Commit
•
35cea74
1
Parent(s):
b83af74
Upload 11 files
Browse files- added_tokens.json +7 -0
- config (6).json +38 -0
- optimizer.pt +3 -0
- pytorch_model (2).bin +3 -0
- rng_state.pth +3 -0
- scheduler.pt +3 -0
- special_tokens_map.json +7 -0
- tokenizer_config.json +54 -0
- trainer_state.json +1293 -0
- training_args.bin +3 -0
- vocab.txt +33 -0
added_tokens.json
ADDED
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{
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"<cls>": 0,
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"<eos>": 2,
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"<mask>": 32,
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"<pad>": 1,
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"<unk>": 3
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}
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config (6).json
ADDED
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{
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"_name_or_path": "facebook/esm2_t6_8M_UR50D",
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"architectures": [
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"EsmForTokenClassification"
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],
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"attention_probs_dropout_prob": 0.5,
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"classifier_dropout": null,
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"emb_layer_norm_before": false,
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"esmfold_config": null,
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"hidden_act": "gelu",
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"hidden_dropout_prob": 0.5,
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"hidden_size": 320,
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"id2label": {
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"0": "No binding site",
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"1": "Binding site"
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},
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"initializer_range": 0.02,
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"intermediate_size": 1280,
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"is_folding_model": false,
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"label2id": {
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"Binding site": 1,
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"No binding site": 0
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},
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"layer_norm_eps": 1e-05,
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"mask_token_id": 32,
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"max_position_embeddings": 1026,
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"model_type": "esm",
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"num_attention_heads": 20,
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"num_hidden_layers": 6,
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"pad_token_id": 1,
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"position_embedding_type": "rotary",
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"token_dropout": true,
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"torch_dtype": "float32",
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"transformers_version": "4.34.0.dev0",
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"use_cache": true,
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"vocab_list": null,
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"vocab_size": 33
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}
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optimizer.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:ed01130202ab25bb28e408aff3d24b21e5262e7b557d9e0cd96d55cac4e0692a
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size 59361093
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pytorch_model (2).bin
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version https://git-lfs.github.com/spec/v1
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oid sha256:0a0e3863ebd00a136b483eb80d58882f03a47f08d7767b8a5158682fd7cc8c5c
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size 30989061
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rng_state.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:1a85c8f82e6ff59890e9b6b487c977f3ce1fcedec53eae378d17f83e2ecbb1a6
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size 14575
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scheduler.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:73eb32d30209f5b72ceb1037fc68aabd56fd23c02d2f88302d7a2c36d742bf16
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size 627
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special_tokens_map.json
ADDED
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{
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"cls_token": "<cls>",
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"eos_token": "<eos>",
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"mask_token": "<mask>",
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"pad_token": "<pad>",
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"unk_token": "<unk>"
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}
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tokenizer_config.json
ADDED
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@@ -0,0 +1,54 @@
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{
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"added_tokens_decoder": {
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"0": {
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"content": "<cls>",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"1": {
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"content": "<pad>",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"2": {
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"content": "<eos>",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"3": {
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"content": "<unk>",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"32": {
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"content": "<mask>",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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}
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},
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"additional_special_tokens": [],
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"clean_up_tokenization_spaces": true,
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"cls_token": "<cls>",
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"eos_token": "<eos>",
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"mask_token": "<mask>",
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"model_max_length": 1024,
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"pad_token": "<pad>",
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"tokenizer_class": "EsmTokenizer",
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"tokenizer_file": null,
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"unk_token": "<unk>"
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}
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trainer_state.json
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|
| 1 |
+
{
|
| 2 |
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"best_metric": 0.23276936632271397,
|
| 3 |
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"best_model_checkpoint": "esm2_t6_8M_finetune_2023-10-08_00-58-24/checkpoint-42015",
|
| 4 |
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"epoch": 1.0,
|
| 5 |
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"eval_steps": 500,
|
| 6 |
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"global_step": 42015,
|
| 7 |
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"is_hyper_param_search": false,
|
| 8 |
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"is_local_process_zero": true,
|
| 9 |
+
"is_world_process_zero": true,
|
| 10 |
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"log_history": [
|
| 11 |
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{
|
| 12 |
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"epoch": 0.0,
|
| 13 |
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"learning_rate": 0.0005701249285950224,
|
| 14 |
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"loss": 0.65,
|
| 15 |
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"step": 200
|
| 16 |
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},
|
| 17 |
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{
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| 18 |
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"epoch": 0.01,
|
| 19 |
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"learning_rate": 0.0005700293047710233,
|
| 20 |
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"loss": 0.5381,
|
| 21 |
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"step": 400
|
| 22 |
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},
|
| 23 |
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{
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| 24 |
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|
| 25 |
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| 26 |
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"loss": 0.5093,
|
| 27 |
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"step": 600
|
| 28 |
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},
|
| 29 |
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{
|
| 30 |
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"epoch": 0.02,
|
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|
| 1257 |
+
"step": 41600
|
| 1258 |
+
},
|
| 1259 |
+
{
|
| 1260 |
+
"epoch": 0.99,
|
| 1261 |
+
"learning_rate": 4.215705833867654e-08,
|
| 1262 |
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"loss": 0.1186,
|
| 1263 |
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"step": 41800
|
| 1264 |
+
},
|
| 1265 |
+
{
|
| 1266 |
+
"epoch": 1.0,
|
| 1267 |
+
"learning_rate": 7.172452126860464e-10,
|
| 1268 |
+
"loss": 0.1156,
|
| 1269 |
+
"step": 42000
|
| 1270 |
+
},
|
| 1271 |
+
{
|
| 1272 |
+
"epoch": 1.0,
|
| 1273 |
+
"eval_accuracy": 0.9232681404353718,
|
| 1274 |
+
"eval_auc": 0.7327222270892191,
|
| 1275 |
+
"eval_f1": 0.23276936632271397,
|
| 1276 |
+
"eval_loss": 1.4070135354995728,
|
| 1277 |
+
"eval_mcc": 0.2532717443913893,
|
| 1278 |
+
"eval_precision": 0.14886006058928025,
|
| 1279 |
+
"eval_recall": 0.5334820519181167,
|
| 1280 |
+
"eval_runtime": 1911.9976,
|
| 1281 |
+
"eval_samples_per_second": 66.763,
|
| 1282 |
+
"eval_steps_per_second": 5.564,
|
| 1283 |
+
"step": 42015
|
| 1284 |
+
}
|
| 1285 |
+
],
|
| 1286 |
+
"logging_steps": 200,
|
| 1287 |
+
"max_steps": 42015,
|
| 1288 |
+
"num_train_epochs": 1,
|
| 1289 |
+
"save_steps": 500,
|
| 1290 |
+
"total_flos": 2.0189159728820676e+16,
|
| 1291 |
+
"trial_name": null,
|
| 1292 |
+
"trial_params": null
|
| 1293 |
+
}
|
training_args.bin
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
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|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:30d2e37dd745b136deee1518b887f496e20443336e529bbeb49feb47e366d3ff
|
| 3 |
+
size 4091
|
vocab.txt
ADDED
|
@@ -0,0 +1,33 @@
|
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|
|
|
|
|
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|
|
|
|
|
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|
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|
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|
|
|
|
|
|
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|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 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>
|