
|
281 |
+
}
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:19560f827f37de980ef9907eb4a996feaadf6e4f6a723cacbef99fc7a0ba1b25
|
3 |
+
size 4155
|
esm2_t6_8M_qlora_binding_sites_2023-09-29_03-34-40/checkpoint-7878/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>
|