Upload folder using huggingface_hub
Browse files- README.md +37 -0
- checkpoint-450/config.json +55 -0
- checkpoint-450/model.safetensors +3 -0
- checkpoint-450/optimizer.pt +3 -0
- checkpoint-450/rng_state.pth +3 -0
- checkpoint-450/scheduler.pt +3 -0
- checkpoint-450/trainer_state.json +523 -0
- checkpoint-450/training_args.bin +3 -0
- config.json +55 -0
- model.safetensors +3 -0
- special_tokens_map.json +7 -0
- tokenizer.json +194 -0
- tokenizer_config.json +58 -0
- training_args.bin +3 -0
- training_params.json +30 -0
- vocab.txt +30 -0
README.md
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---
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tags:
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- autotrain
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- text-classification
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widget:
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- text: "I love AutoTrain"
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datasets:
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- as-cle-bert/AMR-Gene-Families
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---
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# Model Trained Using AutoTrain
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- Problem type: Text Classification
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## Validation Metrics
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loss: 0.08235077559947968
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f1_macro: 0.986759581881533
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f1_micro: 0.99
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f1_weighted: 0.9899790940766551
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precision_macro: 0.9871615312791784
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precision_micro: 0.99
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precision_weighted: 0.9901213818860879
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recall_macro: 0.986574074074074
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recall_micro: 0.99
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recall_weighted: 0.99
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accuracy: 0.99
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checkpoint-450/config.json
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{
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"_name_or_path": "Rostlab/prot_bert",
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"_num_labels": 12,
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"architectures": [
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"BertForSequenceClassification"
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],
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"attention_probs_dropout_prob": 0.0,
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"classifier_dropout": null,
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"hidden_act": "gelu",
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"hidden_dropout_prob": 0.0,
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"hidden_size": 1024,
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"id2label": {
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"0": "PDC beta-lactamase",
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"1": "CTX-M beta-lactamase",
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"2": "SHV beta-lactamase",
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"3": "CMY beta-lactamase",
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"4": "resistance-nodulation-cell division (RND) antibiotic efflux pump",
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"5": "major facilitator superfamily (MFS) antibiotic efflux pump",
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| 19 |
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"6": "quinolone resistance protein (qnr)",
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| 20 |
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"7": "IMP beta-lactamase",
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| 21 |
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"8": "KPC beta-lactamase",
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| 22 |
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"9": "ACT beta-lactamase",
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"10": "MCR phosphoethanolamine transferase",
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"11": "VIM beta-lactamase"
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},
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"initializer_range": 0.02,
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| 27 |
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"intermediate_size": 4096,
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"label2id": {
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"ACT beta-lactamase": 9,
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| 30 |
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"CMY beta-lactamase": 3,
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"CTX-M beta-lactamase": 1,
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| 32 |
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"IMP beta-lactamase": 7,
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| 33 |
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"KPC beta-lactamase": 8,
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| 34 |
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"MCR phosphoethanolamine transferase": 10,
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| 35 |
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"PDC beta-lactamase": 0,
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| 36 |
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"SHV beta-lactamase": 2,
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| 37 |
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"VIM beta-lactamase": 11,
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| 38 |
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"major facilitator superfamily (MFS) antibiotic efflux pump": 5,
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| 39 |
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"quinolone resistance protein (qnr)": 6,
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| 40 |
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"resistance-nodulation-cell division (RND) antibiotic efflux pump": 4
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| 41 |
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},
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| 42 |
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"layer_norm_eps": 1e-12,
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| 43 |
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"max_position_embeddings": 40000,
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| 44 |
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"model_type": "bert",
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| 45 |
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"num_attention_heads": 16,
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| 46 |
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"num_hidden_layers": 30,
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| 47 |
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"pad_token_id": 0,
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| 48 |
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"position_embedding_type": "absolute",
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| 49 |
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"problem_type": "single_label_classification",
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| 50 |
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"torch_dtype": "float32",
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"transformers_version": "4.39.0",
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| 52 |
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"type_vocab_size": 2,
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"use_cache": true,
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"vocab_size": 30
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}
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checkpoint-450/model.safetensors
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version https://git-lfs.github.com/spec/v1
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oid sha256:7b482ed0644cc263571f364d2f8c163134071cf2e1f377000fdb9576dad99882
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size 1679832496
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checkpoint-450/optimizer.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:9309b9d765925a9e41447d54c63767cfe3285429cae7a8e089794f2e91b70bb1
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size 3359943437
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checkpoint-450/rng_state.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:5e721764cfe6d7ef80d19a2ff27d723d65ac25eb377b60bb6e4c10a66202a1bf
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size 13990
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checkpoint-450/scheduler.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:7f2295262c8b0cd31776d8d5f370bfd4d7da47a787dc53758a73b3dbb54b80f3
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size 1064
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checkpoint-450/trainer_state.json
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"id": 3,
|
| 49 |
+
"content": "[SEP]",
|
| 50 |
+
"single_word": false,
|
| 51 |
+
"lstrip": false,
|
| 52 |
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"rstrip": false,
|
| 53 |
+
"normalized": false,
|
| 54 |
+
"special": true
|
| 55 |
+
},
|
| 56 |
+
{
|
| 57 |
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"id": 4,
|
| 58 |
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"content": "[MASK]",
|
| 59 |
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|
| 60 |
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|
| 61 |
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"rstrip": false,
|
| 62 |
+
"normalized": false,
|
| 63 |
+
"special": true
|
| 64 |
+
}
|
| 65 |
+
],
|
| 66 |
+
"normalizer": {
|
| 67 |
+
"type": "BertNormalizer",
|
| 68 |
+
"clean_text": true,
|
| 69 |
+
"handle_chinese_chars": true,
|
| 70 |
+
"strip_accents": null,
|
| 71 |
+
"lowercase": false
|
| 72 |
+
},
|
| 73 |
+
"pre_tokenizer": {
|
| 74 |
+
"type": "BertPreTokenizer"
|
| 75 |
+
},
|
| 76 |
+
"post_processor": {
|
| 77 |
+
"type": "TemplateProcessing",
|
| 78 |
+
"single": [
|
| 79 |
+
{
|
| 80 |
+
"SpecialToken": {
|
| 81 |
+
"id": "[CLS]",
|
| 82 |
+
"type_id": 0
|
| 83 |
+
}
|
| 84 |
+
},
|
| 85 |
+
{
|
| 86 |
+
"Sequence": {
|
| 87 |
+
"id": "A",
|
| 88 |
+
"type_id": 0
|
| 89 |
+
}
|
| 90 |
+
},
|
| 91 |
+
{
|
| 92 |
+
"SpecialToken": {
|
| 93 |
+
"id": "[SEP]",
|
| 94 |
+
"type_id": 0
|
| 95 |
+
}
|
| 96 |
+
}
|
| 97 |
+
],
|
| 98 |
+
"pair": [
|
| 99 |
+
{
|
| 100 |
+
"SpecialToken": {
|
| 101 |
+
"id": "[CLS]",
|
| 102 |
+
"type_id": 0
|
| 103 |
+
}
|
| 104 |
+
},
|
| 105 |
+
{
|
| 106 |
+
"Sequence": {
|
| 107 |
+
"id": "A",
|
| 108 |
+
"type_id": 0
|
| 109 |
+
}
|
| 110 |
+
},
|
| 111 |
+
{
|
| 112 |
+
"SpecialToken": {
|
| 113 |
+
"id": "[SEP]",
|
| 114 |
+
"type_id": 0
|
| 115 |
+
}
|
| 116 |
+
},
|
| 117 |
+
{
|
| 118 |
+
"Sequence": {
|
| 119 |
+
"id": "B",
|
| 120 |
+
"type_id": 1
|
| 121 |
+
}
|
| 122 |
+
},
|
| 123 |
+
{
|
| 124 |
+
"SpecialToken": {
|
| 125 |
+
"id": "[SEP]",
|
| 126 |
+
"type_id": 1
|
| 127 |
+
}
|
| 128 |
+
}
|
| 129 |
+
],
|
| 130 |
+
"special_tokens": {
|
| 131 |
+
"[CLS]": {
|
| 132 |
+
"id": "[CLS]",
|
| 133 |
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"ids": [
|
| 134 |
+
2
|
| 135 |
+
],
|
| 136 |
+
"tokens": [
|
| 137 |
+
"[CLS]"
|
| 138 |
+
]
|
| 139 |
+
},
|
| 140 |
+
"[SEP]": {
|
| 141 |
+
"id": "[SEP]",
|
| 142 |
+
"ids": [
|
| 143 |
+
3
|
| 144 |
+
],
|
| 145 |
+
"tokens": [
|
| 146 |
+
"[SEP]"
|
| 147 |
+
]
|
| 148 |
+
}
|
| 149 |
+
}
|
| 150 |
+
},
|
| 151 |
+
"decoder": {
|
| 152 |
+
"type": "WordPiece",
|
| 153 |
+
"prefix": "##",
|
| 154 |
+
"cleanup": true
|
| 155 |
+
},
|
| 156 |
+
"model": {
|
| 157 |
+
"type": "WordPiece",
|
| 158 |
+
"unk_token": "[UNK]",
|
| 159 |
+
"continuing_subword_prefix": "##",
|
| 160 |
+
"max_input_chars_per_word": 100,
|
| 161 |
+
"vocab": {
|
| 162 |
+
"[PAD]": 0,
|
| 163 |
+
"[UNK]": 1,
|
| 164 |
+
"[CLS]": 2,
|
| 165 |
+
"[SEP]": 3,
|
| 166 |
+
"[MASK]": 4,
|
| 167 |
+
"L": 5,
|
| 168 |
+
"A": 6,
|
| 169 |
+
"G": 7,
|
| 170 |
+
"V": 8,
|
| 171 |
+
"E": 9,
|
| 172 |
+
"S": 10,
|
| 173 |
+
"I": 11,
|
| 174 |
+
"K": 12,
|
| 175 |
+
"R": 13,
|
| 176 |
+
"D": 14,
|
| 177 |
+
"T": 15,
|
| 178 |
+
"P": 16,
|
| 179 |
+
"N": 17,
|
| 180 |
+
"Q": 18,
|
| 181 |
+
"F": 19,
|
| 182 |
+
"Y": 20,
|
| 183 |
+
"M": 21,
|
| 184 |
+
"H": 22,
|
| 185 |
+
"C": 23,
|
| 186 |
+
"W": 24,
|
| 187 |
+
"X": 25,
|
| 188 |
+
"U": 26,
|
| 189 |
+
"B": 27,
|
| 190 |
+
"Z": 28,
|
| 191 |
+
"O": 29
|
| 192 |
+
}
|
| 193 |
+
}
|
| 194 |
+
}
|
tokenizer_config.json
ADDED
|
@@ -0,0 +1,58 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 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 |
+
"clean_up_tokenization_spaces": true,
|
| 45 |
+
"cls_token": "[CLS]",
|
| 46 |
+
"do_basic_tokenize": true,
|
| 47 |
+
"do_lower_case": false,
|
| 48 |
+
"full_tokenizer_file": null,
|
| 49 |
+
"mask_token": "[MASK]",
|
| 50 |
+
"model_max_length": 1000000000000000019884624838656,
|
| 51 |
+
"never_split": null,
|
| 52 |
+
"pad_token": "[PAD]",
|
| 53 |
+
"sep_token": "[SEP]",
|
| 54 |
+
"strip_accents": null,
|
| 55 |
+
"tokenize_chinese_chars": true,
|
| 56 |
+
"tokenizer_class": "BertTokenizer",
|
| 57 |
+
"unk_token": "[UNK]"
|
| 58 |
+
}
|
training_args.bin
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a181d426a846aed31d185c1c8e7462bde216a5de70b47a96fc82542bdb87ea9d
|
| 3 |
+
size 4920
|
training_params.json
ADDED
|
@@ -0,0 +1,30 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"data_path": "as-cle-bert/AMR-Gene-Families",
|
| 3 |
+
"model": "Rostlab/prot_bert",
|
| 4 |
+
"lr": 5e-05,
|
| 5 |
+
"epochs": 3,
|
| 6 |
+
"max_seq_length": 128,
|
| 7 |
+
"batch_size": 8,
|
| 8 |
+
"warmup_ratio": 0.1,
|
| 9 |
+
"gradient_accumulation": 1,
|
| 10 |
+
"optimizer": "adamw_torch",
|
| 11 |
+
"scheduler": "linear",
|
| 12 |
+
"weight_decay": 0.0,
|
| 13 |
+
"max_grad_norm": 1.0,
|
| 14 |
+
"seed": 42,
|
| 15 |
+
"train_split": "train",
|
| 16 |
+
"valid_split": "test",
|
| 17 |
+
"text_column": "text",
|
| 18 |
+
"target_column": "label",
|
| 19 |
+
"logging_steps": -1,
|
| 20 |
+
"project_name": "autotrain-fzudm-korrh",
|
| 21 |
+
"auto_find_batch_size": false,
|
| 22 |
+
"mixed_precision": "no",
|
| 23 |
+
"save_total_limit": 1,
|
| 24 |
+
"save_strategy": "epoch",
|
| 25 |
+
"push_to_hub": true,
|
| 26 |
+
"repo_id": "as-cle-bert/autotrain-fzudm-korrh",
|
| 27 |
+
"evaluation_strategy": "epoch",
|
| 28 |
+
"username": "as-cle-bert",
|
| 29 |
+
"log": "none"
|
| 30 |
+
}
|
vocab.txt
ADDED
|
@@ -0,0 +1,30 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[PAD]
|
| 2 |
+
[UNK]
|
| 3 |
+
[CLS]
|
| 4 |
+
[SEP]
|
| 5 |
+
[MASK]
|
| 6 |
+
L
|
| 7 |
+
A
|
| 8 |
+
G
|
| 9 |
+
V
|
| 10 |
+
E
|
| 11 |
+
S
|
| 12 |
+
I
|
| 13 |
+
K
|
| 14 |
+
R
|
| 15 |
+
D
|
| 16 |
+
T
|
| 17 |
+
P
|
| 18 |
+
N
|
| 19 |
+
Q
|
| 20 |
+
F
|
| 21 |
+
Y
|
| 22 |
+
M
|
| 23 |
+
H
|
| 24 |
+
C
|
| 25 |
+
W
|
| 26 |
+
X
|
| 27 |
+
U
|
| 28 |
+
B
|
| 29 |
+
Z
|
| 30 |
+
O
|