Delete human_enhancers_cohn
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- human_enhancers_cohn/base_3072/checkpoint-200/config.json +0 -27
- human_enhancers_cohn/base_3072/checkpoint-200/model.safetensors +0 -3
- human_enhancers_cohn/base_3072/checkpoint-200/optimizer.pt +0 -3
- human_enhancers_cohn/base_3072/checkpoint-200/rng_state.pth +0 -3
- human_enhancers_cohn/base_3072/checkpoint-200/scheduler.pt +0 -3
- human_enhancers_cohn/base_3072/checkpoint-200/special_tokens_map.json +0 -7
- human_enhancers_cohn/base_3072/checkpoint-200/tokenizer.json +0 -0
- human_enhancers_cohn/base_3072/checkpoint-200/tokenizer_config.json +0 -56
- human_enhancers_cohn/base_3072/checkpoint-200/trainer_state.json +0 -32
- human_enhancers_cohn/base_3072/checkpoint-200/training_args.bin +0 -3
- human_enhancers_cohn/base_3072/checkpoint-400/config.json +0 -27
- human_enhancers_cohn/base_3072/checkpoint-400/model.safetensors +0 -3
- human_enhancers_cohn/base_3072/checkpoint-400/optimizer.pt +0 -3
- human_enhancers_cohn/base_3072/checkpoint-400/rng_state.pth +0 -3
- human_enhancers_cohn/base_3072/checkpoint-400/scheduler.pt +0 -3
- human_enhancers_cohn/base_3072/checkpoint-400/special_tokens_map.json +0 -7
- human_enhancers_cohn/base_3072/checkpoint-400/tokenizer.json +0 -0
- human_enhancers_cohn/base_3072/checkpoint-400/tokenizer_config.json +0 -56
- human_enhancers_cohn/base_3072/checkpoint-400/trainer_state.json +0 -45
- human_enhancers_cohn/base_3072/checkpoint-400/training_args.bin +0 -3
- human_enhancers_cohn/base_3072/results/base_3072_hg38_BPE_3e-5_human_enhancers_cohn_seed42/eval_results.json +0 -1
- human_enhancers_cohn/base_4096/checkpoint-200/config.json +0 -27
- human_enhancers_cohn/base_4096/checkpoint-200/model.safetensors +0 -3
- human_enhancers_cohn/base_4096/checkpoint-200/optimizer.pt +0 -3
- human_enhancers_cohn/base_4096/checkpoint-200/rng_state.pth +0 -3
- human_enhancers_cohn/base_4096/checkpoint-200/scheduler.pt +0 -3
- human_enhancers_cohn/base_4096/checkpoint-200/special_tokens_map.json +0 -7
- human_enhancers_cohn/base_4096/checkpoint-200/tokenizer.json +0 -0
- human_enhancers_cohn/base_4096/checkpoint-200/tokenizer_config.json +0 -56
- human_enhancers_cohn/base_4096/checkpoint-200/trainer_state.json +0 -32
- human_enhancers_cohn/base_4096/checkpoint-200/training_args.bin +0 -3
- human_enhancers_cohn/base_4096/checkpoint-400/config.json +0 -27
- human_enhancers_cohn/base_4096/checkpoint-400/model.safetensors +0 -3
- human_enhancers_cohn/base_4096/checkpoint-400/optimizer.pt +0 -3
- human_enhancers_cohn/base_4096/checkpoint-400/rng_state.pth +0 -3
- human_enhancers_cohn/base_4096/checkpoint-400/scheduler.pt +0 -3
- human_enhancers_cohn/base_4096/checkpoint-400/special_tokens_map.json +0 -7
- human_enhancers_cohn/base_4096/checkpoint-400/tokenizer.json +0 -0
- human_enhancers_cohn/base_4096/checkpoint-400/tokenizer_config.json +0 -56
- human_enhancers_cohn/base_4096/checkpoint-400/trainer_state.json +0 -45
- human_enhancers_cohn/base_4096/checkpoint-400/training_args.bin +0 -3
- human_enhancers_cohn/base_4096/results/base_4096_hg38_BPE_3e-5_human_enhancers_cohn_seed42/eval_results.json +0 -1
- human_enhancers_cohn/len2_4096/checkpoint-200/config.json +0 -27
- human_enhancers_cohn/len2_4096/checkpoint-200/model.safetensors +0 -3
- human_enhancers_cohn/len2_4096/checkpoint-200/optimizer.pt +0 -3
- human_enhancers_cohn/len2_4096/checkpoint-200/rng_state.pth +0 -3
- human_enhancers_cohn/len2_4096/checkpoint-200/scheduler.pt +0 -3
- human_enhancers_cohn/len2_4096/checkpoint-200/special_tokens_map.json +0 -7
- human_enhancers_cohn/len2_4096/checkpoint-200/tokenizer.json +0 -0
- human_enhancers_cohn/len2_4096/checkpoint-200/tokenizer_config.json +0 -15
human_enhancers_cohn/base_3072/checkpoint-200/config.json
DELETED
|
@@ -1,27 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "/root/NaN/dna-tokenizer/pretrain/models/base_3072/checkpoint-100000",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"BertForSequenceClassification"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"classifier_dropout": null,
|
| 8 |
-
"hidden_act": "gelu",
|
| 9 |
-
"hidden_dropout_prob": 0.1,
|
| 10 |
-
"hidden_size": 768,
|
| 11 |
-
"initializer_range": 0.02,
|
| 12 |
-
"intermediate_size": 3072,
|
| 13 |
-
"layer_norm_eps": 1e-12,
|
| 14 |
-
"max_length": 512,
|
| 15 |
-
"max_position_embeddings": 512,
|
| 16 |
-
"model_type": "bert",
|
| 17 |
-
"num_attention_heads": 12,
|
| 18 |
-
"num_hidden_layers": 12,
|
| 19 |
-
"pad_token_id": 0,
|
| 20 |
-
"position_embedding_type": "absolute",
|
| 21 |
-
"problem_type": "single_label_classification",
|
| 22 |
-
"torch_dtype": "float32",
|
| 23 |
-
"transformers_version": "4.35.2",
|
| 24 |
-
"type_vocab_size": 2,
|
| 25 |
-
"use_cache": true,
|
| 26 |
-
"vocab_size": 3072
|
| 27 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/model.safetensors
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:b1c3c78c0f76fa53a518fa1d22f9df99ff736b2ca3a8908cfd0e549b6a22879d
|
| 3 |
-
size 353632152
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/optimizer.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:9a628ae7eab4421da983805cf7f5e6eb448bba273fe46601328c7955019c2d0e
|
| 3 |
-
size 707385995
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/rng_state.pth
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:9e42ae1e4d1487d5e895b4aedb9ab73c4b5e5e7cb820f8e2c7209169be990d46
|
| 3 |
-
size 14709
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/scheduler.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:eb8396a28d05435f8711ed63af5f363fe80d8db70c66f1da4bc3ca37047db868
|
| 3 |
-
size 1465
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/special_tokens_map.json
DELETED
|
@@ -1,7 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"cls_token": "[CLS]",
|
| 3 |
-
"mask_token": "[MASK]",
|
| 4 |
-
"pad_token": "[PAD]",
|
| 5 |
-
"sep_token": "[SEP]",
|
| 6 |
-
"unk_token": "[UNK]"
|
| 7 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/tokenizer.json
DELETED
|
The diff for this file is too large to render.
See raw diff
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/tokenizer_config.json
DELETED
|
@@ -1,56 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"added_tokens_decoder": {
|
| 3 |
-
"0": {
|
| 4 |
-
"content": "[PAD]",
|
| 5 |
-
"lstrip": false,
|
| 6 |
-
"normalized": false,
|
| 7 |
-
"rstrip": false,
|
| 8 |
-
"single_word": false,
|
| 9 |
-
"special": true
|
| 10 |
-
},
|
| 11 |
-
"1": {
|
| 12 |
-
"content": "[UNK]",
|
| 13 |
-
"lstrip": false,
|
| 14 |
-
"normalized": false,
|
| 15 |
-
"rstrip": false,
|
| 16 |
-
"single_word": false,
|
| 17 |
-
"special": true
|
| 18 |
-
},
|
| 19 |
-
"2": {
|
| 20 |
-
"content": "[CLS]",
|
| 21 |
-
"lstrip": false,
|
| 22 |
-
"normalized": false,
|
| 23 |
-
"rstrip": false,
|
| 24 |
-
"single_word": false,
|
| 25 |
-
"special": true
|
| 26 |
-
},
|
| 27 |
-
"3": {
|
| 28 |
-
"content": "[SEP]",
|
| 29 |
-
"lstrip": false,
|
| 30 |
-
"normalized": false,
|
| 31 |
-
"rstrip": false,
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"special": true
|
| 34 |
-
},
|
| 35 |
-
"4": {
|
| 36 |
-
"content": "[MASK]",
|
| 37 |
-
"lstrip": false,
|
| 38 |
-
"normalized": false,
|
| 39 |
-
"rstrip": false,
|
| 40 |
-
"single_word": false,
|
| 41 |
-
"special": true
|
| 42 |
-
}
|
| 43 |
-
},
|
| 44 |
-
"cache_dir": null,
|
| 45 |
-
"clean_up_tokenization_spaces": true,
|
| 46 |
-
"cls_token": "[CLS]",
|
| 47 |
-
"mask_token": "[MASK]",
|
| 48 |
-
"model_max_length": 100,
|
| 49 |
-
"pad_token": "[PAD]",
|
| 50 |
-
"padding_side": "right",
|
| 51 |
-
"sep_token": "[SEP]",
|
| 52 |
-
"tokenizer_class": "PreTrainedTokenizerFast",
|
| 53 |
-
"trust_remote_code": true,
|
| 54 |
-
"unk_token": "[UNK]",
|
| 55 |
-
"use_fast": true
|
| 56 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/trainer_state.json
DELETED
|
@@ -1,32 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"best_metric": null,
|
| 3 |
-
"best_model_checkpoint": null,
|
| 4 |
-
"epoch": 1.1494252873563218,
|
| 5 |
-
"eval_steps": 200,
|
| 6 |
-
"global_step": 200,
|
| 7 |
-
"is_hyper_param_search": false,
|
| 8 |
-
"is_local_process_zero": true,
|
| 9 |
-
"is_world_process_zero": true,
|
| 10 |
-
"log_history": [
|
| 11 |
-
{
|
| 12 |
-
"epoch": 1.15,
|
| 13 |
-
"eval_accuracy": 0.7286793810723282,
|
| 14 |
-
"eval_f1": 0.7271360409211425,
|
| 15 |
-
"eval_loss": 0.5445785522460938,
|
| 16 |
-
"eval_matthews_correlation": 0.46663894149578333,
|
| 17 |
-
"eval_precision": 0.7365956748590126,
|
| 18 |
-
"eval_recall": 0.7300886331185719,
|
| 19 |
-
"eval_runtime": 0.348,
|
| 20 |
-
"eval_samples_per_second": 7985.407,
|
| 21 |
-
"eval_steps_per_second": 63.217,
|
| 22 |
-
"step": 200
|
| 23 |
-
}
|
| 24 |
-
],
|
| 25 |
-
"logging_steps": 100000,
|
| 26 |
-
"max_steps": 522,
|
| 27 |
-
"num_train_epochs": 3,
|
| 28 |
-
"save_steps": 200,
|
| 29 |
-
"total_flos": 1313499783364608.0,
|
| 30 |
-
"trial_name": null,
|
| 31 |
-
"trial_params": null
|
| 32 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-200/training_args.bin
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:b8c6df0d1fd7a8910e91ac2e4665756964d043de7f403929bacfd9e34f1388b5
|
| 3 |
-
size 5329
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/config.json
DELETED
|
@@ -1,27 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "/root/NaN/dna-tokenizer/pretrain/models/base_3072/checkpoint-100000",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"BertForSequenceClassification"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"classifier_dropout": null,
|
| 8 |
-
"hidden_act": "gelu",
|
| 9 |
-
"hidden_dropout_prob": 0.1,
|
| 10 |
-
"hidden_size": 768,
|
| 11 |
-
"initializer_range": 0.02,
|
| 12 |
-
"intermediate_size": 3072,
|
| 13 |
-
"layer_norm_eps": 1e-12,
|
| 14 |
-
"max_length": 512,
|
| 15 |
-
"max_position_embeddings": 512,
|
| 16 |
-
"model_type": "bert",
|
| 17 |
-
"num_attention_heads": 12,
|
| 18 |
-
"num_hidden_layers": 12,
|
| 19 |
-
"pad_token_id": 0,
|
| 20 |
-
"position_embedding_type": "absolute",
|
| 21 |
-
"problem_type": "single_label_classification",
|
| 22 |
-
"torch_dtype": "float32",
|
| 23 |
-
"transformers_version": "4.35.2",
|
| 24 |
-
"type_vocab_size": 2,
|
| 25 |
-
"use_cache": true,
|
| 26 |
-
"vocab_size": 3072
|
| 27 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/model.safetensors
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:ca1bb44d247fe4142437d9c68fc97ec540fca4ad0152b71adb5756435b631832
|
| 3 |
-
size 353632152
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/optimizer.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:9a2fcbac5e10b061d1fba1acef2b3672c839dbf49f2eb95f605f21b20d1303df
|
| 3 |
-
size 707385995
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/rng_state.pth
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:bf4fe29cf4fa8f59481df0375c4e4cf281f735468b247420d21bee83dfb267a0
|
| 3 |
-
size 14709
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/scheduler.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:c56e12e83caf66084bf3a11d3b018aa44e73d3fae41719bdf4ec4aebd71349b8
|
| 3 |
-
size 1465
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/special_tokens_map.json
DELETED
|
@@ -1,7 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"cls_token": "[CLS]",
|
| 3 |
-
"mask_token": "[MASK]",
|
| 4 |
-
"pad_token": "[PAD]",
|
| 5 |
-
"sep_token": "[SEP]",
|
| 6 |
-
"unk_token": "[UNK]"
|
| 7 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/tokenizer.json
DELETED
|
The diff for this file is too large to render.
See raw diff
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/tokenizer_config.json
DELETED
|
@@ -1,56 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"added_tokens_decoder": {
|
| 3 |
-
"0": {
|
| 4 |
-
"content": "[PAD]",
|
| 5 |
-
"lstrip": false,
|
| 6 |
-
"normalized": false,
|
| 7 |
-
"rstrip": false,
|
| 8 |
-
"single_word": false,
|
| 9 |
-
"special": true
|
| 10 |
-
},
|
| 11 |
-
"1": {
|
| 12 |
-
"content": "[UNK]",
|
| 13 |
-
"lstrip": false,
|
| 14 |
-
"normalized": false,
|
| 15 |
-
"rstrip": false,
|
| 16 |
-
"single_word": false,
|
| 17 |
-
"special": true
|
| 18 |
-
},
|
| 19 |
-
"2": {
|
| 20 |
-
"content": "[CLS]",
|
| 21 |
-
"lstrip": false,
|
| 22 |
-
"normalized": false,
|
| 23 |
-
"rstrip": false,
|
| 24 |
-
"single_word": false,
|
| 25 |
-
"special": true
|
| 26 |
-
},
|
| 27 |
-
"3": {
|
| 28 |
-
"content": "[SEP]",
|
| 29 |
-
"lstrip": false,
|
| 30 |
-
"normalized": false,
|
| 31 |
-
"rstrip": false,
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"special": true
|
| 34 |
-
},
|
| 35 |
-
"4": {
|
| 36 |
-
"content": "[MASK]",
|
| 37 |
-
"lstrip": false,
|
| 38 |
-
"normalized": false,
|
| 39 |
-
"rstrip": false,
|
| 40 |
-
"single_word": false,
|
| 41 |
-
"special": true
|
| 42 |
-
}
|
| 43 |
-
},
|
| 44 |
-
"cache_dir": null,
|
| 45 |
-
"clean_up_tokenization_spaces": true,
|
| 46 |
-
"cls_token": "[CLS]",
|
| 47 |
-
"mask_token": "[MASK]",
|
| 48 |
-
"model_max_length": 100,
|
| 49 |
-
"pad_token": "[PAD]",
|
| 50 |
-
"padding_side": "right",
|
| 51 |
-
"sep_token": "[SEP]",
|
| 52 |
-
"tokenizer_class": "PreTrainedTokenizerFast",
|
| 53 |
-
"trust_remote_code": true,
|
| 54 |
-
"unk_token": "[UNK]",
|
| 55 |
-
"use_fast": true
|
| 56 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/trainer_state.json
DELETED
|
@@ -1,45 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"best_metric": null,
|
| 3 |
-
"best_model_checkpoint": null,
|
| 4 |
-
"epoch": 2.2988505747126435,
|
| 5 |
-
"eval_steps": 200,
|
| 6 |
-
"global_step": 400,
|
| 7 |
-
"is_hyper_param_search": false,
|
| 8 |
-
"is_local_process_zero": true,
|
| 9 |
-
"is_world_process_zero": true,
|
| 10 |
-
"log_history": [
|
| 11 |
-
{
|
| 12 |
-
"epoch": 1.15,
|
| 13 |
-
"eval_accuracy": 0.7286793810723282,
|
| 14 |
-
"eval_f1": 0.7271360409211425,
|
| 15 |
-
"eval_loss": 0.5445785522460938,
|
| 16 |
-
"eval_matthews_correlation": 0.46663894149578333,
|
| 17 |
-
"eval_precision": 0.7365956748590126,
|
| 18 |
-
"eval_recall": 0.7300886331185719,
|
| 19 |
-
"eval_runtime": 0.348,
|
| 20 |
-
"eval_samples_per_second": 7985.407,
|
| 21 |
-
"eval_steps_per_second": 63.217,
|
| 22 |
-
"step": 200
|
| 23 |
-
},
|
| 24 |
-
{
|
| 25 |
-
"epoch": 2.3,
|
| 26 |
-
"eval_accuracy": 0.7315581144296509,
|
| 27 |
-
"eval_f1": 0.7303631758953757,
|
| 28 |
-
"eval_loss": 0.5473530292510986,
|
| 29 |
-
"eval_matthews_correlation": 0.4708754627902413,
|
| 30 |
-
"eval_precision": 0.7380764695224866,
|
| 31 |
-
"eval_recall": 0.7328282399166098,
|
| 32 |
-
"eval_runtime": 0.3356,
|
| 33 |
-
"eval_samples_per_second": 8281.835,
|
| 34 |
-
"eval_steps_per_second": 65.563,
|
| 35 |
-
"step": 400
|
| 36 |
-
}
|
| 37 |
-
],
|
| 38 |
-
"logging_steps": 100000,
|
| 39 |
-
"max_steps": 522,
|
| 40 |
-
"num_train_epochs": 3,
|
| 41 |
-
"save_steps": 200,
|
| 42 |
-
"total_flos": 2626999566729216.0,
|
| 43 |
-
"trial_name": null,
|
| 44 |
-
"trial_params": null
|
| 45 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/checkpoint-400/training_args.bin
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:b8c6df0d1fd7a8910e91ac2e4665756964d043de7f403929bacfd9e34f1388b5
|
| 3 |
-
size 5329
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_3072/results/base_3072_hg38_BPE_3e-5_human_enhancers_cohn_seed42/eval_results.json
DELETED
|
@@ -1 +0,0 @@
|
|
| 1 |
-
{"eval_loss": 0.5286217331886292, "eval_accuracy": 0.7478417266187051, "eval_f1": 0.747571248577904, "eval_matthews_correlation": 0.4964151424232939, "eval_precision": 0.7486823947994081, "eval_recall": 0.7477336542318491, "eval_runtime": 0.3382, "eval_samples_per_second": 8219.743, "eval_steps_per_second": 65.048, "epoch": 3.0}
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/config.json
DELETED
|
@@ -1,27 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "/root/NaN/dna-tokenizer/pretrain/models/base_4096/checkpoint-100000",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"BertForSequenceClassification"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"classifier_dropout": null,
|
| 8 |
-
"hidden_act": "gelu",
|
| 9 |
-
"hidden_dropout_prob": 0.1,
|
| 10 |
-
"hidden_size": 768,
|
| 11 |
-
"initializer_range": 0.02,
|
| 12 |
-
"intermediate_size": 3072,
|
| 13 |
-
"layer_norm_eps": 1e-12,
|
| 14 |
-
"max_length": 512,
|
| 15 |
-
"max_position_embeddings": 512,
|
| 16 |
-
"model_type": "bert",
|
| 17 |
-
"num_attention_heads": 12,
|
| 18 |
-
"num_hidden_layers": 12,
|
| 19 |
-
"pad_token_id": 0,
|
| 20 |
-
"position_embedding_type": "absolute",
|
| 21 |
-
"problem_type": "single_label_classification",
|
| 22 |
-
"torch_dtype": "float32",
|
| 23 |
-
"transformers_version": "4.35.2",
|
| 24 |
-
"type_vocab_size": 2,
|
| 25 |
-
"use_cache": true,
|
| 26 |
-
"vocab_size": 4096
|
| 27 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/model.safetensors
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:17f8ea34fd87774272dee433615c534e78b812c987288cc29089ef02640c988c
|
| 3 |
-
size 356777880
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/optimizer.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:ae741782ffa1b91d2583dd6e1adf687fffe531777e99a7871a49bf36deaa1187
|
| 3 |
-
size 713677451
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/rng_state.pth
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:9e42ae1e4d1487d5e895b4aedb9ab73c4b5e5e7cb820f8e2c7209169be990d46
|
| 3 |
-
size 14709
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/scheduler.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:eb8396a28d05435f8711ed63af5f363fe80d8db70c66f1da4bc3ca37047db868
|
| 3 |
-
size 1465
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/special_tokens_map.json
DELETED
|
@@ -1,7 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"cls_token": "[CLS]",
|
| 3 |
-
"mask_token": "[MASK]",
|
| 4 |
-
"pad_token": "[PAD]",
|
| 5 |
-
"sep_token": "[SEP]",
|
| 6 |
-
"unk_token": "[UNK]"
|
| 7 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/tokenizer.json
DELETED
|
The diff for this file is too large to render.
See raw diff
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/tokenizer_config.json
DELETED
|
@@ -1,56 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"added_tokens_decoder": {
|
| 3 |
-
"0": {
|
| 4 |
-
"content": "[PAD]",
|
| 5 |
-
"lstrip": false,
|
| 6 |
-
"normalized": false,
|
| 7 |
-
"rstrip": false,
|
| 8 |
-
"single_word": false,
|
| 9 |
-
"special": true
|
| 10 |
-
},
|
| 11 |
-
"1": {
|
| 12 |
-
"content": "[UNK]",
|
| 13 |
-
"lstrip": false,
|
| 14 |
-
"normalized": false,
|
| 15 |
-
"rstrip": false,
|
| 16 |
-
"single_word": false,
|
| 17 |
-
"special": true
|
| 18 |
-
},
|
| 19 |
-
"2": {
|
| 20 |
-
"content": "[CLS]",
|
| 21 |
-
"lstrip": false,
|
| 22 |
-
"normalized": false,
|
| 23 |
-
"rstrip": false,
|
| 24 |
-
"single_word": false,
|
| 25 |
-
"special": true
|
| 26 |
-
},
|
| 27 |
-
"3": {
|
| 28 |
-
"content": "[SEP]",
|
| 29 |
-
"lstrip": false,
|
| 30 |
-
"normalized": false,
|
| 31 |
-
"rstrip": false,
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"special": true
|
| 34 |
-
},
|
| 35 |
-
"4": {
|
| 36 |
-
"content": "[MASK]",
|
| 37 |
-
"lstrip": false,
|
| 38 |
-
"normalized": false,
|
| 39 |
-
"rstrip": false,
|
| 40 |
-
"single_word": false,
|
| 41 |
-
"special": true
|
| 42 |
-
}
|
| 43 |
-
},
|
| 44 |
-
"cache_dir": null,
|
| 45 |
-
"clean_up_tokenization_spaces": true,
|
| 46 |
-
"cls_token": "[CLS]",
|
| 47 |
-
"mask_token": "[MASK]",
|
| 48 |
-
"model_max_length": 100,
|
| 49 |
-
"pad_token": "[PAD]",
|
| 50 |
-
"padding_side": "right",
|
| 51 |
-
"sep_token": "[SEP]",
|
| 52 |
-
"tokenizer_class": "PreTrainedTokenizerFast",
|
| 53 |
-
"trust_remote_code": true,
|
| 54 |
-
"unk_token": "[UNK]",
|
| 55 |
-
"use_fast": true
|
| 56 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/trainer_state.json
DELETED
|
@@ -1,32 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"best_metric": null,
|
| 3 |
-
"best_model_checkpoint": null,
|
| 4 |
-
"epoch": 1.1494252873563218,
|
| 5 |
-
"eval_steps": 200,
|
| 6 |
-
"global_step": 200,
|
| 7 |
-
"is_hyper_param_search": false,
|
| 8 |
-
"is_local_process_zero": true,
|
| 9 |
-
"is_world_process_zero": true,
|
| 10 |
-
"log_history": [
|
| 11 |
-
{
|
| 12 |
-
"epoch": 1.15,
|
| 13 |
-
"eval_accuracy": 0.7272400143936668,
|
| 14 |
-
"eval_f1": 0.726651008279048,
|
| 15 |
-
"eval_loss": 0.5429649949073792,
|
| 16 |
-
"eval_matthews_correlation": 0.4590420984631282,
|
| 17 |
-
"eval_precision": 0.7308673322297692,
|
| 18 |
-
"eval_recall": 0.7281826169669112,
|
| 19 |
-
"eval_runtime": 0.3499,
|
| 20 |
-
"eval_samples_per_second": 7943.048,
|
| 21 |
-
"eval_steps_per_second": 62.881,
|
| 22 |
-
"step": 200
|
| 23 |
-
}
|
| 24 |
-
],
|
| 25 |
-
"logging_steps": 100000,
|
| 26 |
-
"max_steps": 522,
|
| 27 |
-
"num_train_epochs": 3,
|
| 28 |
-
"save_steps": 200,
|
| 29 |
-
"total_flos": 1313499783364608.0,
|
| 30 |
-
"trial_name": null,
|
| 31 |
-
"trial_params": null
|
| 32 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-200/training_args.bin
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:0a64e6cdb75d2c4c3c7a14d660dc111937f95bed2b6a6945ed2b775bb8a44575
|
| 3 |
-
size 5329
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/config.json
DELETED
|
@@ -1,27 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "/root/NaN/dna-tokenizer/pretrain/models/base_4096/checkpoint-100000",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"BertForSequenceClassification"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"classifier_dropout": null,
|
| 8 |
-
"hidden_act": "gelu",
|
| 9 |
-
"hidden_dropout_prob": 0.1,
|
| 10 |
-
"hidden_size": 768,
|
| 11 |
-
"initializer_range": 0.02,
|
| 12 |
-
"intermediate_size": 3072,
|
| 13 |
-
"layer_norm_eps": 1e-12,
|
| 14 |
-
"max_length": 512,
|
| 15 |
-
"max_position_embeddings": 512,
|
| 16 |
-
"model_type": "bert",
|
| 17 |
-
"num_attention_heads": 12,
|
| 18 |
-
"num_hidden_layers": 12,
|
| 19 |
-
"pad_token_id": 0,
|
| 20 |
-
"position_embedding_type": "absolute",
|
| 21 |
-
"problem_type": "single_label_classification",
|
| 22 |
-
"torch_dtype": "float32",
|
| 23 |
-
"transformers_version": "4.35.2",
|
| 24 |
-
"type_vocab_size": 2,
|
| 25 |
-
"use_cache": true,
|
| 26 |
-
"vocab_size": 4096
|
| 27 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/model.safetensors
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:7a89e0fa0910b22b9665a40cf1ebc94092151a2e6a189c3722f0993a717f95f3
|
| 3 |
-
size 356777880
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/optimizer.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:e696bee8175087f3b9982ebbb087e7cc5bda7fa2993eac0c6153c308dc8e5ee3
|
| 3 |
-
size 713677451
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/rng_state.pth
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:bf4fe29cf4fa8f59481df0375c4e4cf281f735468b247420d21bee83dfb267a0
|
| 3 |
-
size 14709
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/scheduler.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:c56e12e83caf66084bf3a11d3b018aa44e73d3fae41719bdf4ec4aebd71349b8
|
| 3 |
-
size 1465
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/special_tokens_map.json
DELETED
|
@@ -1,7 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"cls_token": "[CLS]",
|
| 3 |
-
"mask_token": "[MASK]",
|
| 4 |
-
"pad_token": "[PAD]",
|
| 5 |
-
"sep_token": "[SEP]",
|
| 6 |
-
"unk_token": "[UNK]"
|
| 7 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/tokenizer.json
DELETED
|
The diff for this file is too large to render.
See raw diff
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/tokenizer_config.json
DELETED
|
@@ -1,56 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"added_tokens_decoder": {
|
| 3 |
-
"0": {
|
| 4 |
-
"content": "[PAD]",
|
| 5 |
-
"lstrip": false,
|
| 6 |
-
"normalized": false,
|
| 7 |
-
"rstrip": false,
|
| 8 |
-
"single_word": false,
|
| 9 |
-
"special": true
|
| 10 |
-
},
|
| 11 |
-
"1": {
|
| 12 |
-
"content": "[UNK]",
|
| 13 |
-
"lstrip": false,
|
| 14 |
-
"normalized": false,
|
| 15 |
-
"rstrip": false,
|
| 16 |
-
"single_word": false,
|
| 17 |
-
"special": true
|
| 18 |
-
},
|
| 19 |
-
"2": {
|
| 20 |
-
"content": "[CLS]",
|
| 21 |
-
"lstrip": false,
|
| 22 |
-
"normalized": false,
|
| 23 |
-
"rstrip": false,
|
| 24 |
-
"single_word": false,
|
| 25 |
-
"special": true
|
| 26 |
-
},
|
| 27 |
-
"3": {
|
| 28 |
-
"content": "[SEP]",
|
| 29 |
-
"lstrip": false,
|
| 30 |
-
"normalized": false,
|
| 31 |
-
"rstrip": false,
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"special": true
|
| 34 |
-
},
|
| 35 |
-
"4": {
|
| 36 |
-
"content": "[MASK]",
|
| 37 |
-
"lstrip": false,
|
| 38 |
-
"normalized": false,
|
| 39 |
-
"rstrip": false,
|
| 40 |
-
"single_word": false,
|
| 41 |
-
"special": true
|
| 42 |
-
}
|
| 43 |
-
},
|
| 44 |
-
"cache_dir": null,
|
| 45 |
-
"clean_up_tokenization_spaces": true,
|
| 46 |
-
"cls_token": "[CLS]",
|
| 47 |
-
"mask_token": "[MASK]",
|
| 48 |
-
"model_max_length": 100,
|
| 49 |
-
"pad_token": "[PAD]",
|
| 50 |
-
"padding_side": "right",
|
| 51 |
-
"sep_token": "[SEP]",
|
| 52 |
-
"tokenizer_class": "PreTrainedTokenizerFast",
|
| 53 |
-
"trust_remote_code": true,
|
| 54 |
-
"unk_token": "[UNK]",
|
| 55 |
-
"use_fast": true
|
| 56 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/trainer_state.json
DELETED
|
@@ -1,45 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"best_metric": null,
|
| 3 |
-
"best_model_checkpoint": null,
|
| 4 |
-
"epoch": 2.2988505747126435,
|
| 5 |
-
"eval_steps": 200,
|
| 6 |
-
"global_step": 400,
|
| 7 |
-
"is_hyper_param_search": false,
|
| 8 |
-
"is_local_process_zero": true,
|
| 9 |
-
"is_world_process_zero": true,
|
| 10 |
-
"log_history": [
|
| 11 |
-
{
|
| 12 |
-
"epoch": 1.15,
|
| 13 |
-
"eval_accuracy": 0.7272400143936668,
|
| 14 |
-
"eval_f1": 0.726651008279048,
|
| 15 |
-
"eval_loss": 0.5429649949073792,
|
| 16 |
-
"eval_matthews_correlation": 0.4590420984631282,
|
| 17 |
-
"eval_precision": 0.7308673322297692,
|
| 18 |
-
"eval_recall": 0.7281826169669112,
|
| 19 |
-
"eval_runtime": 0.3499,
|
| 20 |
-
"eval_samples_per_second": 7943.048,
|
| 21 |
-
"eval_steps_per_second": 62.881,
|
| 22 |
-
"step": 200
|
| 23 |
-
},
|
| 24 |
-
{
|
| 25 |
-
"epoch": 2.3,
|
| 26 |
-
"eval_accuracy": 0.7311982727599856,
|
| 27 |
-
"eval_f1": 0.7303485546869165,
|
| 28 |
-
"eval_loss": 0.5538003444671631,
|
| 29 |
-
"eval_matthews_correlation": 0.46841885139218503,
|
| 30 |
-
"eval_precision": 0.7361352778105461,
|
| 31 |
-
"eval_recall": 0.7322992802833276,
|
| 32 |
-
"eval_runtime": 0.3367,
|
| 33 |
-
"eval_samples_per_second": 8254.814,
|
| 34 |
-
"eval_steps_per_second": 65.349,
|
| 35 |
-
"step": 400
|
| 36 |
-
}
|
| 37 |
-
],
|
| 38 |
-
"logging_steps": 100000,
|
| 39 |
-
"max_steps": 522,
|
| 40 |
-
"num_train_epochs": 3,
|
| 41 |
-
"save_steps": 200,
|
| 42 |
-
"total_flos": 2626999566729216.0,
|
| 43 |
-
"trial_name": null,
|
| 44 |
-
"trial_params": null
|
| 45 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/checkpoint-400/training_args.bin
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:0a64e6cdb75d2c4c3c7a14d660dc111937f95bed2b6a6945ed2b775bb8a44575
|
| 3 |
-
size 5329
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/base_4096/results/base_4096_hg38_BPE_3e-5_human_enhancers_cohn_seed42/eval_results.json
DELETED
|
@@ -1 +0,0 @@
|
|
| 1 |
-
{"eval_loss": 0.5185958743095398, "eval_accuracy": 0.7568345323741007, "eval_f1": 0.7568344065185065, "eval_matthews_correlation": 0.5136970171361614, "eval_precision": 0.7568501038533662, "eval_recall": 0.7568469132927035, "eval_runtime": 0.3402, "eval_samples_per_second": 8172.163, "eval_steps_per_second": 64.672, "epoch": 3.0}
|
|
|
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/config.json
DELETED
|
@@ -1,27 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "/root/NaN/dna-tokenizer/pretrain/models/model_len2_4096/checkpoint-100000",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"BertForSequenceClassification"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"classifier_dropout": null,
|
| 8 |
-
"hidden_act": "gelu",
|
| 9 |
-
"hidden_dropout_prob": 0.1,
|
| 10 |
-
"hidden_size": 768,
|
| 11 |
-
"initializer_range": 0.02,
|
| 12 |
-
"intermediate_size": 3072,
|
| 13 |
-
"layer_norm_eps": 1e-12,
|
| 14 |
-
"max_length": 512,
|
| 15 |
-
"max_position_embeddings": 512,
|
| 16 |
-
"model_type": "bert",
|
| 17 |
-
"num_attention_heads": 12,
|
| 18 |
-
"num_hidden_layers": 12,
|
| 19 |
-
"pad_token_id": 0,
|
| 20 |
-
"position_embedding_type": "absolute",
|
| 21 |
-
"problem_type": "single_label_classification",
|
| 22 |
-
"torch_dtype": "float32",
|
| 23 |
-
"transformers_version": "4.35.2",
|
| 24 |
-
"type_vocab_size": 2,
|
| 25 |
-
"use_cache": true,
|
| 26 |
-
"vocab_size": 4096
|
| 27 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/model.safetensors
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:efcd4d4cbed93bfdbaacc31b84d83bc08e5f225251adfc0636182562c7003d6b
|
| 3 |
-
size 356777880
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/optimizer.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:744f69f215485b9463065926fd18c83fe8a9e9470e0addacb1b680e537c30c66
|
| 3 |
-
size 713677451
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/rng_state.pth
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:9e42ae1e4d1487d5e895b4aedb9ab73c4b5e5e7cb820f8e2c7209169be990d46
|
| 3 |
-
size 14709
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/scheduler.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:eb8396a28d05435f8711ed63af5f363fe80d8db70c66f1da4bc3ca37047db868
|
| 3 |
-
size 1465
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/special_tokens_map.json
DELETED
|
@@ -1,7 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"cls_token": "[CLS]",
|
| 3 |
-
"mask_token": "[MASK]",
|
| 4 |
-
"pad_token": "[PAD]",
|
| 5 |
-
"sep_token": "[SEP]",
|
| 6 |
-
"unk_token": "[UNK]"
|
| 7 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/tokenizer.json
DELETED
|
The diff for this file is too large to render.
See raw diff
|
|
|
human_enhancers_cohn/len2_4096/checkpoint-200/tokenizer_config.json
DELETED
|
@@ -1,15 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"added_tokens_decoder": {},
|
| 3 |
-
"cache_dir": null,
|
| 4 |
-
"clean_up_tokenization_spaces": true,
|
| 5 |
-
"cls_token": "[CLS]",
|
| 6 |
-
"mask_token": "[MASK]",
|
| 7 |
-
"model_max_length": 100,
|
| 8 |
-
"pad_token": "[PAD]",
|
| 9 |
-
"padding_side": "right",
|
| 10 |
-
"sep_token": "[SEP]",
|
| 11 |
-
"tokenizer_class": "PreTrainedTokenizerFast",
|
| 12 |
-
"trust_remote_code": true,
|
| 13 |
-
"unk_token": "[UNK]",
|
| 14 |
-
"use_fast": true
|
| 15 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|