Delete models/finetuned
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- models/finetuned/bace/config.json +0 -28
- models/finetuned/bace/finetuning_optimized_config.json +0 -24
- models/finetuned/bace/merges.txt +0 -162
- models/finetuned/bace/model.pt +0 -3
- models/finetuned/bace/special_tokens_map.json +0 -51
- models/finetuned/bace/tokenizer.json +0 -473
- models/finetuned/bace/tokenizer_config.json +0 -59
- models/finetuned/bace/vocab.json +0 -1
- models/finetuned/bbbp/config.json +0 -28
- models/finetuned/bbbp/finetuning_optimized_config.json +0 -24
- models/finetuned/bbbp/merges.txt +0 -162
- models/finetuned/bbbp/model.pt +0 -3
- models/finetuned/bbbp/special_tokens_map.json +0 -51
- models/finetuned/bbbp/tokenizer.json +0 -473
- models/finetuned/bbbp/tokenizer_config.json +0 -59
- models/finetuned/bbbp/vocab.json +0 -1
- models/finetuned/esol/config.json +0 -28
- models/finetuned/esol/finetuning_optimized_config.json +0 -24
- models/finetuned/esol/merges.txt +0 -162
- models/finetuned/esol/model.pt +0 -3
- models/finetuned/esol/special_tokens_map.json +0 -51
- models/finetuned/esol/tokenizer.json +0 -473
- models/finetuned/esol/tokenizer_config.json +0 -59
- models/finetuned/esol/vocab.json +0 -1
- models/finetuned/freesolv/config.json +0 -28
- models/finetuned/freesolv/finetuning_optimized_config.json +0 -24
- models/finetuned/freesolv/merges.txt +0 -162
- models/finetuned/freesolv/model.pt +0 -3
- models/finetuned/freesolv/special_tokens_map.json +0 -51
- models/finetuned/freesolv/tokenizer.json +0 -473
- models/finetuned/freesolv/tokenizer_config.json +0 -59
- models/finetuned/freesolv/vocab.json +0 -1
- models/finetuned/hiv/config.json +0 -27
- models/finetuned/hiv/finetuning_optimized_config.json +0 -24
- models/finetuned/hiv/merges.txt +0 -378
- models/finetuned/hiv/model.pt +0 -3
- models/finetuned/hiv/special_tokens_map.json +0 -51
- models/finetuned/hiv/tokenizer.json +0 -909
- models/finetuned/hiv/tokenizer_config.json +0 -65
- models/finetuned/hiv/vocab.json +0 -1
- models/finetuned/lipo/config.json +0 -28
- models/finetuned/lipo/finetuning_optimized_config.json +0 -24
- models/finetuned/lipo/merges.txt +0 -162
- models/finetuned/lipo/model.pt +0 -3
- models/finetuned/lipo/special_tokens_map.json +0 -51
- models/finetuned/lipo/tokenizer.json +0 -473
- models/finetuned/lipo/tokenizer_config.json +0 -59
- models/finetuned/lipo/vocab.json +0 -1
- models/finetuned/pdbbind_full/config.json +0 -28
- models/finetuned/pdbbind_full/finetuning_optimized_config.json +0 -24
models/finetuned/bace/config.json
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{
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"_name_or_path": "data/epoch_267/hf",
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"architectures": [
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"RobertaForMaskedLM"
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],
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"attention_probs_dropout_prob": 0.1,
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"bos_token_id": 0,
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"classifier_dropout": null,
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"eos_token_id": 2,
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"hidden_act": "gelu",
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"hidden_dropout_prob": 0.1,
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"hidden_size": 768,
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"initializer_range": 0.02,
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"intermediate_size": 3072,
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"layer_norm_eps": 1e-12,
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"max_position_embeddings": 514,
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"model_type": "roberta",
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"num_attention_heads": 4,
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"num_hidden_layers": 12,
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"output_hidden_states": true,
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"pad_token_id": 1,
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"position_embedding_type": "absolute",
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"torch_dtype": "float32",
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"transformers_version": "4.26.1",
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"type_vocab_size": 1,
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"use_cache": true,
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"vocab_size": 800
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}
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models/finetuned/bace/finetuning_optimized_config.json
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{
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"dataset_meta_csv": "data/finetuning_datasets/classification/bace/bace.csv",
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"dataset_embs_npz": "data/finetuning_datasets/classification/bace/bace_embs.npz",
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"use_scaffold": 1,
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"seed": 42,
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"train_frac": 0.8,
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"val_frac": 0.1,
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"test_frac": 0.1,
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"model_path": "HUBioDataLab/SELFormer",
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"tokenizer_path": "HUBioDataLab/SELFormer",
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"pretrained_multimodal_dir": "data/models/SELFormerMM",
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"task_type": "binary",
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"label_column": "Class",
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"num_labels": 2,
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"batch_size": 16,
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"max_len": 128,
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"epochs": 25,
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"backbone_lr": 5e-06,
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"head_lr": 5e-05,
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"weight_decay": 0.001,
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"checkpoint_every": 25,
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"test_eval_every": 0,
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"save_dir": "data/models/finetuned/bace"
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}
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models/finetuned/bace/merges.txt
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#version: 0.2 - Trained by `huggingface/tokenizers`
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B r
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a n
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c h
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models/finetuned/bace/model.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:f17ebde0f06fdca997a8be88bb399bd42ff14b293ddc28bd8223fcb9253dfb13
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size 1022855293
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models/finetuned/bace/special_tokens_map.json
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{
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"bos_token": {
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"content": "<s>",
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"lstrip": false,
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"normalized": true,
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"rstrip": false,
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"single_word": false
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},
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"cls_token": {
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"content": "<s>",
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"normalized": true,
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"rstrip": false,
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"single_word": false
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},
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"eos_token": {
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"content": "</s>",
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"lstrip": false,
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"normalized": true,
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"rstrip": false,
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"single_word": false
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},
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"mask_token": {
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"content": "<mask>",
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"lstrip": true,
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"normalized": true,
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"rstrip": false,
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"single_word": false
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},
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"pad_token": {
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"content": "<pad>",
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"lstrip": false,
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"normalized": true,
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},
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"content": "</s>",
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"lstrip": false,
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"normalized": true,
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"rstrip": false,
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"single_word": false
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},
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"unk_token": {
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"content": "<unk>",
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"normalized": true,
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}
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}
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models/finetuned/bace/tokenizer.json
DELETED
|
@@ -1,473 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"version": "1.0",
|
| 3 |
-
"truncation": {
|
| 4 |
-
"direction": "Right",
|
| 5 |
-
"max_length": 128,
|
| 6 |
-
"strategy": "LongestFirst",
|
| 7 |
-
"stride": 0
|
| 8 |
-
},
|
| 9 |
-
"padding": {
|
| 10 |
-
"strategy": {
|
| 11 |
-
"Fixed": 128
|
| 12 |
-
},
|
| 13 |
-
"direction": "Right",
|
| 14 |
-
"pad_to_multiple_of": null,
|
| 15 |
-
"pad_id": 3,
|
| 16 |
-
"pad_type_id": 0,
|
| 17 |
-
"pad_token": "<pad>"
|
| 18 |
-
},
|
| 19 |
-
"added_tokens": [
|
| 20 |
-
{
|
| 21 |
-
"id": 0,
|
| 22 |
-
"content": "<unk>",
|
| 23 |
-
"single_word": false,
|
| 24 |
-
"lstrip": false,
|
| 25 |
-
"rstrip": false,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"special": true
|
| 28 |
-
},
|
| 29 |
-
{
|
| 30 |
-
"id": 1,
|
| 31 |
-
"content": "<s>",
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"lstrip": false,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"normalized": true,
|
| 36 |
-
"special": true
|
| 37 |
-
},
|
| 38 |
-
{
|
| 39 |
-
"id": 2,
|
| 40 |
-
"content": "</s>",
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"lstrip": false,
|
| 43 |
-
"rstrip": false,
|
| 44 |
-
"normalized": true,
|
| 45 |
-
"special": true
|
| 46 |
-
},
|
| 47 |
-
{
|
| 48 |
-
"id": 3,
|
| 49 |
-
"content": "<pad>",
|
| 50 |
-
"single_word": false,
|
| 51 |
-
"lstrip": false,
|
| 52 |
-
"rstrip": false,
|
| 53 |
-
"normalized": true,
|
| 54 |
-
"special": true
|
| 55 |
-
},
|
| 56 |
-
{
|
| 57 |
-
"id": 4,
|
| 58 |
-
"content": "<mask>",
|
| 59 |
-
"single_word": false,
|
| 60 |
-
"lstrip": true,
|
| 61 |
-
"rstrip": false,
|
| 62 |
-
"normalized": true,
|
| 63 |
-
"special": true
|
| 64 |
-
}
|
| 65 |
-
],
|
| 66 |
-
"normalizer": null,
|
| 67 |
-
"pre_tokenizer": {
|
| 68 |
-
"type": "ByteLevel",
|
| 69 |
-
"add_prefix_space": false,
|
| 70 |
-
"trim_offsets": true,
|
| 71 |
-
"use_regex": true
|
| 72 |
-
},
|
| 73 |
-
"post_processor": {
|
| 74 |
-
"type": "RobertaProcessing",
|
| 75 |
-
"sep": [
|
| 76 |
-
"</s>",
|
| 77 |
-
2
|
| 78 |
-
],
|
| 79 |
-
"cls": [
|
| 80 |
-
"<s>",
|
| 81 |
-
1
|
| 82 |
-
],
|
| 83 |
-
"trim_offsets": true,
|
| 84 |
-
"add_prefix_space": false
|
| 85 |
-
},
|
| 86 |
-
"decoder": {
|
| 87 |
-
"type": "ByteLevel",
|
| 88 |
-
"add_prefix_space": true,
|
| 89 |
-
"trim_offsets": true,
|
| 90 |
-
"use_regex": true
|
| 91 |
-
},
|
| 92 |
-
"model": {
|
| 93 |
-
"type": "BPE",
|
| 94 |
-
"dropout": null,
|
| 95 |
-
"unk_token": null,
|
| 96 |
-
"continuing_subword_prefix": "",
|
| 97 |
-
"end_of_word_suffix": "",
|
| 98 |
-
"fuse_unk": false,
|
| 99 |
-
"vocab": {
|
| 100 |
-
"<unk>": 0,
|
| 101 |
-
"<s>": 1,
|
| 102 |
-
"</s>": 2,
|
| 103 |
-
"<pad>": 3,
|
| 104 |
-
"<mask>": 4,
|
| 105 |
-
"\n": 5,
|
| 106 |
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"#": 6,
|
| 107 |
-
"+": 7,
|
| 108 |
-
"-": 8,
|
| 109 |
-
".": 9,
|
| 110 |
-
"/": 10,
|
| 111 |
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"0": 11,
|
| 112 |
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"1": 12,
|
| 113 |
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"2": 13,
|
| 114 |
-
"3": 14,
|
| 115 |
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"4": 15,
|
| 116 |
-
"5": 16,
|
| 117 |
-
"8": 17,
|
| 118 |
-
"=": 18,
|
| 119 |
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"@": 19,
|
| 120 |
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"A": 20,
|
| 121 |
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|
| 122 |
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"C": 22,
|
| 123 |
-
"F": 23,
|
| 124 |
-
"H": 24,
|
| 125 |
-
"I": 25,
|
| 126 |
-
"K": 26,
|
| 127 |
-
"L": 27,
|
| 128 |
-
"M": 28,
|
| 129 |
-
"N": 29,
|
| 130 |
-
"O": 30,
|
| 131 |
-
"P": 31,
|
| 132 |
-
"R": 32,
|
| 133 |
-
"S": 33,
|
| 134 |
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"T": 34,
|
| 135 |
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"Z": 35,
|
| 136 |
-
"\\": 36,
|
| 137 |
-
"a": 37,
|
| 138 |
-
"c": 38,
|
| 139 |
-
"e": 39,
|
| 140 |
-
"g": 40,
|
| 141 |
-
"h": 41,
|
| 142 |
-
"i": 42,
|
| 143 |
-
"l": 43,
|
| 144 |
-
"n": 44,
|
| 145 |
-
"r": 45,
|
| 146 |
-
"s": 46,
|
| 147 |
-
"Br": 47,
|
| 148 |
-
"an": 48,
|
| 149 |
-
"ch": 49,
|
| 150 |
-
"Bran": 50,
|
| 151 |
-
"Branch": 51,
|
| 152 |
-
"Branch1": 52,
|
| 153 |
-
"=C": 53,
|
| 154 |
-
"Ri": 54,
|
| 155 |
-
"ng": 55,
|
| 156 |
-
"Ring": 56,
|
| 157 |
-
"Ring1": 57,
|
| 158 |
-
"=Branch1": 58,
|
| 159 |
-
"Branch2": 59,
|
| 160 |
-
"=O": 60,
|
| 161 |
-
"Ring2": 61,
|
| 162 |
-
"H1": 62,
|
| 163 |
-
"C@": 63,
|
| 164 |
-
"=N": 64,
|
| 165 |
-
"#Branch1": 65,
|
| 166 |
-
"C@@": 66,
|
| 167 |
-
"=Branch2": 67,
|
| 168 |
-
"C@H1": 68,
|
| 169 |
-
"C@@H1": 69,
|
| 170 |
-
"#Branch2": 70,
|
| 171 |
-
"Cl": 71,
|
| 172 |
-
"#C": 72,
|
| 173 |
-
"/C": 73,
|
| 174 |
-
"NH1": 74,
|
| 175 |
-
"+1": 75,
|
| 176 |
-
"-1": 76,
|
| 177 |
-
"=Ring1": 77,
|
| 178 |
-
"O-1": 78,
|
| 179 |
-
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|
| 180 |
-
"\\C": 80,
|
| 181 |
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"/N": 81,
|
| 182 |
-
"#N": 82,
|
| 183 |
-
"=Ring2": 83,
|
| 184 |
-
"=S": 84,
|
| 185 |
-
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|
| 186 |
-
"Na": 86,
|
| 187 |
-
"Na+1": 87,
|
| 188 |
-
"\\N": 88,
|
| 189 |
-
"S+1": 89,
|
| 190 |
-
"/O": 90,
|
| 191 |
-
"\\S": 91,
|
| 192 |
-
"\\O": 92,
|
| 193 |
-
"Br-1": 93,
|
| 194 |
-
"I-1": 94,
|
| 195 |
-
"Cl-1": 95,
|
| 196 |
-
"/C@H1": 96,
|
| 197 |
-
"Branch3": 97,
|
| 198 |
-
"/C@@H1": 98,
|
| 199 |
-
"=P": 99,
|
| 200 |
-
"/S": 100,
|
| 201 |
-
"=N-1": 101,
|
| 202 |
-
"Si": 102,
|
| 203 |
-
"K+1": 103,
|
| 204 |
-
"N-1": 104,
|
| 205 |
-
"Se": 105,
|
| 206 |
-
"Li": 106,
|
| 207 |
-
"Li+1": 107,
|
| 208 |
-
"+3": 108,
|
| 209 |
-
"Cl+3": 109,
|
| 210 |
-
"\\C@H1": 110,
|
| 211 |
-
"Ring3": 111,
|
| 212 |
-
"\\C@@H1": 112,
|
| 213 |
-
"/N+1": 113,
|
| 214 |
-
"/P": 114,
|
| 215 |
-
"\\F": 115,
|
| 216 |
-
"P@": 116,
|
| 217 |
-
"2H": 117,
|
| 218 |
-
"PH1": 118,
|
| 219 |
-
"/Br": 119,
|
| 220 |
-
"N@": 120,
|
| 221 |
-
"P+1": 121,
|
| 222 |
-
"/Cl": 122,
|
| 223 |
-
"\\NH1": 123,
|
| 224 |
-
"\\Br": 124,
|
| 225 |
-
"@+1": 125,
|
| 226 |
-
"/I": 126,
|
| 227 |
-
"/C@": 127,
|
| 228 |
-
"Te": 128,
|
| 229 |
-
"\\N+1": 129,
|
| 230 |
-
"P@@": 130,
|
| 231 |
-
"12": 131,
|
| 232 |
-
"5I": 132,
|
| 233 |
-
"\\O-1": 133,
|
| 234 |
-
"125I": 134,
|
| 235 |
-
"/F": 135,
|
| 236 |
-
"#N+1": 136,
|
| 237 |
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"\\Cl": 137,
|
| 238 |
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"N@+1": 138,
|
| 239 |
-
"\\I": 139,
|
| 240 |
-
"-/": 140,
|
| 241 |
-
"/C@@": 141,
|
| 242 |
-
"N@@": 142,
|
| 243 |
-
"N@@+1": 143,
|
| 244 |
-
"-/Ring2": 144,
|
| 245 |
-
"-\\": 145,
|
| 246 |
-
"14": 146,
|
| 247 |
-
"B-1": 147,
|
| 248 |
-
"C-1": 148,
|
| 249 |
-
"S@+1": 149,
|
| 250 |
-
"14C": 150,
|
| 251 |
-
"H2": 151,
|
| 252 |
-
"H4": 152,
|
| 253 |
-
"I+1": 153,
|
| 254 |
-
"S-1": 154,
|
| 255 |
-
"\\P": 155,
|
| 256 |
-
"=S+1": 156,
|
| 257 |
-
"=P@": 157,
|
| 258 |
-
"SiH4": 158,
|
| 259 |
-
"+2": 159,
|
| 260 |
-
"3H": 160,
|
| 261 |
-
"@@+1": 161,
|
| 262 |
-
"Ag": 162,
|
| 263 |
-
"C+1": 163,
|
| 264 |
-
"S@@+1": 164,
|
| 265 |
-
"Cl+1": 165,
|
| 266 |
-
"=Se": 166,
|
| 267 |
-
"-\\Ring1": 167,
|
| 268 |
-
"H0": 168,
|
| 269 |
-
"OH0": 169,
|
| 270 |
-
"11": 170,
|
| 271 |
-
"=Branch3": 171,
|
| 272 |
-
"=Te": 172,
|
| 273 |
-
"Mg": 173,
|
| 274 |
-
"O+1": 174,
|
| 275 |
-
"Zn": 175,
|
| 276 |
-
"\\C@": 176,
|
| 277 |
-
"\\S+1": 177,
|
| 278 |
-
"H1-1": 178,
|
| 279 |
-
"SeH1": 179,
|
| 280 |
-
"P@+1": 180,
|
| 281 |
-
"-\\Ring2": 181,
|
| 282 |
-
"11C": 182,
|
| 283 |
-
"=Te+1": 183,
|
| 284 |
-
"Zn+2": 184,
|
| 285 |
-
"/NH1": 185,
|
| 286 |
-
"18": 186,
|
| 287 |
-
"As": 187,
|
| 288 |
-
"BH2": 188,
|
| 289 |
-
"BH1-1": 189,
|
| 290 |
-
"Ca": 190,
|
| 291 |
-
"H3": 191,
|
| 292 |
-
"OH1-1": 192,
|
| 293 |
-
"SH2": 193,
|
| 294 |
-
"=O+1": 194,
|
| 295 |
-
"Se+1": 195,
|
| 296 |
-
"TeH2": 196,
|
| 297 |
-
"125IH1": 197,
|
| 298 |
-
"-/Ring1": 198,
|
| 299 |
-
"14CH2": 199,
|
| 300 |
-
"Ag+1": 200,
|
| 301 |
-
"=Se+1": 201,
|
| 302 |
-
"MgH2": 202,
|
| 303 |
-
"Mg+2": 203,
|
| 304 |
-
"11CH3": 204,
|
| 305 |
-
"18F": 205,
|
| 306 |
-
"BH2-1": 206,
|
| 307 |
-
"Ca+2": 207
|
| 308 |
-
},
|
| 309 |
-
"merges": [
|
| 310 |
-
"B r",
|
| 311 |
-
"a n",
|
| 312 |
-
"c h",
|
| 313 |
-
"Br an",
|
| 314 |
-
"Bran ch",
|
| 315 |
-
"Branch 1",
|
| 316 |
-
"= C",
|
| 317 |
-
"R i",
|
| 318 |
-
"n g",
|
| 319 |
-
"Ri ng",
|
| 320 |
-
"Ring 1",
|
| 321 |
-
"= Branch1",
|
| 322 |
-
"Branch 2",
|
| 323 |
-
"= O",
|
| 324 |
-
"Ring 2",
|
| 325 |
-
"H 1",
|
| 326 |
-
"C @",
|
| 327 |
-
"= N",
|
| 328 |
-
"# Branch1",
|
| 329 |
-
"C@ @",
|
| 330 |
-
"= Branch2",
|
| 331 |
-
"C@ H1",
|
| 332 |
-
"C@@ H1",
|
| 333 |
-
"# Branch2",
|
| 334 |
-
"C l",
|
| 335 |
-
"# C",
|
| 336 |
-
"/ C",
|
| 337 |
-
"N H1",
|
| 338 |
-
"+ 1",
|
| 339 |
-
"- 1",
|
| 340 |
-
"= Ring1",
|
| 341 |
-
"O -1",
|
| 342 |
-
"N +1",
|
| 343 |
-
"\\ C",
|
| 344 |
-
"/ N",
|
| 345 |
-
"# N",
|
| 346 |
-
"= Ring2",
|
| 347 |
-
"= S",
|
| 348 |
-
"=N +1",
|
| 349 |
-
"N a",
|
| 350 |
-
"Na +1",
|
| 351 |
-
"\\ N",
|
| 352 |
-
"S +1",
|
| 353 |
-
"/ O",
|
| 354 |
-
"\\ S",
|
| 355 |
-
"\\ O",
|
| 356 |
-
"Br -1",
|
| 357 |
-
"I -1",
|
| 358 |
-
"Cl -1",
|
| 359 |
-
"/ C@H1",
|
| 360 |
-
"Branch 3",
|
| 361 |
-
"/ C@@H1",
|
| 362 |
-
"= P",
|
| 363 |
-
"/ S",
|
| 364 |
-
"=N -1",
|
| 365 |
-
"S i",
|
| 366 |
-
"K +1",
|
| 367 |
-
"N -1",
|
| 368 |
-
"S e",
|
| 369 |
-
"L i",
|
| 370 |
-
"Li +1",
|
| 371 |
-
"+ 3",
|
| 372 |
-
"Cl +3",
|
| 373 |
-
"\\ C@H1",
|
| 374 |
-
"Ring 3",
|
| 375 |
-
"\\ C@@H1",
|
| 376 |
-
"/ N+1",
|
| 377 |
-
"/ P",
|
| 378 |
-
"\\ F",
|
| 379 |
-
"P @",
|
| 380 |
-
"2 H",
|
| 381 |
-
"P H1",
|
| 382 |
-
"/ Br",
|
| 383 |
-
"N @",
|
| 384 |
-
"P +1",
|
| 385 |
-
"/ Cl",
|
| 386 |
-
"\\ NH1",
|
| 387 |
-
"\\ Br",
|
| 388 |
-
"@ +1",
|
| 389 |
-
"/ I",
|
| 390 |
-
"/ C@",
|
| 391 |
-
"T e",
|
| 392 |
-
"\\ N+1",
|
| 393 |
-
"P@ @",
|
| 394 |
-
"1 2",
|
| 395 |
-
"5 I",
|
| 396 |
-
"\\ O-1",
|
| 397 |
-
"12 5I",
|
| 398 |
-
"/ F",
|
| 399 |
-
"# N+1",
|
| 400 |
-
"\\ Cl",
|
| 401 |
-
"N@ +1",
|
| 402 |
-
"\\ I",
|
| 403 |
-
"- /",
|
| 404 |
-
"/ C@@",
|
| 405 |
-
"N@ @",
|
| 406 |
-
"N@ @+1",
|
| 407 |
-
"-/ Ring2",
|
| 408 |
-
"- \\",
|
| 409 |
-
"1 4",
|
| 410 |
-
"B -1",
|
| 411 |
-
"C -1",
|
| 412 |
-
"S @+1",
|
| 413 |
-
"14 C",
|
| 414 |
-
"H 2",
|
| 415 |
-
"H 4",
|
| 416 |
-
"I +1",
|
| 417 |
-
"S -1",
|
| 418 |
-
"\\ P",
|
| 419 |
-
"=S +1",
|
| 420 |
-
"=P @",
|
| 421 |
-
"Si H4",
|
| 422 |
-
"+ 2",
|
| 423 |
-
"3 H",
|
| 424 |
-
"@ @+1",
|
| 425 |
-
"A g",
|
| 426 |
-
"C +1",
|
| 427 |
-
"S @@+1",
|
| 428 |
-
"Cl +1",
|
| 429 |
-
"=S e",
|
| 430 |
-
"-\\ Ring1",
|
| 431 |
-
"H 0",
|
| 432 |
-
"O H0",
|
| 433 |
-
"1 1",
|
| 434 |
-
"= Branch3",
|
| 435 |
-
"= Te",
|
| 436 |
-
"M g",
|
| 437 |
-
"O +1",
|
| 438 |
-
"Z n",
|
| 439 |
-
"\\ C@",
|
| 440 |
-
"\\ S+1",
|
| 441 |
-
"H1 -1",
|
| 442 |
-
"Se H1",
|
| 443 |
-
"P@ +1",
|
| 444 |
-
"-\\ Ring2",
|
| 445 |
-
"11 C",
|
| 446 |
-
"=Te +1",
|
| 447 |
-
"Zn +2",
|
| 448 |
-
"/ NH1",
|
| 449 |
-
"1 8",
|
| 450 |
-
"A s",
|
| 451 |
-
"B H2",
|
| 452 |
-
"B H1-1",
|
| 453 |
-
"C a",
|
| 454 |
-
"H 3",
|
| 455 |
-
"O H1-1",
|
| 456 |
-
"S H2",
|
| 457 |
-
"=O +1",
|
| 458 |
-
"Se +1",
|
| 459 |
-
"Te H2",
|
| 460 |
-
"125I H1",
|
| 461 |
-
"-/ Ring1",
|
| 462 |
-
"14C H2",
|
| 463 |
-
"Ag +1",
|
| 464 |
-
"=Se +1",
|
| 465 |
-
"Mg H2",
|
| 466 |
-
"Mg +2",
|
| 467 |
-
"11C H3",
|
| 468 |
-
"18 F",
|
| 469 |
-
"BH2 -1",
|
| 470 |
-
"Ca +2"
|
| 471 |
-
]
|
| 472 |
-
}
|
| 473 |
-
}
|
|
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|
models/finetuned/bace/tokenizer_config.json
DELETED
|
@@ -1,59 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"add_prefix_space": false,
|
| 3 |
-
"added_tokens_decoder": {
|
| 4 |
-
"0": {
|
| 5 |
-
"content": "<unk>",
|
| 6 |
-
"lstrip": false,
|
| 7 |
-
"normalized": true,
|
| 8 |
-
"rstrip": false,
|
| 9 |
-
"single_word": false,
|
| 10 |
-
"special": true
|
| 11 |
-
},
|
| 12 |
-
"1": {
|
| 13 |
-
"content": "<s>",
|
| 14 |
-
"lstrip": false,
|
| 15 |
-
"normalized": true,
|
| 16 |
-
"rstrip": false,
|
| 17 |
-
"single_word": false,
|
| 18 |
-
"special": true
|
| 19 |
-
},
|
| 20 |
-
"2": {
|
| 21 |
-
"content": "</s>",
|
| 22 |
-
"lstrip": false,
|
| 23 |
-
"normalized": true,
|
| 24 |
-
"rstrip": false,
|
| 25 |
-
"single_word": false,
|
| 26 |
-
"special": true
|
| 27 |
-
},
|
| 28 |
-
"3": {
|
| 29 |
-
"content": "<pad>",
|
| 30 |
-
"lstrip": false,
|
| 31 |
-
"normalized": true,
|
| 32 |
-
"rstrip": false,
|
| 33 |
-
"single_word": false,
|
| 34 |
-
"special": true
|
| 35 |
-
},
|
| 36 |
-
"4": {
|
| 37 |
-
"content": "<mask>",
|
| 38 |
-
"lstrip": true,
|
| 39 |
-
"normalized": true,
|
| 40 |
-
"rstrip": false,
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"special": true
|
| 43 |
-
}
|
| 44 |
-
},
|
| 45 |
-
"bos_token": "<s>",
|
| 46 |
-
"clean_up_tokenization_spaces": true,
|
| 47 |
-
"cls_token": "<s>",
|
| 48 |
-
"eos_token": "</s>",
|
| 49 |
-
"errors": "replace",
|
| 50 |
-
"mask_token": "<mask>",
|
| 51 |
-
"model_max_length": 1000000000000000019884624838656,
|
| 52 |
-
"name_or_path": "data/epoch_267/hf",
|
| 53 |
-
"pad_token": "<pad>",
|
| 54 |
-
"sep_token": "</s>",
|
| 55 |
-
"special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
|
| 56 |
-
"tokenizer_class": "RobertaTokenizer",
|
| 57 |
-
"trim_offsets": true,
|
| 58 |
-
"unk_token": "<unk>"
|
| 59 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
models/finetuned/bace/vocab.json
DELETED
|
@@ -1 +0,0 @@
|
|
| 1 |
-
{"<unk>":0,"<s>":1,"</s>":2,"<pad>":3,"<mask>":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
|
|
|
|
|
|
models/finetuned/bbbp/config.json
DELETED
|
@@ -1,28 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "data/epoch_267/hf",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"RobertaForMaskedLM"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"bos_token_id": 0,
|
| 8 |
-
"classifier_dropout": null,
|
| 9 |
-
"eos_token_id": 2,
|
| 10 |
-
"hidden_act": "gelu",
|
| 11 |
-
"hidden_dropout_prob": 0.1,
|
| 12 |
-
"hidden_size": 768,
|
| 13 |
-
"initializer_range": 0.02,
|
| 14 |
-
"intermediate_size": 3072,
|
| 15 |
-
"layer_norm_eps": 1e-12,
|
| 16 |
-
"max_position_embeddings": 514,
|
| 17 |
-
"model_type": "roberta",
|
| 18 |
-
"num_attention_heads": 4,
|
| 19 |
-
"num_hidden_layers": 12,
|
| 20 |
-
"output_hidden_states": true,
|
| 21 |
-
"pad_token_id": 1,
|
| 22 |
-
"position_embedding_type": "absolute",
|
| 23 |
-
"torch_dtype": "float32",
|
| 24 |
-
"transformers_version": "4.26.1",
|
| 25 |
-
"type_vocab_size": 1,
|
| 26 |
-
"use_cache": true,
|
| 27 |
-
"vocab_size": 800
|
| 28 |
-
}
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models/finetuned/bbbp/finetuning_optimized_config.json
DELETED
|
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|
| 1 |
-
{
|
| 2 |
-
"dataset_meta_csv": "data/finetuning_datasets/classification/bbbp/bbbp.csv",
|
| 3 |
-
"dataset_embs_npz": "data/finetuning_datasets/classification/bbbp/bbbp_embs.npz",
|
| 4 |
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"use_scaffold": 1,
|
| 5 |
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"seed": 42,
|
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"train_frac": 0.8,
|
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"val_frac": 0.1,
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"test_frac": 0.1,
|
| 9 |
-
"model_path": "HUBioDataLab/SELFormer",
|
| 10 |
-
"tokenizer_path": "HUBioDataLab/SELFormer",
|
| 11 |
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"pretrained_multimodal_dir": "data/models/SELFormerMM",
|
| 12 |
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"task_type": "binary",
|
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"label_column": "p_np",
|
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"num_labels": 2,
|
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"batch_size": 32,
|
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"max_len": 128,
|
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"epochs": 25,
|
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"backbone_lr": 5e-05,
|
| 19 |
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"head_lr": 1e-05,
|
| 20 |
-
"weight_decay": 0.1,
|
| 21 |
-
"checkpoint_every": 25,
|
| 22 |
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"test_eval_every": 0,
|
| 23 |
-
"save_dir": "data/models/finetuned/bbbp"
|
| 24 |
-
}
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models/finetuned/bbbp/merges.txt
DELETED
|
@@ -1,162 +0,0 @@
|
|
| 1 |
-
#version: 0.2 - Trained by `huggingface/tokenizers`
|
| 2 |
-
B r
|
| 3 |
-
a n
|
| 4 |
-
c h
|
| 5 |
-
Br an
|
| 6 |
-
Bran ch
|
| 7 |
-
Branch 1
|
| 8 |
-
= C
|
| 9 |
-
R i
|
| 10 |
-
n g
|
| 11 |
-
Ri ng
|
| 12 |
-
Ring 1
|
| 13 |
-
= Branch1
|
| 14 |
-
Branch 2
|
| 15 |
-
= O
|
| 16 |
-
Ring 2
|
| 17 |
-
H 1
|
| 18 |
-
C @
|
| 19 |
-
= N
|
| 20 |
-
# Branch1
|
| 21 |
-
C@ @
|
| 22 |
-
= Branch2
|
| 23 |
-
C@ H1
|
| 24 |
-
C@@ H1
|
| 25 |
-
# Branch2
|
| 26 |
-
C l
|
| 27 |
-
# C
|
| 28 |
-
/ C
|
| 29 |
-
N H1
|
| 30 |
-
+ 1
|
| 31 |
-
- 1
|
| 32 |
-
= Ring1
|
| 33 |
-
O -1
|
| 34 |
-
N +1
|
| 35 |
-
\ C
|
| 36 |
-
/ N
|
| 37 |
-
# N
|
| 38 |
-
= Ring2
|
| 39 |
-
= S
|
| 40 |
-
=N +1
|
| 41 |
-
N a
|
| 42 |
-
Na +1
|
| 43 |
-
\ N
|
| 44 |
-
S +1
|
| 45 |
-
/ O
|
| 46 |
-
\ S
|
| 47 |
-
\ O
|
| 48 |
-
Br -1
|
| 49 |
-
I -1
|
| 50 |
-
Cl -1
|
| 51 |
-
/ C@H1
|
| 52 |
-
Branch 3
|
| 53 |
-
/ C@@H1
|
| 54 |
-
= P
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| 55 |
-
/ S
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| 56 |
-
=N -1
|
| 57 |
-
S i
|
| 58 |
-
K +1
|
| 59 |
-
N -1
|
| 60 |
-
S e
|
| 61 |
-
L i
|
| 62 |
-
Li +1
|
| 63 |
-
+ 3
|
| 64 |
-
Cl +3
|
| 65 |
-
\ C@H1
|
| 66 |
-
Ring 3
|
| 67 |
-
\ C@@H1
|
| 68 |
-
/ N+1
|
| 69 |
-
/ P
|
| 70 |
-
\ F
|
| 71 |
-
P @
|
| 72 |
-
2 H
|
| 73 |
-
P H1
|
| 74 |
-
/ Br
|
| 75 |
-
N @
|
| 76 |
-
P +1
|
| 77 |
-
/ Cl
|
| 78 |
-
\ NH1
|
| 79 |
-
\ Br
|
| 80 |
-
@ +1
|
| 81 |
-
/ I
|
| 82 |
-
/ C@
|
| 83 |
-
T e
|
| 84 |
-
\ N+1
|
| 85 |
-
P@ @
|
| 86 |
-
1 2
|
| 87 |
-
5 I
|
| 88 |
-
\ O-1
|
| 89 |
-
12 5I
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| 90 |
-
/ F
|
| 91 |
-
# N+1
|
| 92 |
-
\ Cl
|
| 93 |
-
N@ +1
|
| 94 |
-
\ I
|
| 95 |
-
- /
|
| 96 |
-
/ C@@
|
| 97 |
-
N@ @
|
| 98 |
-
N@ @+1
|
| 99 |
-
-/ Ring2
|
| 100 |
-
- \
|
| 101 |
-
1 4
|
| 102 |
-
B -1
|
| 103 |
-
C -1
|
| 104 |
-
S @+1
|
| 105 |
-
14 C
|
| 106 |
-
H 2
|
| 107 |
-
H 4
|
| 108 |
-
I +1
|
| 109 |
-
S -1
|
| 110 |
-
\ P
|
| 111 |
-
=S +1
|
| 112 |
-
=P @
|
| 113 |
-
Si H4
|
| 114 |
-
+ 2
|
| 115 |
-
3 H
|
| 116 |
-
@ @+1
|
| 117 |
-
A g
|
| 118 |
-
C +1
|
| 119 |
-
S @@+1
|
| 120 |
-
Cl +1
|
| 121 |
-
=S e
|
| 122 |
-
-\ Ring1
|
| 123 |
-
H 0
|
| 124 |
-
O H0
|
| 125 |
-
1 1
|
| 126 |
-
= Branch3
|
| 127 |
-
= Te
|
| 128 |
-
M g
|
| 129 |
-
O +1
|
| 130 |
-
Z n
|
| 131 |
-
\ C@
|
| 132 |
-
\ S+1
|
| 133 |
-
H1 -1
|
| 134 |
-
Se H1
|
| 135 |
-
P@ +1
|
| 136 |
-
-\ Ring2
|
| 137 |
-
11 C
|
| 138 |
-
=Te +1
|
| 139 |
-
Zn +2
|
| 140 |
-
/ NH1
|
| 141 |
-
1 8
|
| 142 |
-
A s
|
| 143 |
-
B H2
|
| 144 |
-
B H1-1
|
| 145 |
-
C a
|
| 146 |
-
H 3
|
| 147 |
-
O H1-1
|
| 148 |
-
S H2
|
| 149 |
-
=O +1
|
| 150 |
-
Se +1
|
| 151 |
-
Te H2
|
| 152 |
-
125I H1
|
| 153 |
-
-/ Ring1
|
| 154 |
-
14C H2
|
| 155 |
-
Ag +1
|
| 156 |
-
=Se +1
|
| 157 |
-
Mg H2
|
| 158 |
-
Mg +2
|
| 159 |
-
11C H3
|
| 160 |
-
18 F
|
| 161 |
-
BH2 -1
|
| 162 |
-
Ca +2
|
|
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models/finetuned/bbbp/model.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:bfd9b008df03c05aeba73099ed9af31c62e30b961ae1d0946e486465996ae64b
|
| 3 |
-
size 1022855293
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models/finetuned/bbbp/special_tokens_map.json
DELETED
|
@@ -1,51 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"bos_token": {
|
| 3 |
-
"content": "<s>",
|
| 4 |
-
"lstrip": false,
|
| 5 |
-
"normalized": true,
|
| 6 |
-
"rstrip": false,
|
| 7 |
-
"single_word": false
|
| 8 |
-
},
|
| 9 |
-
"cls_token": {
|
| 10 |
-
"content": "<s>",
|
| 11 |
-
"lstrip": false,
|
| 12 |
-
"normalized": true,
|
| 13 |
-
"rstrip": false,
|
| 14 |
-
"single_word": false
|
| 15 |
-
},
|
| 16 |
-
"eos_token": {
|
| 17 |
-
"content": "</s>",
|
| 18 |
-
"lstrip": false,
|
| 19 |
-
"normalized": true,
|
| 20 |
-
"rstrip": false,
|
| 21 |
-
"single_word": false
|
| 22 |
-
},
|
| 23 |
-
"mask_token": {
|
| 24 |
-
"content": "<mask>",
|
| 25 |
-
"lstrip": true,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"rstrip": false,
|
| 28 |
-
"single_word": false
|
| 29 |
-
},
|
| 30 |
-
"pad_token": {
|
| 31 |
-
"content": "<pad>",
|
| 32 |
-
"lstrip": false,
|
| 33 |
-
"normalized": true,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"single_word": false
|
| 36 |
-
},
|
| 37 |
-
"sep_token": {
|
| 38 |
-
"content": "</s>",
|
| 39 |
-
"lstrip": false,
|
| 40 |
-
"normalized": true,
|
| 41 |
-
"rstrip": false,
|
| 42 |
-
"single_word": false
|
| 43 |
-
},
|
| 44 |
-
"unk_token": {
|
| 45 |
-
"content": "<unk>",
|
| 46 |
-
"lstrip": false,
|
| 47 |
-
"normalized": true,
|
| 48 |
-
"rstrip": false,
|
| 49 |
-
"single_word": false
|
| 50 |
-
}
|
| 51 |
-
}
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models/finetuned/bbbp/tokenizer.json
DELETED
|
@@ -1,473 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"version": "1.0",
|
| 3 |
-
"truncation": {
|
| 4 |
-
"direction": "Right",
|
| 5 |
-
"max_length": 128,
|
| 6 |
-
"strategy": "LongestFirst",
|
| 7 |
-
"stride": 0
|
| 8 |
-
},
|
| 9 |
-
"padding": {
|
| 10 |
-
"strategy": {
|
| 11 |
-
"Fixed": 128
|
| 12 |
-
},
|
| 13 |
-
"direction": "Right",
|
| 14 |
-
"pad_to_multiple_of": null,
|
| 15 |
-
"pad_id": 3,
|
| 16 |
-
"pad_type_id": 0,
|
| 17 |
-
"pad_token": "<pad>"
|
| 18 |
-
},
|
| 19 |
-
"added_tokens": [
|
| 20 |
-
{
|
| 21 |
-
"id": 0,
|
| 22 |
-
"content": "<unk>",
|
| 23 |
-
"single_word": false,
|
| 24 |
-
"lstrip": false,
|
| 25 |
-
"rstrip": false,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"special": true
|
| 28 |
-
},
|
| 29 |
-
{
|
| 30 |
-
"id": 1,
|
| 31 |
-
"content": "<s>",
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"lstrip": false,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"normalized": true,
|
| 36 |
-
"special": true
|
| 37 |
-
},
|
| 38 |
-
{
|
| 39 |
-
"id": 2,
|
| 40 |
-
"content": "</s>",
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"lstrip": false,
|
| 43 |
-
"rstrip": false,
|
| 44 |
-
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-
"type": "ByteLevel",
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-
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-
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-
"post_processor": {
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| 74 |
-
"type": "RobertaProcessing",
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| 75 |
-
"sep": [
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| 76 |
-
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| 77 |
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],
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-
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| 80 |
-
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| 81 |
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1
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| 82 |
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],
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-
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"model": {
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|
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|
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
-
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|
| 163 |
-
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|
| 164 |
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|
| 165 |
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|
| 166 |
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|
| 167 |
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|
| 168 |
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|
| 169 |
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|
| 170 |
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|
| 171 |
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|
| 172 |
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|
| 173 |
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"/C": 73,
|
| 174 |
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|
| 175 |
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"+1": 75,
|
| 176 |
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|
| 177 |
-
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|
| 178 |
-
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|
| 179 |
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|
| 180 |
-
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|
| 181 |
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|
| 182 |
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|
| 183 |
-
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|
| 184 |
-
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|
| 185 |
-
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|
| 186 |
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|
| 187 |
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|
| 188 |
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|
| 189 |
-
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|
| 190 |
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|
| 191 |
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|
| 192 |
-
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|
| 193 |
-
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|
| 194 |
-
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|
| 195 |
-
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|
| 196 |
-
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|
| 197 |
-
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|
| 198 |
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|
| 199 |
-
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|
| 200 |
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|
| 201 |
-
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|
| 202 |
-
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|
| 203 |
-
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|
| 204 |
-
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|
| 205 |
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|
| 206 |
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|
| 207 |
-
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|
| 208 |
-
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|
| 209 |
-
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|
| 210 |
-
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|
| 211 |
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|
| 212 |
-
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|
| 213 |
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|
| 214 |
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|
| 215 |
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|
| 216 |
-
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|
| 217 |
-
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|
| 218 |
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|
| 219 |
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|
| 220 |
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|
| 221 |
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|
| 222 |
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|
| 223 |
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|
| 224 |
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|
| 225 |
-
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|
| 226 |
-
"/I": 126,
|
| 227 |
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|
| 228 |
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|
| 229 |
-
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|
| 230 |
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|
| 231 |
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|
| 232 |
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|
| 233 |
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|
| 234 |
-
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|
| 235 |
-
"/F": 135,
|
| 236 |
-
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|
| 237 |
-
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|
| 238 |
-
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|
| 239 |
-
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|
| 240 |
-
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|
| 241 |
-
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|
| 242 |
-
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|
| 243 |
-
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|
| 244 |
-
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|
| 245 |
-
"-\\": 145,
|
| 246 |
-
"14": 146,
|
| 247 |
-
"B-1": 147,
|
| 248 |
-
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|
| 249 |
-
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|
| 250 |
-
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|
| 251 |
-
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|
| 252 |
-
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|
| 253 |
-
"I+1": 153,
|
| 254 |
-
"S-1": 154,
|
| 255 |
-
"\\P": 155,
|
| 256 |
-
"=S+1": 156,
|
| 257 |
-
"=P@": 157,
|
| 258 |
-
"SiH4": 158,
|
| 259 |
-
"+2": 159,
|
| 260 |
-
"3H": 160,
|
| 261 |
-
"@@+1": 161,
|
| 262 |
-
"Ag": 162,
|
| 263 |
-
"C+1": 163,
|
| 264 |
-
"S@@+1": 164,
|
| 265 |
-
"Cl+1": 165,
|
| 266 |
-
"=Se": 166,
|
| 267 |
-
"-\\Ring1": 167,
|
| 268 |
-
"H0": 168,
|
| 269 |
-
"OH0": 169,
|
| 270 |
-
"11": 170,
|
| 271 |
-
"=Branch3": 171,
|
| 272 |
-
"=Te": 172,
|
| 273 |
-
"Mg": 173,
|
| 274 |
-
"O+1": 174,
|
| 275 |
-
"Zn": 175,
|
| 276 |
-
"\\C@": 176,
|
| 277 |
-
"\\S+1": 177,
|
| 278 |
-
"H1-1": 178,
|
| 279 |
-
"SeH1": 179,
|
| 280 |
-
"P@+1": 180,
|
| 281 |
-
"-\\Ring2": 181,
|
| 282 |
-
"11C": 182,
|
| 283 |
-
"=Te+1": 183,
|
| 284 |
-
"Zn+2": 184,
|
| 285 |
-
"/NH1": 185,
|
| 286 |
-
"18": 186,
|
| 287 |
-
"As": 187,
|
| 288 |
-
"BH2": 188,
|
| 289 |
-
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|
| 290 |
-
"Ca": 190,
|
| 291 |
-
"H3": 191,
|
| 292 |
-
"OH1-1": 192,
|
| 293 |
-
"SH2": 193,
|
| 294 |
-
"=O+1": 194,
|
| 295 |
-
"Se+1": 195,
|
| 296 |
-
"TeH2": 196,
|
| 297 |
-
"125IH1": 197,
|
| 298 |
-
"-/Ring1": 198,
|
| 299 |
-
"14CH2": 199,
|
| 300 |
-
"Ag+1": 200,
|
| 301 |
-
"=Se+1": 201,
|
| 302 |
-
"MgH2": 202,
|
| 303 |
-
"Mg+2": 203,
|
| 304 |
-
"11CH3": 204,
|
| 305 |
-
"18F": 205,
|
| 306 |
-
"BH2-1": 206,
|
| 307 |
-
"Ca+2": 207
|
| 308 |
-
},
|
| 309 |
-
"merges": [
|
| 310 |
-
"B r",
|
| 311 |
-
"a n",
|
| 312 |
-
"c h",
|
| 313 |
-
"Br an",
|
| 314 |
-
"Bran ch",
|
| 315 |
-
"Branch 1",
|
| 316 |
-
"= C",
|
| 317 |
-
"R i",
|
| 318 |
-
"n g",
|
| 319 |
-
"Ri ng",
|
| 320 |
-
"Ring 1",
|
| 321 |
-
"= Branch1",
|
| 322 |
-
"Branch 2",
|
| 323 |
-
"= O",
|
| 324 |
-
"Ring 2",
|
| 325 |
-
"H 1",
|
| 326 |
-
"C @",
|
| 327 |
-
"= N",
|
| 328 |
-
"# Branch1",
|
| 329 |
-
"C@ @",
|
| 330 |
-
"= Branch2",
|
| 331 |
-
"C@ H1",
|
| 332 |
-
"C@@ H1",
|
| 333 |
-
"# Branch2",
|
| 334 |
-
"C l",
|
| 335 |
-
"# C",
|
| 336 |
-
"/ C",
|
| 337 |
-
"N H1",
|
| 338 |
-
"+ 1",
|
| 339 |
-
"- 1",
|
| 340 |
-
"= Ring1",
|
| 341 |
-
"O -1",
|
| 342 |
-
"N +1",
|
| 343 |
-
"\\ C",
|
| 344 |
-
"/ N",
|
| 345 |
-
"# N",
|
| 346 |
-
"= Ring2",
|
| 347 |
-
"= S",
|
| 348 |
-
"=N +1",
|
| 349 |
-
"N a",
|
| 350 |
-
"Na +1",
|
| 351 |
-
"\\ N",
|
| 352 |
-
"S +1",
|
| 353 |
-
"/ O",
|
| 354 |
-
"\\ S",
|
| 355 |
-
"\\ O",
|
| 356 |
-
"Br -1",
|
| 357 |
-
"I -1",
|
| 358 |
-
"Cl -1",
|
| 359 |
-
"/ C@H1",
|
| 360 |
-
"Branch 3",
|
| 361 |
-
"/ C@@H1",
|
| 362 |
-
"= P",
|
| 363 |
-
"/ S",
|
| 364 |
-
"=N -1",
|
| 365 |
-
"S i",
|
| 366 |
-
"K +1",
|
| 367 |
-
"N -1",
|
| 368 |
-
"S e",
|
| 369 |
-
"L i",
|
| 370 |
-
"Li +1",
|
| 371 |
-
"+ 3",
|
| 372 |
-
"Cl +3",
|
| 373 |
-
"\\ C@H1",
|
| 374 |
-
"Ring 3",
|
| 375 |
-
"\\ C@@H1",
|
| 376 |
-
"/ N+1",
|
| 377 |
-
"/ P",
|
| 378 |
-
"\\ F",
|
| 379 |
-
"P @",
|
| 380 |
-
"2 H",
|
| 381 |
-
"P H1",
|
| 382 |
-
"/ Br",
|
| 383 |
-
"N @",
|
| 384 |
-
"P +1",
|
| 385 |
-
"/ Cl",
|
| 386 |
-
"\\ NH1",
|
| 387 |
-
"\\ Br",
|
| 388 |
-
"@ +1",
|
| 389 |
-
"/ I",
|
| 390 |
-
"/ C@",
|
| 391 |
-
"T e",
|
| 392 |
-
"\\ N+1",
|
| 393 |
-
"P@ @",
|
| 394 |
-
"1 2",
|
| 395 |
-
"5 I",
|
| 396 |
-
"\\ O-1",
|
| 397 |
-
"12 5I",
|
| 398 |
-
"/ F",
|
| 399 |
-
"# N+1",
|
| 400 |
-
"\\ Cl",
|
| 401 |
-
"N@ +1",
|
| 402 |
-
"\\ I",
|
| 403 |
-
"- /",
|
| 404 |
-
"/ C@@",
|
| 405 |
-
"N@ @",
|
| 406 |
-
"N@ @+1",
|
| 407 |
-
"-/ Ring2",
|
| 408 |
-
"- \\",
|
| 409 |
-
"1 4",
|
| 410 |
-
"B -1",
|
| 411 |
-
"C -1",
|
| 412 |
-
"S @+1",
|
| 413 |
-
"14 C",
|
| 414 |
-
"H 2",
|
| 415 |
-
"H 4",
|
| 416 |
-
"I +1",
|
| 417 |
-
"S -1",
|
| 418 |
-
"\\ P",
|
| 419 |
-
"=S +1",
|
| 420 |
-
"=P @",
|
| 421 |
-
"Si H4",
|
| 422 |
-
"+ 2",
|
| 423 |
-
"3 H",
|
| 424 |
-
"@ @+1",
|
| 425 |
-
"A g",
|
| 426 |
-
"C +1",
|
| 427 |
-
"S @@+1",
|
| 428 |
-
"Cl +1",
|
| 429 |
-
"=S e",
|
| 430 |
-
"-\\ Ring1",
|
| 431 |
-
"H 0",
|
| 432 |
-
"O H0",
|
| 433 |
-
"1 1",
|
| 434 |
-
"= Branch3",
|
| 435 |
-
"= Te",
|
| 436 |
-
"M g",
|
| 437 |
-
"O +1",
|
| 438 |
-
"Z n",
|
| 439 |
-
"\\ C@",
|
| 440 |
-
"\\ S+1",
|
| 441 |
-
"H1 -1",
|
| 442 |
-
"Se H1",
|
| 443 |
-
"P@ +1",
|
| 444 |
-
"-\\ Ring2",
|
| 445 |
-
"11 C",
|
| 446 |
-
"=Te +1",
|
| 447 |
-
"Zn +2",
|
| 448 |
-
"/ NH1",
|
| 449 |
-
"1 8",
|
| 450 |
-
"A s",
|
| 451 |
-
"B H2",
|
| 452 |
-
"B H1-1",
|
| 453 |
-
"C a",
|
| 454 |
-
"H 3",
|
| 455 |
-
"O H1-1",
|
| 456 |
-
"S H2",
|
| 457 |
-
"=O +1",
|
| 458 |
-
"Se +1",
|
| 459 |
-
"Te H2",
|
| 460 |
-
"125I H1",
|
| 461 |
-
"-/ Ring1",
|
| 462 |
-
"14C H2",
|
| 463 |
-
"Ag +1",
|
| 464 |
-
"=Se +1",
|
| 465 |
-
"Mg H2",
|
| 466 |
-
"Mg +2",
|
| 467 |
-
"11C H3",
|
| 468 |
-
"18 F",
|
| 469 |
-
"BH2 -1",
|
| 470 |
-
"Ca +2"
|
| 471 |
-
]
|
| 472 |
-
}
|
| 473 |
-
}
|
|
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|
models/finetuned/bbbp/tokenizer_config.json
DELETED
|
@@ -1,59 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"add_prefix_space": false,
|
| 3 |
-
"added_tokens_decoder": {
|
| 4 |
-
"0": {
|
| 5 |
-
"content": "<unk>",
|
| 6 |
-
"lstrip": false,
|
| 7 |
-
"normalized": true,
|
| 8 |
-
"rstrip": false,
|
| 9 |
-
"single_word": false,
|
| 10 |
-
"special": true
|
| 11 |
-
},
|
| 12 |
-
"1": {
|
| 13 |
-
"content": "<s>",
|
| 14 |
-
"lstrip": false,
|
| 15 |
-
"normalized": true,
|
| 16 |
-
"rstrip": false,
|
| 17 |
-
"single_word": false,
|
| 18 |
-
"special": true
|
| 19 |
-
},
|
| 20 |
-
"2": {
|
| 21 |
-
"content": "</s>",
|
| 22 |
-
"lstrip": false,
|
| 23 |
-
"normalized": true,
|
| 24 |
-
"rstrip": false,
|
| 25 |
-
"single_word": false,
|
| 26 |
-
"special": true
|
| 27 |
-
},
|
| 28 |
-
"3": {
|
| 29 |
-
"content": "<pad>",
|
| 30 |
-
"lstrip": false,
|
| 31 |
-
"normalized": true,
|
| 32 |
-
"rstrip": false,
|
| 33 |
-
"single_word": false,
|
| 34 |
-
"special": true
|
| 35 |
-
},
|
| 36 |
-
"4": {
|
| 37 |
-
"content": "<mask>",
|
| 38 |
-
"lstrip": true,
|
| 39 |
-
"normalized": true,
|
| 40 |
-
"rstrip": false,
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"special": true
|
| 43 |
-
}
|
| 44 |
-
},
|
| 45 |
-
"bos_token": "<s>",
|
| 46 |
-
"clean_up_tokenization_spaces": true,
|
| 47 |
-
"cls_token": "<s>",
|
| 48 |
-
"eos_token": "</s>",
|
| 49 |
-
"errors": "replace",
|
| 50 |
-
"mask_token": "<mask>",
|
| 51 |
-
"model_max_length": 1000000000000000019884624838656,
|
| 52 |
-
"name_or_path": "data/epoch_267/hf",
|
| 53 |
-
"pad_token": "<pad>",
|
| 54 |
-
"sep_token": "</s>",
|
| 55 |
-
"special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
|
| 56 |
-
"tokenizer_class": "RobertaTokenizer",
|
| 57 |
-
"trim_offsets": true,
|
| 58 |
-
"unk_token": "<unk>"
|
| 59 |
-
}
|
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|
models/finetuned/bbbp/vocab.json
DELETED
|
@@ -1 +0,0 @@
|
|
| 1 |
-
{"<unk>":0,"<s>":1,"</s>":2,"<pad>":3,"<mask>":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
|
|
|
|
|
|
models/finetuned/esol/config.json
DELETED
|
@@ -1,28 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "data/epoch_267/hf",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"RobertaForMaskedLM"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"bos_token_id": 0,
|
| 8 |
-
"classifier_dropout": null,
|
| 9 |
-
"eos_token_id": 2,
|
| 10 |
-
"hidden_act": "gelu",
|
| 11 |
-
"hidden_dropout_prob": 0.1,
|
| 12 |
-
"hidden_size": 768,
|
| 13 |
-
"initializer_range": 0.02,
|
| 14 |
-
"intermediate_size": 3072,
|
| 15 |
-
"layer_norm_eps": 1e-12,
|
| 16 |
-
"max_position_embeddings": 514,
|
| 17 |
-
"model_type": "roberta",
|
| 18 |
-
"num_attention_heads": 4,
|
| 19 |
-
"num_hidden_layers": 12,
|
| 20 |
-
"output_hidden_states": true,
|
| 21 |
-
"pad_token_id": 1,
|
| 22 |
-
"position_embedding_type": "absolute",
|
| 23 |
-
"torch_dtype": "float32",
|
| 24 |
-
"transformers_version": "4.26.1",
|
| 25 |
-
"type_vocab_size": 1,
|
| 26 |
-
"use_cache": true,
|
| 27 |
-
"vocab_size": 800
|
| 28 |
-
}
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|
models/finetuned/esol/finetuning_optimized_config.json
DELETED
|
@@ -1,24 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"dataset_meta_csv": "data/finetuning_datasets/regression/esol/esol.csv",
|
| 3 |
-
"dataset_embs_npz": "data/finetuning_datasets/regression/esol/esol_embs.npz",
|
| 4 |
-
"use_scaffold": 0,
|
| 5 |
-
"seed": 42,
|
| 6 |
-
"train_frac": 0.8,
|
| 7 |
-
"val_frac": 0.1,
|
| 8 |
-
"test_frac": 0.1,
|
| 9 |
-
"model_path": "HUBioDataLab/SELFormer",
|
| 10 |
-
"tokenizer_path": "HUBioDataLab/SELFormer",
|
| 11 |
-
"pretrained_multimodal_dir": "data/models/SELFormerMM",
|
| 12 |
-
"task_type": "regression",
|
| 13 |
-
"label_column": "measured log solubility in mols per litre",
|
| 14 |
-
"num_labels": 1,
|
| 15 |
-
"batch_size": 8,
|
| 16 |
-
"max_len": 128,
|
| 17 |
-
"epochs": 100,
|
| 18 |
-
"backbone_lr": 5e-05,
|
| 19 |
-
"head_lr": 5e-05,
|
| 20 |
-
"weight_decay": 0.1,
|
| 21 |
-
"checkpoint_every": 25,
|
| 22 |
-
"test_eval_every": 0,
|
| 23 |
-
"save_dir": "data/models/finetuned/esol"
|
| 24 |
-
}
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models/finetuned/esol/merges.txt
DELETED
|
@@ -1,162 +0,0 @@
|
|
| 1 |
-
#version: 0.2 - Trained by `huggingface/tokenizers`
|
| 2 |
-
B r
|
| 3 |
-
a n
|
| 4 |
-
c h
|
| 5 |
-
Br an
|
| 6 |
-
Bran ch
|
| 7 |
-
Branch 1
|
| 8 |
-
= C
|
| 9 |
-
R i
|
| 10 |
-
n g
|
| 11 |
-
Ri ng
|
| 12 |
-
Ring 1
|
| 13 |
-
= Branch1
|
| 14 |
-
Branch 2
|
| 15 |
-
= O
|
| 16 |
-
Ring 2
|
| 17 |
-
H 1
|
| 18 |
-
C @
|
| 19 |
-
= N
|
| 20 |
-
# Branch1
|
| 21 |
-
C@ @
|
| 22 |
-
= Branch2
|
| 23 |
-
C@ H1
|
| 24 |
-
C@@ H1
|
| 25 |
-
# Branch2
|
| 26 |
-
C l
|
| 27 |
-
# C
|
| 28 |
-
/ C
|
| 29 |
-
N H1
|
| 30 |
-
+ 1
|
| 31 |
-
- 1
|
| 32 |
-
= Ring1
|
| 33 |
-
O -1
|
| 34 |
-
N +1
|
| 35 |
-
\ C
|
| 36 |
-
/ N
|
| 37 |
-
# N
|
| 38 |
-
= Ring2
|
| 39 |
-
= S
|
| 40 |
-
=N +1
|
| 41 |
-
N a
|
| 42 |
-
Na +1
|
| 43 |
-
\ N
|
| 44 |
-
S +1
|
| 45 |
-
/ O
|
| 46 |
-
\ S
|
| 47 |
-
\ O
|
| 48 |
-
Br -1
|
| 49 |
-
I -1
|
| 50 |
-
Cl -1
|
| 51 |
-
/ C@H1
|
| 52 |
-
Branch 3
|
| 53 |
-
/ C@@H1
|
| 54 |
-
= P
|
| 55 |
-
/ S
|
| 56 |
-
=N -1
|
| 57 |
-
S i
|
| 58 |
-
K +1
|
| 59 |
-
N -1
|
| 60 |
-
S e
|
| 61 |
-
L i
|
| 62 |
-
Li +1
|
| 63 |
-
+ 3
|
| 64 |
-
Cl +3
|
| 65 |
-
\ C@H1
|
| 66 |
-
Ring 3
|
| 67 |
-
\ C@@H1
|
| 68 |
-
/ N+1
|
| 69 |
-
/ P
|
| 70 |
-
\ F
|
| 71 |
-
P @
|
| 72 |
-
2 H
|
| 73 |
-
P H1
|
| 74 |
-
/ Br
|
| 75 |
-
N @
|
| 76 |
-
P +1
|
| 77 |
-
/ Cl
|
| 78 |
-
\ NH1
|
| 79 |
-
\ Br
|
| 80 |
-
@ +1
|
| 81 |
-
/ I
|
| 82 |
-
/ C@
|
| 83 |
-
T e
|
| 84 |
-
\ N+1
|
| 85 |
-
P@ @
|
| 86 |
-
1 2
|
| 87 |
-
5 I
|
| 88 |
-
\ O-1
|
| 89 |
-
12 5I
|
| 90 |
-
/ F
|
| 91 |
-
# N+1
|
| 92 |
-
\ Cl
|
| 93 |
-
N@ +1
|
| 94 |
-
\ I
|
| 95 |
-
- /
|
| 96 |
-
/ C@@
|
| 97 |
-
N@ @
|
| 98 |
-
N@ @+1
|
| 99 |
-
-/ Ring2
|
| 100 |
-
- \
|
| 101 |
-
1 4
|
| 102 |
-
B -1
|
| 103 |
-
C -1
|
| 104 |
-
S @+1
|
| 105 |
-
14 C
|
| 106 |
-
H 2
|
| 107 |
-
H 4
|
| 108 |
-
I +1
|
| 109 |
-
S -1
|
| 110 |
-
\ P
|
| 111 |
-
=S +1
|
| 112 |
-
=P @
|
| 113 |
-
Si H4
|
| 114 |
-
+ 2
|
| 115 |
-
3 H
|
| 116 |
-
@ @+1
|
| 117 |
-
A g
|
| 118 |
-
C +1
|
| 119 |
-
S @@+1
|
| 120 |
-
Cl +1
|
| 121 |
-
=S e
|
| 122 |
-
-\ Ring1
|
| 123 |
-
H 0
|
| 124 |
-
O H0
|
| 125 |
-
1 1
|
| 126 |
-
= Branch3
|
| 127 |
-
= Te
|
| 128 |
-
M g
|
| 129 |
-
O +1
|
| 130 |
-
Z n
|
| 131 |
-
\ C@
|
| 132 |
-
\ S+1
|
| 133 |
-
H1 -1
|
| 134 |
-
Se H1
|
| 135 |
-
P@ +1
|
| 136 |
-
-\ Ring2
|
| 137 |
-
11 C
|
| 138 |
-
=Te +1
|
| 139 |
-
Zn +2
|
| 140 |
-
/ NH1
|
| 141 |
-
1 8
|
| 142 |
-
A s
|
| 143 |
-
B H2
|
| 144 |
-
B H1-1
|
| 145 |
-
C a
|
| 146 |
-
H 3
|
| 147 |
-
O H1-1
|
| 148 |
-
S H2
|
| 149 |
-
=O +1
|
| 150 |
-
Se +1
|
| 151 |
-
Te H2
|
| 152 |
-
125I H1
|
| 153 |
-
-/ Ring1
|
| 154 |
-
14C H2
|
| 155 |
-
Ag +1
|
| 156 |
-
=Se +1
|
| 157 |
-
Mg H2
|
| 158 |
-
Mg +2
|
| 159 |
-
11C H3
|
| 160 |
-
18 F
|
| 161 |
-
BH2 -1
|
| 162 |
-
Ca +2
|
|
|
|
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models/finetuned/esol/model.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:eed86c02f896cfdf36e8f5e519d66ae82d7eae4a0993911ee8f89ceb76e8b07b
|
| 3 |
-
size 1022843005
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|
models/finetuned/esol/special_tokens_map.json
DELETED
|
@@ -1,51 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"bos_token": {
|
| 3 |
-
"content": "<s>",
|
| 4 |
-
"lstrip": false,
|
| 5 |
-
"normalized": true,
|
| 6 |
-
"rstrip": false,
|
| 7 |
-
"single_word": false
|
| 8 |
-
},
|
| 9 |
-
"cls_token": {
|
| 10 |
-
"content": "<s>",
|
| 11 |
-
"lstrip": false,
|
| 12 |
-
"normalized": true,
|
| 13 |
-
"rstrip": false,
|
| 14 |
-
"single_word": false
|
| 15 |
-
},
|
| 16 |
-
"eos_token": {
|
| 17 |
-
"content": "</s>",
|
| 18 |
-
"lstrip": false,
|
| 19 |
-
"normalized": true,
|
| 20 |
-
"rstrip": false,
|
| 21 |
-
"single_word": false
|
| 22 |
-
},
|
| 23 |
-
"mask_token": {
|
| 24 |
-
"content": "<mask>",
|
| 25 |
-
"lstrip": true,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"rstrip": false,
|
| 28 |
-
"single_word": false
|
| 29 |
-
},
|
| 30 |
-
"pad_token": {
|
| 31 |
-
"content": "<pad>",
|
| 32 |
-
"lstrip": false,
|
| 33 |
-
"normalized": true,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"single_word": false
|
| 36 |
-
},
|
| 37 |
-
"sep_token": {
|
| 38 |
-
"content": "</s>",
|
| 39 |
-
"lstrip": false,
|
| 40 |
-
"normalized": true,
|
| 41 |
-
"rstrip": false,
|
| 42 |
-
"single_word": false
|
| 43 |
-
},
|
| 44 |
-
"unk_token": {
|
| 45 |
-
"content": "<unk>",
|
| 46 |
-
"lstrip": false,
|
| 47 |
-
"normalized": true,
|
| 48 |
-
"rstrip": false,
|
| 49 |
-
"single_word": false
|
| 50 |
-
}
|
| 51 |
-
}
|
|
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|
models/finetuned/esol/tokenizer.json
DELETED
|
@@ -1,473 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"version": "1.0",
|
| 3 |
-
"truncation": {
|
| 4 |
-
"direction": "Right",
|
| 5 |
-
"max_length": 128,
|
| 6 |
-
"strategy": "LongestFirst",
|
| 7 |
-
"stride": 0
|
| 8 |
-
},
|
| 9 |
-
"padding": {
|
| 10 |
-
"strategy": {
|
| 11 |
-
"Fixed": 128
|
| 12 |
-
},
|
| 13 |
-
"direction": "Right",
|
| 14 |
-
"pad_to_multiple_of": null,
|
| 15 |
-
"pad_id": 3,
|
| 16 |
-
"pad_type_id": 0,
|
| 17 |
-
"pad_token": "<pad>"
|
| 18 |
-
},
|
| 19 |
-
"added_tokens": [
|
| 20 |
-
{
|
| 21 |
-
"id": 0,
|
| 22 |
-
"content": "<unk>",
|
| 23 |
-
"single_word": false,
|
| 24 |
-
"lstrip": false,
|
| 25 |
-
"rstrip": false,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"special": true
|
| 28 |
-
},
|
| 29 |
-
{
|
| 30 |
-
"id": 1,
|
| 31 |
-
"content": "<s>",
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"lstrip": false,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"normalized": true,
|
| 36 |
-
"special": true
|
| 37 |
-
},
|
| 38 |
-
{
|
| 39 |
-
"id": 2,
|
| 40 |
-
"content": "</s>",
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"lstrip": false,
|
| 43 |
-
"rstrip": false,
|
| 44 |
-
"normalized": true,
|
| 45 |
-
"special": true
|
| 46 |
-
},
|
| 47 |
-
{
|
| 48 |
-
"id": 3,
|
| 49 |
-
"content": "<pad>",
|
| 50 |
-
"single_word": false,
|
| 51 |
-
"lstrip": false,
|
| 52 |
-
"rstrip": false,
|
| 53 |
-
"normalized": true,
|
| 54 |
-
"special": true
|
| 55 |
-
},
|
| 56 |
-
{
|
| 57 |
-
"id": 4,
|
| 58 |
-
"content": "<mask>",
|
| 59 |
-
"single_word": false,
|
| 60 |
-
"lstrip": true,
|
| 61 |
-
"rstrip": false,
|
| 62 |
-
"normalized": true,
|
| 63 |
-
"special": true
|
| 64 |
-
}
|
| 65 |
-
],
|
| 66 |
-
"normalizer": null,
|
| 67 |
-
"pre_tokenizer": {
|
| 68 |
-
"type": "ByteLevel",
|
| 69 |
-
"add_prefix_space": false,
|
| 70 |
-
"trim_offsets": true,
|
| 71 |
-
"use_regex": true
|
| 72 |
-
},
|
| 73 |
-
"post_processor": {
|
| 74 |
-
"type": "RobertaProcessing",
|
| 75 |
-
"sep": [
|
| 76 |
-
"</s>",
|
| 77 |
-
2
|
| 78 |
-
],
|
| 79 |
-
"cls": [
|
| 80 |
-
"<s>",
|
| 81 |
-
1
|
| 82 |
-
],
|
| 83 |
-
"trim_offsets": true,
|
| 84 |
-
"add_prefix_space": false
|
| 85 |
-
},
|
| 86 |
-
"decoder": {
|
| 87 |
-
"type": "ByteLevel",
|
| 88 |
-
"add_prefix_space": true,
|
| 89 |
-
"trim_offsets": true,
|
| 90 |
-
"use_regex": true
|
| 91 |
-
},
|
| 92 |
-
"model": {
|
| 93 |
-
"type": "BPE",
|
| 94 |
-
"dropout": null,
|
| 95 |
-
"unk_token": null,
|
| 96 |
-
"continuing_subword_prefix": "",
|
| 97 |
-
"end_of_word_suffix": "",
|
| 98 |
-
"fuse_unk": false,
|
| 99 |
-
"vocab": {
|
| 100 |
-
"<unk>": 0,
|
| 101 |
-
"<s>": 1,
|
| 102 |
-
"</s>": 2,
|
| 103 |
-
"<pad>": 3,
|
| 104 |
-
"<mask>": 4,
|
| 105 |
-
"\n": 5,
|
| 106 |
-
"#": 6,
|
| 107 |
-
"+": 7,
|
| 108 |
-
"-": 8,
|
| 109 |
-
".": 9,
|
| 110 |
-
"/": 10,
|
| 111 |
-
"0": 11,
|
| 112 |
-
"1": 12,
|
| 113 |
-
"2": 13,
|
| 114 |
-
"3": 14,
|
| 115 |
-
"4": 15,
|
| 116 |
-
"5": 16,
|
| 117 |
-
"8": 17,
|
| 118 |
-
"=": 18,
|
| 119 |
-
"@": 19,
|
| 120 |
-
"A": 20,
|
| 121 |
-
"B": 21,
|
| 122 |
-
"C": 22,
|
| 123 |
-
"F": 23,
|
| 124 |
-
"H": 24,
|
| 125 |
-
"I": 25,
|
| 126 |
-
"K": 26,
|
| 127 |
-
"L": 27,
|
| 128 |
-
"M": 28,
|
| 129 |
-
"N": 29,
|
| 130 |
-
"O": 30,
|
| 131 |
-
"P": 31,
|
| 132 |
-
"R": 32,
|
| 133 |
-
"S": 33,
|
| 134 |
-
"T": 34,
|
| 135 |
-
"Z": 35,
|
| 136 |
-
"\\": 36,
|
| 137 |
-
"a": 37,
|
| 138 |
-
"c": 38,
|
| 139 |
-
"e": 39,
|
| 140 |
-
"g": 40,
|
| 141 |
-
"h": 41,
|
| 142 |
-
"i": 42,
|
| 143 |
-
"l": 43,
|
| 144 |
-
"n": 44,
|
| 145 |
-
"r": 45,
|
| 146 |
-
"s": 46,
|
| 147 |
-
"Br": 47,
|
| 148 |
-
"an": 48,
|
| 149 |
-
"ch": 49,
|
| 150 |
-
"Bran": 50,
|
| 151 |
-
"Branch": 51,
|
| 152 |
-
"Branch1": 52,
|
| 153 |
-
"=C": 53,
|
| 154 |
-
"Ri": 54,
|
| 155 |
-
"ng": 55,
|
| 156 |
-
"Ring": 56,
|
| 157 |
-
"Ring1": 57,
|
| 158 |
-
"=Branch1": 58,
|
| 159 |
-
"Branch2": 59,
|
| 160 |
-
"=O": 60,
|
| 161 |
-
"Ring2": 61,
|
| 162 |
-
"H1": 62,
|
| 163 |
-
"C@": 63,
|
| 164 |
-
"=N": 64,
|
| 165 |
-
"#Branch1": 65,
|
| 166 |
-
"C@@": 66,
|
| 167 |
-
"=Branch2": 67,
|
| 168 |
-
"C@H1": 68,
|
| 169 |
-
"C@@H1": 69,
|
| 170 |
-
"#Branch2": 70,
|
| 171 |
-
"Cl": 71,
|
| 172 |
-
"#C": 72,
|
| 173 |
-
"/C": 73,
|
| 174 |
-
"NH1": 74,
|
| 175 |
-
"+1": 75,
|
| 176 |
-
"-1": 76,
|
| 177 |
-
"=Ring1": 77,
|
| 178 |
-
"O-1": 78,
|
| 179 |
-
"N+1": 79,
|
| 180 |
-
"\\C": 80,
|
| 181 |
-
"/N": 81,
|
| 182 |
-
"#N": 82,
|
| 183 |
-
"=Ring2": 83,
|
| 184 |
-
"=S": 84,
|
| 185 |
-
"=N+1": 85,
|
| 186 |
-
"Na": 86,
|
| 187 |
-
"Na+1": 87,
|
| 188 |
-
"\\N": 88,
|
| 189 |
-
"S+1": 89,
|
| 190 |
-
"/O": 90,
|
| 191 |
-
"\\S": 91,
|
| 192 |
-
"\\O": 92,
|
| 193 |
-
"Br-1": 93,
|
| 194 |
-
"I-1": 94,
|
| 195 |
-
"Cl-1": 95,
|
| 196 |
-
"/C@H1": 96,
|
| 197 |
-
"Branch3": 97,
|
| 198 |
-
"/C@@H1": 98,
|
| 199 |
-
"=P": 99,
|
| 200 |
-
"/S": 100,
|
| 201 |
-
"=N-1": 101,
|
| 202 |
-
"Si": 102,
|
| 203 |
-
"K+1": 103,
|
| 204 |
-
"N-1": 104,
|
| 205 |
-
"Se": 105,
|
| 206 |
-
"Li": 106,
|
| 207 |
-
"Li+1": 107,
|
| 208 |
-
"+3": 108,
|
| 209 |
-
"Cl+3": 109,
|
| 210 |
-
"\\C@H1": 110,
|
| 211 |
-
"Ring3": 111,
|
| 212 |
-
"\\C@@H1": 112,
|
| 213 |
-
"/N+1": 113,
|
| 214 |
-
"/P": 114,
|
| 215 |
-
"\\F": 115,
|
| 216 |
-
"P@": 116,
|
| 217 |
-
"2H": 117,
|
| 218 |
-
"PH1": 118,
|
| 219 |
-
"/Br": 119,
|
| 220 |
-
"N@": 120,
|
| 221 |
-
"P+1": 121,
|
| 222 |
-
"/Cl": 122,
|
| 223 |
-
"\\NH1": 123,
|
| 224 |
-
"\\Br": 124,
|
| 225 |
-
"@+1": 125,
|
| 226 |
-
"/I": 126,
|
| 227 |
-
"/C@": 127,
|
| 228 |
-
"Te": 128,
|
| 229 |
-
"\\N+1": 129,
|
| 230 |
-
"P@@": 130,
|
| 231 |
-
"12": 131,
|
| 232 |
-
"5I": 132,
|
| 233 |
-
"\\O-1": 133,
|
| 234 |
-
"125I": 134,
|
| 235 |
-
"/F": 135,
|
| 236 |
-
"#N+1": 136,
|
| 237 |
-
"\\Cl": 137,
|
| 238 |
-
"N@+1": 138,
|
| 239 |
-
"\\I": 139,
|
| 240 |
-
"-/": 140,
|
| 241 |
-
"/C@@": 141,
|
| 242 |
-
"N@@": 142,
|
| 243 |
-
"N@@+1": 143,
|
| 244 |
-
"-/Ring2": 144,
|
| 245 |
-
"-\\": 145,
|
| 246 |
-
"14": 146,
|
| 247 |
-
"B-1": 147,
|
| 248 |
-
"C-1": 148,
|
| 249 |
-
"S@+1": 149,
|
| 250 |
-
"14C": 150,
|
| 251 |
-
"H2": 151,
|
| 252 |
-
"H4": 152,
|
| 253 |
-
"I+1": 153,
|
| 254 |
-
"S-1": 154,
|
| 255 |
-
"\\P": 155,
|
| 256 |
-
"=S+1": 156,
|
| 257 |
-
"=P@": 157,
|
| 258 |
-
"SiH4": 158,
|
| 259 |
-
"+2": 159,
|
| 260 |
-
"3H": 160,
|
| 261 |
-
"@@+1": 161,
|
| 262 |
-
"Ag": 162,
|
| 263 |
-
"C+1": 163,
|
| 264 |
-
"S@@+1": 164,
|
| 265 |
-
"Cl+1": 165,
|
| 266 |
-
"=Se": 166,
|
| 267 |
-
"-\\Ring1": 167,
|
| 268 |
-
"H0": 168,
|
| 269 |
-
"OH0": 169,
|
| 270 |
-
"11": 170,
|
| 271 |
-
"=Branch3": 171,
|
| 272 |
-
"=Te": 172,
|
| 273 |
-
"Mg": 173,
|
| 274 |
-
"O+1": 174,
|
| 275 |
-
"Zn": 175,
|
| 276 |
-
"\\C@": 176,
|
| 277 |
-
"\\S+1": 177,
|
| 278 |
-
"H1-1": 178,
|
| 279 |
-
"SeH1": 179,
|
| 280 |
-
"P@+1": 180,
|
| 281 |
-
"-\\Ring2": 181,
|
| 282 |
-
"11C": 182,
|
| 283 |
-
"=Te+1": 183,
|
| 284 |
-
"Zn+2": 184,
|
| 285 |
-
"/NH1": 185,
|
| 286 |
-
"18": 186,
|
| 287 |
-
"As": 187,
|
| 288 |
-
"BH2": 188,
|
| 289 |
-
"BH1-1": 189,
|
| 290 |
-
"Ca": 190,
|
| 291 |
-
"H3": 191,
|
| 292 |
-
"OH1-1": 192,
|
| 293 |
-
"SH2": 193,
|
| 294 |
-
"=O+1": 194,
|
| 295 |
-
"Se+1": 195,
|
| 296 |
-
"TeH2": 196,
|
| 297 |
-
"125IH1": 197,
|
| 298 |
-
"-/Ring1": 198,
|
| 299 |
-
"14CH2": 199,
|
| 300 |
-
"Ag+1": 200,
|
| 301 |
-
"=Se+1": 201,
|
| 302 |
-
"MgH2": 202,
|
| 303 |
-
"Mg+2": 203,
|
| 304 |
-
"11CH3": 204,
|
| 305 |
-
"18F": 205,
|
| 306 |
-
"BH2-1": 206,
|
| 307 |
-
"Ca+2": 207
|
| 308 |
-
},
|
| 309 |
-
"merges": [
|
| 310 |
-
"B r",
|
| 311 |
-
"a n",
|
| 312 |
-
"c h",
|
| 313 |
-
"Br an",
|
| 314 |
-
"Bran ch",
|
| 315 |
-
"Branch 1",
|
| 316 |
-
"= C",
|
| 317 |
-
"R i",
|
| 318 |
-
"n g",
|
| 319 |
-
"Ri ng",
|
| 320 |
-
"Ring 1",
|
| 321 |
-
"= Branch1",
|
| 322 |
-
"Branch 2",
|
| 323 |
-
"= O",
|
| 324 |
-
"Ring 2",
|
| 325 |
-
"H 1",
|
| 326 |
-
"C @",
|
| 327 |
-
"= N",
|
| 328 |
-
"# Branch1",
|
| 329 |
-
"C@ @",
|
| 330 |
-
"= Branch2",
|
| 331 |
-
"C@ H1",
|
| 332 |
-
"C@@ H1",
|
| 333 |
-
"# Branch2",
|
| 334 |
-
"C l",
|
| 335 |
-
"# C",
|
| 336 |
-
"/ C",
|
| 337 |
-
"N H1",
|
| 338 |
-
"+ 1",
|
| 339 |
-
"- 1",
|
| 340 |
-
"= Ring1",
|
| 341 |
-
"O -1",
|
| 342 |
-
"N +1",
|
| 343 |
-
"\\ C",
|
| 344 |
-
"/ N",
|
| 345 |
-
"# N",
|
| 346 |
-
"= Ring2",
|
| 347 |
-
"= S",
|
| 348 |
-
"=N +1",
|
| 349 |
-
"N a",
|
| 350 |
-
"Na +1",
|
| 351 |
-
"\\ N",
|
| 352 |
-
"S +1",
|
| 353 |
-
"/ O",
|
| 354 |
-
"\\ S",
|
| 355 |
-
"\\ O",
|
| 356 |
-
"Br -1",
|
| 357 |
-
"I -1",
|
| 358 |
-
"Cl -1",
|
| 359 |
-
"/ C@H1",
|
| 360 |
-
"Branch 3",
|
| 361 |
-
"/ C@@H1",
|
| 362 |
-
"= P",
|
| 363 |
-
"/ S",
|
| 364 |
-
"=N -1",
|
| 365 |
-
"S i",
|
| 366 |
-
"K +1",
|
| 367 |
-
"N -1",
|
| 368 |
-
"S e",
|
| 369 |
-
"L i",
|
| 370 |
-
"Li +1",
|
| 371 |
-
"+ 3",
|
| 372 |
-
"Cl +3",
|
| 373 |
-
"\\ C@H1",
|
| 374 |
-
"Ring 3",
|
| 375 |
-
"\\ C@@H1",
|
| 376 |
-
"/ N+1",
|
| 377 |
-
"/ P",
|
| 378 |
-
"\\ F",
|
| 379 |
-
"P @",
|
| 380 |
-
"2 H",
|
| 381 |
-
"P H1",
|
| 382 |
-
"/ Br",
|
| 383 |
-
"N @",
|
| 384 |
-
"P +1",
|
| 385 |
-
"/ Cl",
|
| 386 |
-
"\\ NH1",
|
| 387 |
-
"\\ Br",
|
| 388 |
-
"@ +1",
|
| 389 |
-
"/ I",
|
| 390 |
-
"/ C@",
|
| 391 |
-
"T e",
|
| 392 |
-
"\\ N+1",
|
| 393 |
-
"P@ @",
|
| 394 |
-
"1 2",
|
| 395 |
-
"5 I",
|
| 396 |
-
"\\ O-1",
|
| 397 |
-
"12 5I",
|
| 398 |
-
"/ F",
|
| 399 |
-
"# N+1",
|
| 400 |
-
"\\ Cl",
|
| 401 |
-
"N@ +1",
|
| 402 |
-
"\\ I",
|
| 403 |
-
"- /",
|
| 404 |
-
"/ C@@",
|
| 405 |
-
"N@ @",
|
| 406 |
-
"N@ @+1",
|
| 407 |
-
"-/ Ring2",
|
| 408 |
-
"- \\",
|
| 409 |
-
"1 4",
|
| 410 |
-
"B -1",
|
| 411 |
-
"C -1",
|
| 412 |
-
"S @+1",
|
| 413 |
-
"14 C",
|
| 414 |
-
"H 2",
|
| 415 |
-
"H 4",
|
| 416 |
-
"I +1",
|
| 417 |
-
"S -1",
|
| 418 |
-
"\\ P",
|
| 419 |
-
"=S +1",
|
| 420 |
-
"=P @",
|
| 421 |
-
"Si H4",
|
| 422 |
-
"+ 2",
|
| 423 |
-
"3 H",
|
| 424 |
-
"@ @+1",
|
| 425 |
-
"A g",
|
| 426 |
-
"C +1",
|
| 427 |
-
"S @@+1",
|
| 428 |
-
"Cl +1",
|
| 429 |
-
"=S e",
|
| 430 |
-
"-\\ Ring1",
|
| 431 |
-
"H 0",
|
| 432 |
-
"O H0",
|
| 433 |
-
"1 1",
|
| 434 |
-
"= Branch3",
|
| 435 |
-
"= Te",
|
| 436 |
-
"M g",
|
| 437 |
-
"O +1",
|
| 438 |
-
"Z n",
|
| 439 |
-
"\\ C@",
|
| 440 |
-
"\\ S+1",
|
| 441 |
-
"H1 -1",
|
| 442 |
-
"Se H1",
|
| 443 |
-
"P@ +1",
|
| 444 |
-
"-\\ Ring2",
|
| 445 |
-
"11 C",
|
| 446 |
-
"=Te +1",
|
| 447 |
-
"Zn +2",
|
| 448 |
-
"/ NH1",
|
| 449 |
-
"1 8",
|
| 450 |
-
"A s",
|
| 451 |
-
"B H2",
|
| 452 |
-
"B H1-1",
|
| 453 |
-
"C a",
|
| 454 |
-
"H 3",
|
| 455 |
-
"O H1-1",
|
| 456 |
-
"S H2",
|
| 457 |
-
"=O +1",
|
| 458 |
-
"Se +1",
|
| 459 |
-
"Te H2",
|
| 460 |
-
"125I H1",
|
| 461 |
-
"-/ Ring1",
|
| 462 |
-
"14C H2",
|
| 463 |
-
"Ag +1",
|
| 464 |
-
"=Se +1",
|
| 465 |
-
"Mg H2",
|
| 466 |
-
"Mg +2",
|
| 467 |
-
"11C H3",
|
| 468 |
-
"18 F",
|
| 469 |
-
"BH2 -1",
|
| 470 |
-
"Ca +2"
|
| 471 |
-
]
|
| 472 |
-
}
|
| 473 |
-
}
|
|
|
|
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|
models/finetuned/esol/tokenizer_config.json
DELETED
|
@@ -1,59 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"add_prefix_space": false,
|
| 3 |
-
"added_tokens_decoder": {
|
| 4 |
-
"0": {
|
| 5 |
-
"content": "<unk>",
|
| 6 |
-
"lstrip": false,
|
| 7 |
-
"normalized": true,
|
| 8 |
-
"rstrip": false,
|
| 9 |
-
"single_word": false,
|
| 10 |
-
"special": true
|
| 11 |
-
},
|
| 12 |
-
"1": {
|
| 13 |
-
"content": "<s>",
|
| 14 |
-
"lstrip": false,
|
| 15 |
-
"normalized": true,
|
| 16 |
-
"rstrip": false,
|
| 17 |
-
"single_word": false,
|
| 18 |
-
"special": true
|
| 19 |
-
},
|
| 20 |
-
"2": {
|
| 21 |
-
"content": "</s>",
|
| 22 |
-
"lstrip": false,
|
| 23 |
-
"normalized": true,
|
| 24 |
-
"rstrip": false,
|
| 25 |
-
"single_word": false,
|
| 26 |
-
"special": true
|
| 27 |
-
},
|
| 28 |
-
"3": {
|
| 29 |
-
"content": "<pad>",
|
| 30 |
-
"lstrip": false,
|
| 31 |
-
"normalized": true,
|
| 32 |
-
"rstrip": false,
|
| 33 |
-
"single_word": false,
|
| 34 |
-
"special": true
|
| 35 |
-
},
|
| 36 |
-
"4": {
|
| 37 |
-
"content": "<mask>",
|
| 38 |
-
"lstrip": true,
|
| 39 |
-
"normalized": true,
|
| 40 |
-
"rstrip": false,
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"special": true
|
| 43 |
-
}
|
| 44 |
-
},
|
| 45 |
-
"bos_token": "<s>",
|
| 46 |
-
"clean_up_tokenization_spaces": true,
|
| 47 |
-
"cls_token": "<s>",
|
| 48 |
-
"eos_token": "</s>",
|
| 49 |
-
"errors": "replace",
|
| 50 |
-
"mask_token": "<mask>",
|
| 51 |
-
"model_max_length": 1000000000000000019884624838656,
|
| 52 |
-
"name_or_path": "data/epoch_267/hf",
|
| 53 |
-
"pad_token": "<pad>",
|
| 54 |
-
"sep_token": "</s>",
|
| 55 |
-
"special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
|
| 56 |
-
"tokenizer_class": "RobertaTokenizer",
|
| 57 |
-
"trim_offsets": true,
|
| 58 |
-
"unk_token": "<unk>"
|
| 59 |
-
}
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|
models/finetuned/esol/vocab.json
DELETED
|
@@ -1 +0,0 @@
|
|
| 1 |
-
{"<unk>":0,"<s>":1,"</s>":2,"<pad>":3,"<mask>":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
|
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|
models/finetuned/freesolv/config.json
DELETED
|
@@ -1,28 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "data/epoch_267/hf",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"RobertaForMaskedLM"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"bos_token_id": 0,
|
| 8 |
-
"classifier_dropout": null,
|
| 9 |
-
"eos_token_id": 2,
|
| 10 |
-
"hidden_act": "gelu",
|
| 11 |
-
"hidden_dropout_prob": 0.1,
|
| 12 |
-
"hidden_size": 768,
|
| 13 |
-
"initializer_range": 0.02,
|
| 14 |
-
"intermediate_size": 3072,
|
| 15 |
-
"layer_norm_eps": 1e-12,
|
| 16 |
-
"max_position_embeddings": 514,
|
| 17 |
-
"model_type": "roberta",
|
| 18 |
-
"num_attention_heads": 4,
|
| 19 |
-
"num_hidden_layers": 12,
|
| 20 |
-
"output_hidden_states": true,
|
| 21 |
-
"pad_token_id": 1,
|
| 22 |
-
"position_embedding_type": "absolute",
|
| 23 |
-
"torch_dtype": "float32",
|
| 24 |
-
"transformers_version": "4.26.1",
|
| 25 |
-
"type_vocab_size": 1,
|
| 26 |
-
"use_cache": true,
|
| 27 |
-
"vocab_size": 800
|
| 28 |
-
}
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|
models/finetuned/freesolv/finetuning_optimized_config.json
DELETED
|
@@ -1,24 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"dataset_meta_csv": "data/finetuning_datasets/regression/freesolv/freesolv.csv",
|
| 3 |
-
"dataset_embs_npz": "data/finetuning_datasets/regression/freesolv/freesolv_embs.npz",
|
| 4 |
-
"use_scaffold": 0,
|
| 5 |
-
"seed": 42,
|
| 6 |
-
"train_frac": 0.8,
|
| 7 |
-
"val_frac": 0.1,
|
| 8 |
-
"test_frac": 0.1,
|
| 9 |
-
"model_path": "HUBioDataLab/SELFormer",
|
| 10 |
-
"tokenizer_path": "HUBioDataLab/SELFormer",
|
| 11 |
-
"pretrained_multimodal_dir": "data/models/SELFormerMM",
|
| 12 |
-
"task_type": "regression",
|
| 13 |
-
"label_column": "freesolv",
|
| 14 |
-
"num_labels": 1,
|
| 15 |
-
"batch_size": 4,
|
| 16 |
-
"max_len": 128,
|
| 17 |
-
"epochs": 25,
|
| 18 |
-
"backbone_lr": 5e-05,
|
| 19 |
-
"head_lr": 0.0002,
|
| 20 |
-
"weight_decay": 0.001,
|
| 21 |
-
"checkpoint_every": 25,
|
| 22 |
-
"test_eval_every": 0,
|
| 23 |
-
"save_dir": "data/models/finetuned/freesolv"
|
| 24 |
-
}
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|
models/finetuned/freesolv/merges.txt
DELETED
|
@@ -1,162 +0,0 @@
|
|
| 1 |
-
#version: 0.2 - Trained by `huggingface/tokenizers`
|
| 2 |
-
B r
|
| 3 |
-
a n
|
| 4 |
-
c h
|
| 5 |
-
Br an
|
| 6 |
-
Bran ch
|
| 7 |
-
Branch 1
|
| 8 |
-
= C
|
| 9 |
-
R i
|
| 10 |
-
n g
|
| 11 |
-
Ri ng
|
| 12 |
-
Ring 1
|
| 13 |
-
= Branch1
|
| 14 |
-
Branch 2
|
| 15 |
-
= O
|
| 16 |
-
Ring 2
|
| 17 |
-
H 1
|
| 18 |
-
C @
|
| 19 |
-
= N
|
| 20 |
-
# Branch1
|
| 21 |
-
C@ @
|
| 22 |
-
= Branch2
|
| 23 |
-
C@ H1
|
| 24 |
-
C@@ H1
|
| 25 |
-
# Branch2
|
| 26 |
-
C l
|
| 27 |
-
# C
|
| 28 |
-
/ C
|
| 29 |
-
N H1
|
| 30 |
-
+ 1
|
| 31 |
-
- 1
|
| 32 |
-
= Ring1
|
| 33 |
-
O -1
|
| 34 |
-
N +1
|
| 35 |
-
\ C
|
| 36 |
-
/ N
|
| 37 |
-
# N
|
| 38 |
-
= Ring2
|
| 39 |
-
= S
|
| 40 |
-
=N +1
|
| 41 |
-
N a
|
| 42 |
-
Na +1
|
| 43 |
-
\ N
|
| 44 |
-
S +1
|
| 45 |
-
/ O
|
| 46 |
-
\ S
|
| 47 |
-
\ O
|
| 48 |
-
Br -1
|
| 49 |
-
I -1
|
| 50 |
-
Cl -1
|
| 51 |
-
/ C@H1
|
| 52 |
-
Branch 3
|
| 53 |
-
/ C@@H1
|
| 54 |
-
= P
|
| 55 |
-
/ S
|
| 56 |
-
=N -1
|
| 57 |
-
S i
|
| 58 |
-
K +1
|
| 59 |
-
N -1
|
| 60 |
-
S e
|
| 61 |
-
L i
|
| 62 |
-
Li +1
|
| 63 |
-
+ 3
|
| 64 |
-
Cl +3
|
| 65 |
-
\ C@H1
|
| 66 |
-
Ring 3
|
| 67 |
-
\ C@@H1
|
| 68 |
-
/ N+1
|
| 69 |
-
/ P
|
| 70 |
-
\ F
|
| 71 |
-
P @
|
| 72 |
-
2 H
|
| 73 |
-
P H1
|
| 74 |
-
/ Br
|
| 75 |
-
N @
|
| 76 |
-
P +1
|
| 77 |
-
/ Cl
|
| 78 |
-
\ NH1
|
| 79 |
-
\ Br
|
| 80 |
-
@ +1
|
| 81 |
-
/ I
|
| 82 |
-
/ C@
|
| 83 |
-
T e
|
| 84 |
-
\ N+1
|
| 85 |
-
P@ @
|
| 86 |
-
1 2
|
| 87 |
-
5 I
|
| 88 |
-
\ O-1
|
| 89 |
-
12 5I
|
| 90 |
-
/ F
|
| 91 |
-
# N+1
|
| 92 |
-
\ Cl
|
| 93 |
-
N@ +1
|
| 94 |
-
\ I
|
| 95 |
-
- /
|
| 96 |
-
/ C@@
|
| 97 |
-
N@ @
|
| 98 |
-
N@ @+1
|
| 99 |
-
-/ Ring2
|
| 100 |
-
- \
|
| 101 |
-
1 4
|
| 102 |
-
B -1
|
| 103 |
-
C -1
|
| 104 |
-
S @+1
|
| 105 |
-
14 C
|
| 106 |
-
H 2
|
| 107 |
-
H 4
|
| 108 |
-
I +1
|
| 109 |
-
S -1
|
| 110 |
-
\ P
|
| 111 |
-
=S +1
|
| 112 |
-
=P @
|
| 113 |
-
Si H4
|
| 114 |
-
+ 2
|
| 115 |
-
3 H
|
| 116 |
-
@ @+1
|
| 117 |
-
A g
|
| 118 |
-
C +1
|
| 119 |
-
S @@+1
|
| 120 |
-
Cl +1
|
| 121 |
-
=S e
|
| 122 |
-
-\ Ring1
|
| 123 |
-
H 0
|
| 124 |
-
O H0
|
| 125 |
-
1 1
|
| 126 |
-
= Branch3
|
| 127 |
-
= Te
|
| 128 |
-
M g
|
| 129 |
-
O +1
|
| 130 |
-
Z n
|
| 131 |
-
\ C@
|
| 132 |
-
\ S+1
|
| 133 |
-
H1 -1
|
| 134 |
-
Se H1
|
| 135 |
-
P@ +1
|
| 136 |
-
-\ Ring2
|
| 137 |
-
11 C
|
| 138 |
-
=Te +1
|
| 139 |
-
Zn +2
|
| 140 |
-
/ NH1
|
| 141 |
-
1 8
|
| 142 |
-
A s
|
| 143 |
-
B H2
|
| 144 |
-
B H1-1
|
| 145 |
-
C a
|
| 146 |
-
H 3
|
| 147 |
-
O H1-1
|
| 148 |
-
S H2
|
| 149 |
-
=O +1
|
| 150 |
-
Se +1
|
| 151 |
-
Te H2
|
| 152 |
-
125I H1
|
| 153 |
-
-/ Ring1
|
| 154 |
-
14C H2
|
| 155 |
-
Ag +1
|
| 156 |
-
=Se +1
|
| 157 |
-
Mg H2
|
| 158 |
-
Mg +2
|
| 159 |
-
11C H3
|
| 160 |
-
18 F
|
| 161 |
-
BH2 -1
|
| 162 |
-
Ca +2
|
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models/finetuned/freesolv/model.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:bc69910d6e2d4ebf7f440f7737b3c3360533076dea6d985b22f8882bc795237a
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| 3 |
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size 1022843005
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models/finetuned/freesolv/special_tokens_map.json
DELETED
|
@@ -1,51 +0,0 @@
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|
| 1 |
-
{
|
| 2 |
-
"bos_token": {
|
| 3 |
-
"content": "<s>",
|
| 4 |
-
"lstrip": false,
|
| 5 |
-
"normalized": true,
|
| 6 |
-
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|
| 7 |
-
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| 8 |
-
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| 9 |
-
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| 10 |
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| 11 |
-
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| 12 |
-
"normalized": true,
|
| 13 |
-
"rstrip": false,
|
| 14 |
-
"single_word": false
|
| 15 |
-
},
|
| 16 |
-
"eos_token": {
|
| 17 |
-
"content": "</s>",
|
| 18 |
-
"lstrip": false,
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| 19 |
-
"normalized": true,
|
| 20 |
-
"rstrip": false,
|
| 21 |
-
"single_word": false
|
| 22 |
-
},
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| 23 |
-
"mask_token": {
|
| 24 |
-
"content": "<mask>",
|
| 25 |
-
"lstrip": true,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"rstrip": false,
|
| 28 |
-
"single_word": false
|
| 29 |
-
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| 30 |
-
"pad_token": {
|
| 31 |
-
"content": "<pad>",
|
| 32 |
-
"lstrip": false,
|
| 33 |
-
"normalized": true,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"single_word": false
|
| 36 |
-
},
|
| 37 |
-
"sep_token": {
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| 38 |
-
"content": "</s>",
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| 39 |
-
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| 40 |
-
"normalized": true,
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| 41 |
-
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| 42 |
-
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| 43 |
-
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| 44 |
-
"unk_token": {
|
| 45 |
-
"content": "<unk>",
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| 46 |
-
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|
| 47 |
-
"normalized": true,
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| 48 |
-
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| 49 |
-
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| 50 |
-
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| 51 |
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|
models/finetuned/freesolv/tokenizer.json
DELETED
|
@@ -1,473 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"version": "1.0",
|
| 3 |
-
"truncation": {
|
| 4 |
-
"direction": "Right",
|
| 5 |
-
"max_length": 128,
|
| 6 |
-
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| 7 |
-
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| 8 |
-
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| 9 |
-
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| 10 |
-
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| 11 |
-
"Fixed": 128
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| 12 |
-
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| 13 |
-
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|
| 14 |
-
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| 15 |
-
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| 16 |
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| 17 |
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"pad_token": "<pad>"
|
| 18 |
-
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| 19 |
-
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| 20 |
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{
|
| 21 |
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| 22 |
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| 23 |
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| 24 |
-
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| 25 |
-
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| 26 |
-
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| 27 |
-
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|
| 28 |
-
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| 29 |
-
{
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| 30 |
-
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|
| 31 |
-
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| 32 |
-
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| 33 |
-
"lstrip": false,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
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|
| 36 |
-
"special": true
|
| 37 |
-
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|
| 38 |
-
{
|
| 39 |
-
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|
| 40 |
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| 41 |
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| 42 |
-
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| 43 |
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| 44 |
-
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|
| 45 |
-
"special": true
|
| 46 |
-
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| 47 |
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|
| 48 |
-
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|
| 49 |
-
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| 50 |
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| 51 |
-
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| 52 |
-
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| 53 |
-
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|
| 54 |
-
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|
| 55 |
-
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|
| 56 |
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|
| 57 |
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|
| 58 |
-
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|
| 59 |
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| 60 |
-
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| 61 |
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|
| 62 |
-
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| 63 |
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| 64 |
-
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| 65 |
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| 66 |
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| 67 |
-
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|
| 68 |
-
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|
| 69 |
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|
| 70 |
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"trim_offsets": true,
|
| 71 |
-
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|
| 72 |
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| 73 |
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"post_processor": {
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| 74 |
-
"type": "RobertaProcessing",
|
| 75 |
-
"sep": [
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| 76 |
-
"</s>",
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| 77 |
-
2
|
| 78 |
-
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|
| 79 |
-
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|
| 80 |
-
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|
| 81 |
-
1
|
| 82 |
-
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| 83 |
-
"trim_offsets": true,
|
| 84 |
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| 85 |
-
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| 86 |
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| 87 |
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|
| 88 |
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| 89 |
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|
| 90 |
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| 91 |
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| 92 |
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| 93 |
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| 94 |
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| 96 |
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| 97 |
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| 98 |
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|
| 99 |
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|
| 100 |
-
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| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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|
| 111 |
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|
| 112 |
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|
| 113 |
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|
| 114 |
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|
| 115 |
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|
| 116 |
-
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|
| 117 |
-
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|
| 118 |
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|
| 119 |
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|
| 120 |
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|
| 121 |
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|
| 122 |
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|
| 123 |
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|
| 124 |
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"H": 24,
|
| 125 |
-
"I": 25,
|
| 126 |
-
"K": 26,
|
| 127 |
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"L": 27,
|
| 128 |
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"M": 28,
|
| 129 |
-
"N": 29,
|
| 130 |
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"O": 30,
|
| 131 |
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|
| 132 |
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"R": 32,
|
| 133 |
-
"S": 33,
|
| 134 |
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"T": 34,
|
| 135 |
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"Z": 35,
|
| 136 |
-
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|
| 137 |
-
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|
| 138 |
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|
| 139 |
-
"e": 39,
|
| 140 |
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|
| 141 |
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|
| 142 |
-
"i": 42,
|
| 143 |
-
"l": 43,
|
| 144 |
-
"n": 44,
|
| 145 |
-
"r": 45,
|
| 146 |
-
"s": 46,
|
| 147 |
-
"Br": 47,
|
| 148 |
-
"an": 48,
|
| 149 |
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"ch": 49,
|
| 150 |
-
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|
| 151 |
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|
| 152 |
-
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|
| 153 |
-
"=C": 53,
|
| 154 |
-
"Ri": 54,
|
| 155 |
-
"ng": 55,
|
| 156 |
-
"Ring": 56,
|
| 157 |
-
"Ring1": 57,
|
| 158 |
-
"=Branch1": 58,
|
| 159 |
-
"Branch2": 59,
|
| 160 |
-
"=O": 60,
|
| 161 |
-
"Ring2": 61,
|
| 162 |
-
"H1": 62,
|
| 163 |
-
"C@": 63,
|
| 164 |
-
"=N": 64,
|
| 165 |
-
"#Branch1": 65,
|
| 166 |
-
"C@@": 66,
|
| 167 |
-
"=Branch2": 67,
|
| 168 |
-
"C@H1": 68,
|
| 169 |
-
"C@@H1": 69,
|
| 170 |
-
"#Branch2": 70,
|
| 171 |
-
"Cl": 71,
|
| 172 |
-
"#C": 72,
|
| 173 |
-
"/C": 73,
|
| 174 |
-
"NH1": 74,
|
| 175 |
-
"+1": 75,
|
| 176 |
-
"-1": 76,
|
| 177 |
-
"=Ring1": 77,
|
| 178 |
-
"O-1": 78,
|
| 179 |
-
"N+1": 79,
|
| 180 |
-
"\\C": 80,
|
| 181 |
-
"/N": 81,
|
| 182 |
-
"#N": 82,
|
| 183 |
-
"=Ring2": 83,
|
| 184 |
-
"=S": 84,
|
| 185 |
-
"=N+1": 85,
|
| 186 |
-
"Na": 86,
|
| 187 |
-
"Na+1": 87,
|
| 188 |
-
"\\N": 88,
|
| 189 |
-
"S+1": 89,
|
| 190 |
-
"/O": 90,
|
| 191 |
-
"\\S": 91,
|
| 192 |
-
"\\O": 92,
|
| 193 |
-
"Br-1": 93,
|
| 194 |
-
"I-1": 94,
|
| 195 |
-
"Cl-1": 95,
|
| 196 |
-
"/C@H1": 96,
|
| 197 |
-
"Branch3": 97,
|
| 198 |
-
"/C@@H1": 98,
|
| 199 |
-
"=P": 99,
|
| 200 |
-
"/S": 100,
|
| 201 |
-
"=N-1": 101,
|
| 202 |
-
"Si": 102,
|
| 203 |
-
"K+1": 103,
|
| 204 |
-
"N-1": 104,
|
| 205 |
-
"Se": 105,
|
| 206 |
-
"Li": 106,
|
| 207 |
-
"Li+1": 107,
|
| 208 |
-
"+3": 108,
|
| 209 |
-
"Cl+3": 109,
|
| 210 |
-
"\\C@H1": 110,
|
| 211 |
-
"Ring3": 111,
|
| 212 |
-
"\\C@@H1": 112,
|
| 213 |
-
"/N+1": 113,
|
| 214 |
-
"/P": 114,
|
| 215 |
-
"\\F": 115,
|
| 216 |
-
"P@": 116,
|
| 217 |
-
"2H": 117,
|
| 218 |
-
"PH1": 118,
|
| 219 |
-
"/Br": 119,
|
| 220 |
-
"N@": 120,
|
| 221 |
-
"P+1": 121,
|
| 222 |
-
"/Cl": 122,
|
| 223 |
-
"\\NH1": 123,
|
| 224 |
-
"\\Br": 124,
|
| 225 |
-
"@+1": 125,
|
| 226 |
-
"/I": 126,
|
| 227 |
-
"/C@": 127,
|
| 228 |
-
"Te": 128,
|
| 229 |
-
"\\N+1": 129,
|
| 230 |
-
"P@@": 130,
|
| 231 |
-
"12": 131,
|
| 232 |
-
"5I": 132,
|
| 233 |
-
"\\O-1": 133,
|
| 234 |
-
"125I": 134,
|
| 235 |
-
"/F": 135,
|
| 236 |
-
"#N+1": 136,
|
| 237 |
-
"\\Cl": 137,
|
| 238 |
-
"N@+1": 138,
|
| 239 |
-
"\\I": 139,
|
| 240 |
-
"-/": 140,
|
| 241 |
-
"/C@@": 141,
|
| 242 |
-
"N@@": 142,
|
| 243 |
-
"N@@+1": 143,
|
| 244 |
-
"-/Ring2": 144,
|
| 245 |
-
"-\\": 145,
|
| 246 |
-
"14": 146,
|
| 247 |
-
"B-1": 147,
|
| 248 |
-
"C-1": 148,
|
| 249 |
-
"S@+1": 149,
|
| 250 |
-
"14C": 150,
|
| 251 |
-
"H2": 151,
|
| 252 |
-
"H4": 152,
|
| 253 |
-
"I+1": 153,
|
| 254 |
-
"S-1": 154,
|
| 255 |
-
"\\P": 155,
|
| 256 |
-
"=S+1": 156,
|
| 257 |
-
"=P@": 157,
|
| 258 |
-
"SiH4": 158,
|
| 259 |
-
"+2": 159,
|
| 260 |
-
"3H": 160,
|
| 261 |
-
"@@+1": 161,
|
| 262 |
-
"Ag": 162,
|
| 263 |
-
"C+1": 163,
|
| 264 |
-
"S@@+1": 164,
|
| 265 |
-
"Cl+1": 165,
|
| 266 |
-
"=Se": 166,
|
| 267 |
-
"-\\Ring1": 167,
|
| 268 |
-
"H0": 168,
|
| 269 |
-
"OH0": 169,
|
| 270 |
-
"11": 170,
|
| 271 |
-
"=Branch3": 171,
|
| 272 |
-
"=Te": 172,
|
| 273 |
-
"Mg": 173,
|
| 274 |
-
"O+1": 174,
|
| 275 |
-
"Zn": 175,
|
| 276 |
-
"\\C@": 176,
|
| 277 |
-
"\\S+1": 177,
|
| 278 |
-
"H1-1": 178,
|
| 279 |
-
"SeH1": 179,
|
| 280 |
-
"P@+1": 180,
|
| 281 |
-
"-\\Ring2": 181,
|
| 282 |
-
"11C": 182,
|
| 283 |
-
"=Te+1": 183,
|
| 284 |
-
"Zn+2": 184,
|
| 285 |
-
"/NH1": 185,
|
| 286 |
-
"18": 186,
|
| 287 |
-
"As": 187,
|
| 288 |
-
"BH2": 188,
|
| 289 |
-
"BH1-1": 189,
|
| 290 |
-
"Ca": 190,
|
| 291 |
-
"H3": 191,
|
| 292 |
-
"OH1-1": 192,
|
| 293 |
-
"SH2": 193,
|
| 294 |
-
"=O+1": 194,
|
| 295 |
-
"Se+1": 195,
|
| 296 |
-
"TeH2": 196,
|
| 297 |
-
"125IH1": 197,
|
| 298 |
-
"-/Ring1": 198,
|
| 299 |
-
"14CH2": 199,
|
| 300 |
-
"Ag+1": 200,
|
| 301 |
-
"=Se+1": 201,
|
| 302 |
-
"MgH2": 202,
|
| 303 |
-
"Mg+2": 203,
|
| 304 |
-
"11CH3": 204,
|
| 305 |
-
"18F": 205,
|
| 306 |
-
"BH2-1": 206,
|
| 307 |
-
"Ca+2": 207
|
| 308 |
-
},
|
| 309 |
-
"merges": [
|
| 310 |
-
"B r",
|
| 311 |
-
"a n",
|
| 312 |
-
"c h",
|
| 313 |
-
"Br an",
|
| 314 |
-
"Bran ch",
|
| 315 |
-
"Branch 1",
|
| 316 |
-
"= C",
|
| 317 |
-
"R i",
|
| 318 |
-
"n g",
|
| 319 |
-
"Ri ng",
|
| 320 |
-
"Ring 1",
|
| 321 |
-
"= Branch1",
|
| 322 |
-
"Branch 2",
|
| 323 |
-
"= O",
|
| 324 |
-
"Ring 2",
|
| 325 |
-
"H 1",
|
| 326 |
-
"C @",
|
| 327 |
-
"= N",
|
| 328 |
-
"# Branch1",
|
| 329 |
-
"C@ @",
|
| 330 |
-
"= Branch2",
|
| 331 |
-
"C@ H1",
|
| 332 |
-
"C@@ H1",
|
| 333 |
-
"# Branch2",
|
| 334 |
-
"C l",
|
| 335 |
-
"# C",
|
| 336 |
-
"/ C",
|
| 337 |
-
"N H1",
|
| 338 |
-
"+ 1",
|
| 339 |
-
"- 1",
|
| 340 |
-
"= Ring1",
|
| 341 |
-
"O -1",
|
| 342 |
-
"N +1",
|
| 343 |
-
"\\ C",
|
| 344 |
-
"/ N",
|
| 345 |
-
"# N",
|
| 346 |
-
"= Ring2",
|
| 347 |
-
"= S",
|
| 348 |
-
"=N +1",
|
| 349 |
-
"N a",
|
| 350 |
-
"Na +1",
|
| 351 |
-
"\\ N",
|
| 352 |
-
"S +1",
|
| 353 |
-
"/ O",
|
| 354 |
-
"\\ S",
|
| 355 |
-
"\\ O",
|
| 356 |
-
"Br -1",
|
| 357 |
-
"I -1",
|
| 358 |
-
"Cl -1",
|
| 359 |
-
"/ C@H1",
|
| 360 |
-
"Branch 3",
|
| 361 |
-
"/ C@@H1",
|
| 362 |
-
"= P",
|
| 363 |
-
"/ S",
|
| 364 |
-
"=N -1",
|
| 365 |
-
"S i",
|
| 366 |
-
"K +1",
|
| 367 |
-
"N -1",
|
| 368 |
-
"S e",
|
| 369 |
-
"L i",
|
| 370 |
-
"Li +1",
|
| 371 |
-
"+ 3",
|
| 372 |
-
"Cl +3",
|
| 373 |
-
"\\ C@H1",
|
| 374 |
-
"Ring 3",
|
| 375 |
-
"\\ C@@H1",
|
| 376 |
-
"/ N+1",
|
| 377 |
-
"/ P",
|
| 378 |
-
"\\ F",
|
| 379 |
-
"P @",
|
| 380 |
-
"2 H",
|
| 381 |
-
"P H1",
|
| 382 |
-
"/ Br",
|
| 383 |
-
"N @",
|
| 384 |
-
"P +1",
|
| 385 |
-
"/ Cl",
|
| 386 |
-
"\\ NH1",
|
| 387 |
-
"\\ Br",
|
| 388 |
-
"@ +1",
|
| 389 |
-
"/ I",
|
| 390 |
-
"/ C@",
|
| 391 |
-
"T e",
|
| 392 |
-
"\\ N+1",
|
| 393 |
-
"P@ @",
|
| 394 |
-
"1 2",
|
| 395 |
-
"5 I",
|
| 396 |
-
"\\ O-1",
|
| 397 |
-
"12 5I",
|
| 398 |
-
"/ F",
|
| 399 |
-
"# N+1",
|
| 400 |
-
"\\ Cl",
|
| 401 |
-
"N@ +1",
|
| 402 |
-
"\\ I",
|
| 403 |
-
"- /",
|
| 404 |
-
"/ C@@",
|
| 405 |
-
"N@ @",
|
| 406 |
-
"N@ @+1",
|
| 407 |
-
"-/ Ring2",
|
| 408 |
-
"- \\",
|
| 409 |
-
"1 4",
|
| 410 |
-
"B -1",
|
| 411 |
-
"C -1",
|
| 412 |
-
"S @+1",
|
| 413 |
-
"14 C",
|
| 414 |
-
"H 2",
|
| 415 |
-
"H 4",
|
| 416 |
-
"I +1",
|
| 417 |
-
"S -1",
|
| 418 |
-
"\\ P",
|
| 419 |
-
"=S +1",
|
| 420 |
-
"=P @",
|
| 421 |
-
"Si H4",
|
| 422 |
-
"+ 2",
|
| 423 |
-
"3 H",
|
| 424 |
-
"@ @+1",
|
| 425 |
-
"A g",
|
| 426 |
-
"C +1",
|
| 427 |
-
"S @@+1",
|
| 428 |
-
"Cl +1",
|
| 429 |
-
"=S e",
|
| 430 |
-
"-\\ Ring1",
|
| 431 |
-
"H 0",
|
| 432 |
-
"O H0",
|
| 433 |
-
"1 1",
|
| 434 |
-
"= Branch3",
|
| 435 |
-
"= Te",
|
| 436 |
-
"M g",
|
| 437 |
-
"O +1",
|
| 438 |
-
"Z n",
|
| 439 |
-
"\\ C@",
|
| 440 |
-
"\\ S+1",
|
| 441 |
-
"H1 -1",
|
| 442 |
-
"Se H1",
|
| 443 |
-
"P@ +1",
|
| 444 |
-
"-\\ Ring2",
|
| 445 |
-
"11 C",
|
| 446 |
-
"=Te +1",
|
| 447 |
-
"Zn +2",
|
| 448 |
-
"/ NH1",
|
| 449 |
-
"1 8",
|
| 450 |
-
"A s",
|
| 451 |
-
"B H2",
|
| 452 |
-
"B H1-1",
|
| 453 |
-
"C a",
|
| 454 |
-
"H 3",
|
| 455 |
-
"O H1-1",
|
| 456 |
-
"S H2",
|
| 457 |
-
"=O +1",
|
| 458 |
-
"Se +1",
|
| 459 |
-
"Te H2",
|
| 460 |
-
"125I H1",
|
| 461 |
-
"-/ Ring1",
|
| 462 |
-
"14C H2",
|
| 463 |
-
"Ag +1",
|
| 464 |
-
"=Se +1",
|
| 465 |
-
"Mg H2",
|
| 466 |
-
"Mg +2",
|
| 467 |
-
"11C H3",
|
| 468 |
-
"18 F",
|
| 469 |
-
"BH2 -1",
|
| 470 |
-
"Ca +2"
|
| 471 |
-
]
|
| 472 |
-
}
|
| 473 |
-
}
|
|
|
|
|
|
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models/finetuned/freesolv/tokenizer_config.json
DELETED
|
@@ -1,59 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"add_prefix_space": false,
|
| 3 |
-
"added_tokens_decoder": {
|
| 4 |
-
"0": {
|
| 5 |
-
"content": "<unk>",
|
| 6 |
-
"lstrip": false,
|
| 7 |
-
"normalized": true,
|
| 8 |
-
"rstrip": false,
|
| 9 |
-
"single_word": false,
|
| 10 |
-
"special": true
|
| 11 |
-
},
|
| 12 |
-
"1": {
|
| 13 |
-
"content": "<s>",
|
| 14 |
-
"lstrip": false,
|
| 15 |
-
"normalized": true,
|
| 16 |
-
"rstrip": false,
|
| 17 |
-
"single_word": false,
|
| 18 |
-
"special": true
|
| 19 |
-
},
|
| 20 |
-
"2": {
|
| 21 |
-
"content": "</s>",
|
| 22 |
-
"lstrip": false,
|
| 23 |
-
"normalized": true,
|
| 24 |
-
"rstrip": false,
|
| 25 |
-
"single_word": false,
|
| 26 |
-
"special": true
|
| 27 |
-
},
|
| 28 |
-
"3": {
|
| 29 |
-
"content": "<pad>",
|
| 30 |
-
"lstrip": false,
|
| 31 |
-
"normalized": true,
|
| 32 |
-
"rstrip": false,
|
| 33 |
-
"single_word": false,
|
| 34 |
-
"special": true
|
| 35 |
-
},
|
| 36 |
-
"4": {
|
| 37 |
-
"content": "<mask>",
|
| 38 |
-
"lstrip": true,
|
| 39 |
-
"normalized": true,
|
| 40 |
-
"rstrip": false,
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"special": true
|
| 43 |
-
}
|
| 44 |
-
},
|
| 45 |
-
"bos_token": "<s>",
|
| 46 |
-
"clean_up_tokenization_spaces": true,
|
| 47 |
-
"cls_token": "<s>",
|
| 48 |
-
"eos_token": "</s>",
|
| 49 |
-
"errors": "replace",
|
| 50 |
-
"mask_token": "<mask>",
|
| 51 |
-
"model_max_length": 1000000000000000019884624838656,
|
| 52 |
-
"name_or_path": "data/epoch_267/hf",
|
| 53 |
-
"pad_token": "<pad>",
|
| 54 |
-
"sep_token": "</s>",
|
| 55 |
-
"special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
|
| 56 |
-
"tokenizer_class": "RobertaTokenizer",
|
| 57 |
-
"trim_offsets": true,
|
| 58 |
-
"unk_token": "<unk>"
|
| 59 |
-
}
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models/finetuned/freesolv/vocab.json
DELETED
|
@@ -1 +0,0 @@
|
|
| 1 |
-
{"<unk>":0,"<s>":1,"</s>":2,"<pad>":3,"<mask>":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
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|
models/finetuned/hiv/config.json
DELETED
|
@@ -1,27 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"RobertaForMaskedLM"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"bos_token_id": 0,
|
| 8 |
-
"classifier_dropout": null,
|
| 9 |
-
"eos_token_id": 2,
|
| 10 |
-
"hidden_act": "gelu",
|
| 11 |
-
"hidden_dropout_prob": 0.1,
|
| 12 |
-
"hidden_size": 768,
|
| 13 |
-
"initializer_range": 0.02,
|
| 14 |
-
"intermediate_size": 3072,
|
| 15 |
-
"layer_norm_eps": 1e-12,
|
| 16 |
-
"max_position_embeddings": 514,
|
| 17 |
-
"model_type": "roberta",
|
| 18 |
-
"num_attention_heads": 4,
|
| 19 |
-
"num_hidden_layers": 12,
|
| 20 |
-
"pad_token_id": 1,
|
| 21 |
-
"position_embedding_type": "absolute",
|
| 22 |
-
"torch_dtype": "float32",
|
| 23 |
-
"transformers_version": "4.26.1",
|
| 24 |
-
"type_vocab_size": 1,
|
| 25 |
-
"use_cache": true,
|
| 26 |
-
"vocab_size": 800
|
| 27 |
-
}
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models/finetuned/hiv/finetuning_optimized_config.json
DELETED
|
@@ -1,24 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"dataset_meta_csv": "data/finetuning_datasets/classification/hiv/hiv.csv",
|
| 3 |
-
"dataset_embs_npz": "data/finetuning_datasets/classification/hiv/hiv_embs.npz",
|
| 4 |
-
"use_scaffold": 1,
|
| 5 |
-
"seed": 42,
|
| 6 |
-
"train_frac": 0.8,
|
| 7 |
-
"val_frac": 0.1,
|
| 8 |
-
"test_frac": 0.1,
|
| 9 |
-
"model_path": "HUBioDataLab/SELFormer",
|
| 10 |
-
"tokenizer_path": "HUBioDataLab/SELFormer",
|
| 11 |
-
"pretrained_multimodal_dir": "data/models/SELFormerMM",
|
| 12 |
-
"task_type": "binary",
|
| 13 |
-
"label_column": "HIV_active",
|
| 14 |
-
"num_labels": 2,
|
| 15 |
-
"batch_size": 16,
|
| 16 |
-
"max_len": 128,
|
| 17 |
-
"epochs": 50,
|
| 18 |
-
"backbone_lr": 5e-5,
|
| 19 |
-
"head_lr": 5e-5,
|
| 20 |
-
"weight_decay": 0.0,
|
| 21 |
-
"checkpoint_every": 25,
|
| 22 |
-
"test_eval_every": 0,
|
| 23 |
-
"save_dir": "data/models/finetuned/hiv"
|
| 24 |
-
}
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|
models/finetuned/hiv/merges.txt
DELETED
|
@@ -1,378 +0,0 @@
|
|
| 1 |
-
#version: 0.2 - Trained by `huggingface/tokenizers`
|
| 2 |
-
B r
|
| 3 |
-
a n
|
| 4 |
-
c h
|
| 5 |
-
Br an
|
| 6 |
-
Bran ch
|
| 7 |
-
Branch 1
|
| 8 |
-
= C
|
| 9 |
-
R i
|
| 10 |
-
n g
|
| 11 |
-
Ri ng
|
| 12 |
-
Ring 1
|
| 13 |
-
= Branch1
|
| 14 |
-
Branch 2
|
| 15 |
-
= O
|
| 16 |
-
Ring 2
|
| 17 |
-
H 1
|
| 18 |
-
C @
|
| 19 |
-
= N
|
| 20 |
-
# Branch1
|
| 21 |
-
C@ @
|
| 22 |
-
= Branch2
|
| 23 |
-
C@ H1
|
| 24 |
-
C@@ H1
|
| 25 |
-
# Branch2
|
| 26 |
-
# C
|
| 27 |
-
C l
|
| 28 |
-
/ C
|
| 29 |
-
N H1
|
| 30 |
-
= Ring1
|
| 31 |
-
+ 1
|
| 32 |
-
- 1
|
| 33 |
-
O -1
|
| 34 |
-
N +1
|
| 35 |
-
\ C
|
| 36 |
-
# N
|
| 37 |
-
/ N
|
| 38 |
-
= Ring2
|
| 39 |
-
= S
|
| 40 |
-
=N +1
|
| 41 |
-
\ N
|
| 42 |
-
N a
|
| 43 |
-
Na +1
|
| 44 |
-
/ O
|
| 45 |
-
\ O
|
| 46 |
-
Br -1
|
| 47 |
-
Branch 3
|
| 48 |
-
\ S
|
| 49 |
-
S +1
|
| 50 |
-
Cl -1
|
| 51 |
-
I -1
|
| 52 |
-
/ C@@H1
|
| 53 |
-
S i
|
| 54 |
-
/ C@H1
|
| 55 |
-
/ S
|
| 56 |
-
=N -1
|
| 57 |
-
S e
|
| 58 |
-
= P
|
| 59 |
-
N -1
|
| 60 |
-
Ring 3
|
| 61 |
-
2 H
|
| 62 |
-
P +1
|
| 63 |
-
K +1
|
| 64 |
-
\ C@@H1
|
| 65 |
-
\ C@H1
|
| 66 |
-
/ N+1
|
| 67 |
-
@ @
|
| 68 |
-
C -1
|
| 69 |
-
# N+1
|
| 70 |
-
B -1
|
| 71 |
-
+ 3
|
| 72 |
-
Cl +3
|
| 73 |
-
\ NH1
|
| 74 |
-
L i
|
| 75 |
-
Li +1
|
| 76 |
-
P H1
|
| 77 |
-
1 8
|
| 78 |
-
18 F
|
| 79 |
-
@ +1
|
| 80 |
-
3 H
|
| 81 |
-
P @@
|
| 82 |
-
H 0
|
| 83 |
-
O H0
|
| 84 |
-
1 2
|
| 85 |
-
P @
|
| 86 |
-
+ 2
|
| 87 |
-
@@ +1
|
| 88 |
-
S -1
|
| 89 |
-
/ Br
|
| 90 |
-
- /
|
| 91 |
-
\ Cl
|
| 92 |
-
-/ Ring2
|
| 93 |
-
\ O-1
|
| 94 |
-
1 1
|
| 95 |
-
5 I
|
| 96 |
-
12 5I
|
| 97 |
-
11 C
|
| 98 |
-
H 3
|
| 99 |
-
\ N+1
|
| 100 |
-
- \
|
| 101 |
-
/ C@@
|
| 102 |
-
S @+1
|
| 103 |
-
A s
|
| 104 |
-
/ Cl
|
| 105 |
-
11C H3
|
| 106 |
-
=S e
|
| 107 |
-
S @@+1
|
| 108 |
-
N @+1
|
| 109 |
-
1 4
|
| 110 |
-
-\ Ring2
|
| 111 |
-
14 C
|
| 112 |
-
\ F
|
| 113 |
-
/ C@
|
| 114 |
-
T e
|
| 115 |
-
H 2
|
| 116 |
-
H1 -1
|
| 117 |
-
=O +1
|
| 118 |
-
N @@+1
|
| 119 |
-
C +1
|
| 120 |
-
=S +1
|
| 121 |
-
Z n
|
| 122 |
-
/ P
|
| 123 |
-
a +2
|
| 124 |
-
/ I
|
| 125 |
-
O H1-1
|
| 126 |
-
C a+2
|
| 127 |
-
\ Br
|
| 128 |
-
M g
|
| 129 |
-
Zn +2
|
| 130 |
-
A l
|
| 131 |
-
/ F
|
| 132 |
-
Mg +2
|
| 133 |
-
12 3
|
| 134 |
-
123 I
|
| 135 |
-
1 3
|
| 136 |
-
I +1
|
| 137 |
-
/ O-1
|
| 138 |
-
-\ Ring1
|
| 139 |
-
B H2
|
| 140 |
-
BH2 -1
|
| 141 |
-
\ I
|
| 142 |
-
/ NH1
|
| 143 |
-
O +1
|
| 144 |
-
13 1
|
| 145 |
-
131 I
|
| 146 |
-
= 14C
|
| 147 |
-
/ S+1
|
| 148 |
-
= Ring3
|
| 149 |
-
\ C@@
|
| 150 |
-
H2 +1
|
| 151 |
-
\ C@
|
| 152 |
-
A g
|
| 153 |
-
= As
|
| 154 |
-
=Se +1
|
| 155 |
-
N H2+1
|
| 156 |
-
Se H1
|
| 157 |
-
-/ Ring1
|
| 158 |
-
= Te
|
| 159 |
-
Al +3
|
| 160 |
-
Na H1
|
| 161 |
-
=Te +1
|
| 162 |
-
NH1 +1
|
| 163 |
-
Ag +1
|
| 164 |
-
H1 +1
|
| 165 |
-
NH1 -1
|
| 166 |
-
\ P
|
| 167 |
-
14C H2
|
| 168 |
-
13 C
|
| 169 |
-
14C H1
|
| 170 |
-
= 11C
|
| 171 |
-
S @@
|
| 172 |
-
=P @@
|
| 173 |
-
Si H2
|
| 174 |
-
H3 -1
|
| 175 |
-
14C H3
|
| 176 |
-
B H3-1
|
| 177 |
-
S @
|
| 178 |
-
=14C H1
|
| 179 |
-
=P H1
|
| 180 |
-
=P @
|
| 181 |
-
=N H1+1
|
| 182 |
-
\S +1
|
| 183 |
-
12 4
|
| 184 |
-
C H1-1
|
| 185 |
-
S r
|
| 186 |
-
=S i
|
| 187 |
-
124 I
|
| 188 |
-
Sr +2
|
| 189 |
-
#C -1
|
| 190 |
-
/C -1
|
| 191 |
-
N @
|
| 192 |
-
/N -1
|
| 193 |
-
13C H1
|
| 194 |
-
/ B
|
| 195 |
-
1 9
|
| 196 |
-
B a+2
|
| 197 |
-
H 4
|
| 198 |
-
S H1+1
|
| 199 |
-
Se +1
|
| 200 |
-
19 F
|
| 201 |
-
/ 125I
|
| 202 |
-
P @+1
|
| 203 |
-
R b
|
| 204 |
-
Cl +1
|
| 205 |
-
Si H4
|
| 206 |
-
Rb +1
|
| 207 |
-
= Branch3
|
| 208 |
-
N @@
|
| 209 |
-
As +1
|
| 210 |
-
/ Si
|
| 211 |
-
B H1-1
|
| 212 |
-
S H1
|
| 213 |
-
/ 123I
|
| 214 |
-
3 2
|
| 215 |
-
= Mg
|
| 216 |
-
H +1
|
| 217 |
-
\ B
|
| 218 |
-
Si H1
|
| 219 |
-
P@@ +1
|
| 220 |
-
- 2
|
| 221 |
-
1 5
|
| 222 |
-
1 7
|
| 223 |
-
3 5
|
| 224 |
-
= 13CH1
|
| 225 |
-
C s
|
| 226 |
-
=N H2+1
|
| 227 |
-
=S H1
|
| 228 |
-
Mg H2
|
| 229 |
-
32 P
|
| 230 |
-
17 F
|
| 231 |
-
35 S
|
| 232 |
-
Cs +1
|
| 233 |
-
# 11C
|
| 234 |
-
/ 131I
|
| 235 |
-
B i
|
| 236 |
-
\ 125I
|
| 237 |
-
=S @@
|
| 238 |
-
\S -1
|
| 239 |
-
6 Br
|
| 240 |
-
7 I
|
| 241 |
-
7 6Br
|
| 242 |
-
= B
|
| 243 |
-
e H1
|
| 244 |
-
\N -1
|
| 245 |
-
18 O
|
| 246 |
-
12 7I
|
| 247 |
-
11C H2
|
| 248 |
-
14 C@@H1
|
| 249 |
-
Te H2
|
| 250 |
-
15 NH1
|
| 251 |
-
Bi +3
|
| 252 |
-
/ P+1
|
| 253 |
-
/ 13C
|
| 254 |
-
/ 13CH1
|
| 255 |
-
0 B
|
| 256 |
-
1 0B
|
| 257 |
-
= Al
|
| 258 |
-
= 18O
|
| 259 |
-
B H0
|
| 260 |
-
F -1
|
| 261 |
-
N H3
|
| 262 |
-
S -2
|
| 263 |
-
Br +2
|
| 264 |
-
Cl +2
|
| 265 |
-
\S i
|
| 266 |
-
/S -1
|
| 267 |
-
=P H2
|
| 268 |
-
14 C@H1
|
| 269 |
-
NH3 +1
|
| 270 |
-
# 14C
|
| 271 |
-
# O+1
|
| 272 |
-
- 3
|
| 273 |
-
2 2
|
| 274 |
-
4 H
|
| 275 |
-
5 Se
|
| 276 |
-
5 Sr+2
|
| 277 |
-
7 5Se
|
| 278 |
-
8 5Sr+2
|
| 279 |
-
= B-1
|
| 280 |
-
= 13C
|
| 281 |
-
@ -1
|
| 282 |
-
B e
|
| 283 |
-
B @@
|
| 284 |
-
B @-1
|
| 285 |
-
C a
|
| 286 |
-
C H1
|
| 287 |
-
I +3
|
| 288 |
-
K H1
|
| 289 |
-
O H1+1
|
| 290 |
-
R a+2
|
| 291 |
-
S H1-1
|
| 292 |
-
\ PH1
|
| 293 |
-
\ 123I
|
| 294 |
-
=C a
|
| 295 |
-
\C H1-1
|
| 296 |
-
=S @
|
| 297 |
-
\S eH1
|
| 298 |
-
/S eH1
|
| 299 |
-
Se -1
|
| 300 |
-
Li H1
|
| 301 |
-
18F -1
|
| 302 |
-
125I H1
|
| 303 |
-
11C H1
|
| 304 |
-
Te H1
|
| 305 |
-
Zn +1
|
| 306 |
-
Zn -2
|
| 307 |
-
Al -3
|
| 308 |
-
13C H3
|
| 309 |
-
15 N
|
| 310 |
-
Be +2
|
| 311 |
-
B@@ -1
|
| 312 |
-
# P
|
| 313 |
-
# S
|
| 314 |
-
- 4
|
| 315 |
-
/ PH1
|
| 316 |
-
/ P@@
|
| 317 |
-
/ As
|
| 318 |
-
/ 14C
|
| 319 |
-
/ 14CH1
|
| 320 |
-
2 K+1
|
| 321 |
-
2 Rb+1
|
| 322 |
-
3 Se
|
| 323 |
-
3 Ra+2
|
| 324 |
-
4 5
|
| 325 |
-
4 7
|
| 326 |
-
4 2K+1
|
| 327 |
-
5 I-1
|
| 328 |
-
7 3Se
|
| 329 |
-
8 9
|
| 330 |
-
8 2Rb+1
|
| 331 |
-
= 32
|
| 332 |
-
= 32P
|
| 333 |
-
C H0
|
| 334 |
-
C H2
|
| 335 |
-
I +2
|
| 336 |
-
N H0
|
| 337 |
-
N H4
|
| 338 |
-
O H1
|
| 339 |
-
P H2+1
|
| 340 |
-
S H0
|
| 341 |
-
S H2
|
| 342 |
-
\ 3H
|
| 343 |
-
\ 11CH3
|
| 344 |
-
\C -1
|
| 345 |
-
\S e
|
| 346 |
-
Si @
|
| 347 |
-
Si -1
|
| 348 |
-
Si H1-1
|
| 349 |
-
Si H3-1
|
| 350 |
-
/S e
|
| 351 |
-
Se -2
|
| 352 |
-
\NH1 -1
|
| 353 |
-
18F H1
|
| 354 |
-
12 5I-1
|
| 355 |
-
11 C@@H1
|
| 356 |
-
11 C-1
|
| 357 |
-
As H1
|
| 358 |
-
As -1
|
| 359 |
-
14 C@@
|
| 360 |
-
Te -1
|
| 361 |
-
Mg +1
|
| 362 |
-
123 I-1
|
| 363 |
-
123 Te
|
| 364 |
-
123I H1
|
| 365 |
-
13 5I
|
| 366 |
-
131 I-1
|
| 367 |
-
Ag -4
|
| 368 |
-
124 I-1
|
| 369 |
-
76Br H1
|
| 370 |
-
18O H1
|
| 371 |
-
22 Na+1
|
| 372 |
-
22 3Ra+2
|
| 373 |
-
Ca H2
|
| 374 |
-
45 Ca+2
|
| 375 |
-
47 Ca+2
|
| 376 |
-
89 Sr+2
|
| 377 |
-
=32 PH1
|
| 378 |
-
NH4 +1
|
|
|
|
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|
models/finetuned/hiv/model.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:e256d9c1f34dc1d3521586b383cb58b01238a2d5229e4383cb7a0cae792fb7a8
|
| 3 |
-
size 1022855293
|
|
|
|
|
|
|
|
|
|
|
|
models/finetuned/hiv/special_tokens_map.json
DELETED
|
@@ -1,51 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"bos_token": {
|
| 3 |
-
"content": "<s>",
|
| 4 |
-
"lstrip": false,
|
| 5 |
-
"normalized": true,
|
| 6 |
-
"rstrip": false,
|
| 7 |
-
"single_word": false
|
| 8 |
-
},
|
| 9 |
-
"cls_token": {
|
| 10 |
-
"content": "<s>",
|
| 11 |
-
"lstrip": false,
|
| 12 |
-
"normalized": true,
|
| 13 |
-
"rstrip": false,
|
| 14 |
-
"single_word": false
|
| 15 |
-
},
|
| 16 |
-
"eos_token": {
|
| 17 |
-
"content": "</s>",
|
| 18 |
-
"lstrip": false,
|
| 19 |
-
"normalized": true,
|
| 20 |
-
"rstrip": false,
|
| 21 |
-
"single_word": false
|
| 22 |
-
},
|
| 23 |
-
"mask_token": {
|
| 24 |
-
"content": "<mask>",
|
| 25 |
-
"lstrip": true,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"rstrip": false,
|
| 28 |
-
"single_word": false
|
| 29 |
-
},
|
| 30 |
-
"pad_token": {
|
| 31 |
-
"content": "<pad>",
|
| 32 |
-
"lstrip": false,
|
| 33 |
-
"normalized": true,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"single_word": false
|
| 36 |
-
},
|
| 37 |
-
"sep_token": {
|
| 38 |
-
"content": "</s>",
|
| 39 |
-
"lstrip": false,
|
| 40 |
-
"normalized": true,
|
| 41 |
-
"rstrip": false,
|
| 42 |
-
"single_word": false
|
| 43 |
-
},
|
| 44 |
-
"unk_token": {
|
| 45 |
-
"content": "<unk>",
|
| 46 |
-
"lstrip": false,
|
| 47 |
-
"normalized": true,
|
| 48 |
-
"rstrip": false,
|
| 49 |
-
"single_word": false
|
| 50 |
-
}
|
| 51 |
-
}
|
|
|
|
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|
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|
models/finetuned/hiv/tokenizer.json
DELETED
|
@@ -1,909 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"version": "1.0",
|
| 3 |
-
"truncation": {
|
| 4 |
-
"direction": "Right",
|
| 5 |
-
"max_length": 128,
|
| 6 |
-
"strategy": "LongestFirst",
|
| 7 |
-
"stride": 0
|
| 8 |
-
},
|
| 9 |
-
"padding": {
|
| 10 |
-
"strategy": {
|
| 11 |
-
"Fixed": 128
|
| 12 |
-
},
|
| 13 |
-
"direction": "Right",
|
| 14 |
-
"pad_to_multiple_of": null,
|
| 15 |
-
"pad_id": 3,
|
| 16 |
-
"pad_type_id": 0,
|
| 17 |
-
"pad_token": "<pad>"
|
| 18 |
-
},
|
| 19 |
-
"added_tokens": [
|
| 20 |
-
{
|
| 21 |
-
"id": 0,
|
| 22 |
-
"content": "<unk>",
|
| 23 |
-
"single_word": false,
|
| 24 |
-
"lstrip": false,
|
| 25 |
-
"rstrip": false,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"special": true
|
| 28 |
-
},
|
| 29 |
-
{
|
| 30 |
-
"id": 1,
|
| 31 |
-
"content": "<s>",
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"lstrip": false,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"normalized": true,
|
| 36 |
-
"special": true
|
| 37 |
-
},
|
| 38 |
-
{
|
| 39 |
-
"id": 2,
|
| 40 |
-
"content": "</s>",
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"lstrip": false,
|
| 43 |
-
"rstrip": false,
|
| 44 |
-
"normalized": true,
|
| 45 |
-
"special": true
|
| 46 |
-
},
|
| 47 |
-
{
|
| 48 |
-
"id": 3,
|
| 49 |
-
"content": "<pad>",
|
| 50 |
-
"single_word": false,
|
| 51 |
-
"lstrip": false,
|
| 52 |
-
"rstrip": false,
|
| 53 |
-
"normalized": true,
|
| 54 |
-
"special": true
|
| 55 |
-
},
|
| 56 |
-
{
|
| 57 |
-
"id": 4,
|
| 58 |
-
"content": "<mask>",
|
| 59 |
-
"single_word": false,
|
| 60 |
-
"lstrip": true,
|
| 61 |
-
"rstrip": false,
|
| 62 |
-
"normalized": true,
|
| 63 |
-
"special": true
|
| 64 |
-
}
|
| 65 |
-
],
|
| 66 |
-
"normalizer": null,
|
| 67 |
-
"pre_tokenizer": {
|
| 68 |
-
"type": "ByteLevel",
|
| 69 |
-
"add_prefix_space": false,
|
| 70 |
-
"trim_offsets": true,
|
| 71 |
-
"use_regex": true
|
| 72 |
-
},
|
| 73 |
-
"post_processor": {
|
| 74 |
-
"type": "RobertaProcessing",
|
| 75 |
-
"sep": [
|
| 76 |
-
"</s>",
|
| 77 |
-
2
|
| 78 |
-
],
|
| 79 |
-
"cls": [
|
| 80 |
-
"<s>",
|
| 81 |
-
1
|
| 82 |
-
],
|
| 83 |
-
"trim_offsets": true,
|
| 84 |
-
"add_prefix_space": false
|
| 85 |
-
},
|
| 86 |
-
"decoder": {
|
| 87 |
-
"type": "ByteLevel",
|
| 88 |
-
"add_prefix_space": true,
|
| 89 |
-
"trim_offsets": true,
|
| 90 |
-
"use_regex": true
|
| 91 |
-
},
|
| 92 |
-
"model": {
|
| 93 |
-
"type": "BPE",
|
| 94 |
-
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|
| 95 |
-
"unk_token": null,
|
| 96 |
-
"continuing_subword_prefix": "",
|
| 97 |
-
"end_of_word_suffix": "",
|
| 98 |
-
"fuse_unk": false,
|
| 99 |
-
"vocab": {
|
| 100 |
-
"<unk>": 0,
|
| 101 |
-
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|
| 102 |
-
"</s>": 2,
|
| 103 |
-
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|
| 104 |
-
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|
| 105 |
-
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|
| 106 |
-
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|
| 107 |
-
"+": 7,
|
| 108 |
-
"-": 8,
|
| 109 |
-
".": 9,
|
| 110 |
-
"/": 10,
|
| 111 |
-
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|
| 112 |
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|
| 113 |
-
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|
| 114 |
-
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|
| 115 |
-
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|
| 116 |
-
"5": 16,
|
| 117 |
-
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|
| 118 |
-
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|
| 119 |
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|
| 120 |
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|
| 121 |
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|
| 122 |
-
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|
| 123 |
-
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|
| 124 |
-
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|
| 125 |
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|
| 126 |
-
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|
| 127 |
-
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|
| 128 |
-
"I": 28,
|
| 129 |
-
"K": 29,
|
| 130 |
-
"L": 30,
|
| 131 |
-
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|
| 132 |
-
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|
| 133 |
-
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|
| 134 |
-
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|
| 135 |
-
"R": 35,
|
| 136 |
-
"S": 36,
|
| 137 |
-
"T": 37,
|
| 138 |
-
"Z": 38,
|
| 139 |
-
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|
| 140 |
-
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|
| 141 |
-
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|
| 142 |
-
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|
| 143 |
-
"e": 43,
|
| 144 |
-
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|
| 145 |
-
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|
| 146 |
-
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|
| 147 |
-
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|
| 148 |
-
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|
| 149 |
-
"r": 49,
|
| 150 |
-
"s": 50,
|
| 151 |
-
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|
| 152 |
-
"an": 52,
|
| 153 |
-
"ch": 53,
|
| 154 |
-
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|
| 155 |
-
"Branch": 55,
|
| 156 |
-
"Branch1": 56,
|
| 157 |
-
"=C": 57,
|
| 158 |
-
"Ri": 58,
|
| 159 |
-
"ng": 59,
|
| 160 |
-
"Ring": 60,
|
| 161 |
-
"Ring1": 61,
|
| 162 |
-
"=Branch1": 62,
|
| 163 |
-
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|
| 164 |
-
"=O": 64,
|
| 165 |
-
"Ring2": 65,
|
| 166 |
-
"H1": 66,
|
| 167 |
-
"C@": 67,
|
| 168 |
-
"=N": 68,
|
| 169 |
-
"#Branch1": 69,
|
| 170 |
-
"C@@": 70,
|
| 171 |
-
"=Branch2": 71,
|
| 172 |
-
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|
| 173 |
-
"C@@H1": 73,
|
| 174 |
-
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|
| 175 |
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|
| 176 |
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|
| 177 |
-
"/C": 77,
|
| 178 |
-
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|
| 179 |
-
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|
| 180 |
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"+1": 80,
|
| 181 |
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|
| 182 |
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|
| 183 |
-
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|
| 184 |
-
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|
| 185 |
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|
| 186 |
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|
| 187 |
-
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|
| 188 |
-
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|
| 189 |
-
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|
| 190 |
-
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|
| 191 |
-
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|
| 192 |
-
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|
| 193 |
-
"/O": 93,
|
| 194 |
-
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|
| 195 |
-
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|
| 196 |
-
"Branch3": 96,
|
| 197 |
-
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|
| 198 |
-
"S+1": 98,
|
| 199 |
-
"Cl-1": 99,
|
| 200 |
-
"I-1": 100,
|
| 201 |
-
"/C@@H1": 101,
|
| 202 |
-
"Si": 102,
|
| 203 |
-
"/C@H1": 103,
|
| 204 |
-
"/S": 104,
|
| 205 |
-
"=N-1": 105,
|
| 206 |
-
"Se": 106,
|
| 207 |
-
"=P": 107,
|
| 208 |
-
"N-1": 108,
|
| 209 |
-
"Ring3": 109,
|
| 210 |
-
"2H": 110,
|
| 211 |
-
"P+1": 111,
|
| 212 |
-
"K+1": 112,
|
| 213 |
-
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|
| 214 |
-
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|
| 215 |
-
"/N+1": 115,
|
| 216 |
-
"@@": 116,
|
| 217 |
-
"C-1": 117,
|
| 218 |
-
"#N+1": 118,
|
| 219 |
-
"B-1": 119,
|
| 220 |
-
"+3": 120,
|
| 221 |
-
"Cl+3": 121,
|
| 222 |
-
"\\NH1": 122,
|
| 223 |
-
"Li": 123,
|
| 224 |
-
"Li+1": 124,
|
| 225 |
-
"PH1": 125,
|
| 226 |
-
"18": 126,
|
| 227 |
-
"18F": 127,
|
| 228 |
-
"@+1": 128,
|
| 229 |
-
"3H": 129,
|
| 230 |
-
"P@@": 130,
|
| 231 |
-
"H0": 131,
|
| 232 |
-
"OH0": 132,
|
| 233 |
-
"12": 133,
|
| 234 |
-
"P@": 134,
|
| 235 |
-
"+2": 135,
|
| 236 |
-
"@@+1": 136,
|
| 237 |
-
"S-1": 137,
|
| 238 |
-
"/Br": 138,
|
| 239 |
-
"-/": 139,
|
| 240 |
-
"\\Cl": 140,
|
| 241 |
-
"-/Ring2": 141,
|
| 242 |
-
"\\O-1": 142,
|
| 243 |
-
"11": 143,
|
| 244 |
-
"5I": 144,
|
| 245 |
-
"125I": 145,
|
| 246 |
-
"11C": 146,
|
| 247 |
-
"H3": 147,
|
| 248 |
-
"\\N+1": 148,
|
| 249 |
-
"-\\": 149,
|
| 250 |
-
"/C@@": 150,
|
| 251 |
-
"S@+1": 151,
|
| 252 |
-
"As": 152,
|
| 253 |
-
"/Cl": 153,
|
| 254 |
-
"11CH3": 154,
|
| 255 |
-
"=Se": 155,
|
| 256 |
-
"S@@+1": 156,
|
| 257 |
-
"N@+1": 157,
|
| 258 |
-
"14": 158,
|
| 259 |
-
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|
| 260 |
-
"14C": 160,
|
| 261 |
-
"\\F": 161,
|
| 262 |
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"/C@": 162,
|
| 263 |
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"Te": 163,
|
| 264 |
-
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|
| 265 |
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|
| 266 |
-
"=O+1": 166,
|
| 267 |
-
"N@@+1": 167,
|
| 268 |
-
"C+1": 168,
|
| 269 |
-
"=S+1": 169,
|
| 270 |
-
"Zn": 170,
|
| 271 |
-
"/P": 171,
|
| 272 |
-
"a+2": 172,
|
| 273 |
-
"/I": 173,
|
| 274 |
-
"OH1-1": 174,
|
| 275 |
-
"Ca+2": 175,
|
| 276 |
-
"\\Br": 176,
|
| 277 |
-
"Mg": 177,
|
| 278 |
-
"Zn+2": 178,
|
| 279 |
-
"Al": 179,
|
| 280 |
-
"/F": 180,
|
| 281 |
-
"Mg+2": 181,
|
| 282 |
-
"123": 182,
|
| 283 |
-
"123I": 183,
|
| 284 |
-
"13": 184,
|
| 285 |
-
"I+1": 185,
|
| 286 |
-
"/O-1": 186,
|
| 287 |
-
"-\\Ring1": 187,
|
| 288 |
-
"BH2": 188,
|
| 289 |
-
"BH2-1": 189,
|
| 290 |
-
"\\I": 190,
|
| 291 |
-
"/NH1": 191,
|
| 292 |
-
"O+1": 192,
|
| 293 |
-
"131": 193,
|
| 294 |
-
"131I": 194,
|
| 295 |
-
"=14C": 195,
|
| 296 |
-
"/S+1": 196,
|
| 297 |
-
"=Ring3": 197,
|
| 298 |
-
"\\C@@": 198,
|
| 299 |
-
"H2+1": 199,
|
| 300 |
-
"\\C@": 200,
|
| 301 |
-
"Ag": 201,
|
| 302 |
-
"=As": 202,
|
| 303 |
-
"=Se+1": 203,
|
| 304 |
-
"NH2+1": 204,
|
| 305 |
-
"SeH1": 205,
|
| 306 |
-
"-/Ring1": 206,
|
| 307 |
-
"=Te": 207,
|
| 308 |
-
"Al+3": 208,
|
| 309 |
-
"NaH1": 209,
|
| 310 |
-
"=Te+1": 210,
|
| 311 |
-
"NH1+1": 211,
|
| 312 |
-
"Ag+1": 212,
|
| 313 |
-
"H1+1": 213,
|
| 314 |
-
"NH1-1": 214,
|
| 315 |
-
"\\P": 215,
|
| 316 |
-
"14CH2": 216,
|
| 317 |
-
"13C": 217,
|
| 318 |
-
"14CH1": 218,
|
| 319 |
-
"=11C": 219,
|
| 320 |
-
"S@@": 220,
|
| 321 |
-
"=P@@": 221,
|
| 322 |
-
"SiH2": 222,
|
| 323 |
-
"H3-1": 223,
|
| 324 |
-
"14CH3": 224,
|
| 325 |
-
"BH3-1": 225,
|
| 326 |
-
"S@": 226,
|
| 327 |
-
"=14CH1": 227,
|
| 328 |
-
"=PH1": 228,
|
| 329 |
-
"=P@": 229,
|
| 330 |
-
"=NH1+1": 230,
|
| 331 |
-
"\\S+1": 231,
|
| 332 |
-
"124": 232,
|
| 333 |
-
"CH1-1": 233,
|
| 334 |
-
"Sr": 234,
|
| 335 |
-
"=Si": 235,
|
| 336 |
-
"124I": 236,
|
| 337 |
-
"Sr+2": 237,
|
| 338 |
-
"#C-1": 238,
|
| 339 |
-
"/C-1": 239,
|
| 340 |
-
"N@": 240,
|
| 341 |
-
"/N-1": 241,
|
| 342 |
-
"13CH1": 242,
|
| 343 |
-
"/B": 243,
|
| 344 |
-
"19": 244,
|
| 345 |
-
"Ba+2": 245,
|
| 346 |
-
"H4": 246,
|
| 347 |
-
"SH1+1": 247,
|
| 348 |
-
"Se+1": 248,
|
| 349 |
-
"19F": 249,
|
| 350 |
-
"/125I": 250,
|
| 351 |
-
"P@+1": 251,
|
| 352 |
-
"Rb": 252,
|
| 353 |
-
"Cl+1": 253,
|
| 354 |
-
"SiH4": 254,
|
| 355 |
-
"Rb+1": 255,
|
| 356 |
-
"=Branch3": 256,
|
| 357 |
-
"N@@": 257,
|
| 358 |
-
"As+1": 258,
|
| 359 |
-
"/Si": 259,
|
| 360 |
-
"BH1-1": 260,
|
| 361 |
-
"SH1": 261,
|
| 362 |
-
"/123I": 262,
|
| 363 |
-
"32": 263,
|
| 364 |
-
"=Mg": 264,
|
| 365 |
-
"H+1": 265,
|
| 366 |
-
"\\B": 266,
|
| 367 |
-
"SiH1": 267,
|
| 368 |
-
"P@@+1": 268,
|
| 369 |
-
"-2": 269,
|
| 370 |
-
"15": 270,
|
| 371 |
-
"17": 271,
|
| 372 |
-
"35": 272,
|
| 373 |
-
"=13CH1": 273,
|
| 374 |
-
"Cs": 274,
|
| 375 |
-
"=NH2+1": 275,
|
| 376 |
-
"=SH1": 276,
|
| 377 |
-
"MgH2": 277,
|
| 378 |
-
"32P": 278,
|
| 379 |
-
"17F": 279,
|
| 380 |
-
"35S": 280,
|
| 381 |
-
"Cs+1": 281,
|
| 382 |
-
"#11C": 282,
|
| 383 |
-
"/131I": 283,
|
| 384 |
-
"Bi": 284,
|
| 385 |
-
"\\125I": 285,
|
| 386 |
-
"=S@@": 286,
|
| 387 |
-
"\\S-1": 287,
|
| 388 |
-
"6Br": 288,
|
| 389 |
-
"7I": 289,
|
| 390 |
-
"76Br": 290,
|
| 391 |
-
"=B": 291,
|
| 392 |
-
"eH1": 292,
|
| 393 |
-
"\\N-1": 293,
|
| 394 |
-
"18O": 294,
|
| 395 |
-
"127I": 295,
|
| 396 |
-
"11CH2": 296,
|
| 397 |
-
"14C@@H1": 297,
|
| 398 |
-
"TeH2": 298,
|
| 399 |
-
"15NH1": 299,
|
| 400 |
-
"Bi+3": 300,
|
| 401 |
-
"/P+1": 301,
|
| 402 |
-
"/13C": 302,
|
| 403 |
-
"/13CH1": 303,
|
| 404 |
-
"0B": 304,
|
| 405 |
-
"10B": 305,
|
| 406 |
-
"=Al": 306,
|
| 407 |
-
"=18O": 307,
|
| 408 |
-
"BH0": 308,
|
| 409 |
-
"F-1": 309,
|
| 410 |
-
"NH3": 310,
|
| 411 |
-
"S-2": 311,
|
| 412 |
-
"Br+2": 312,
|
| 413 |
-
"Cl+2": 313,
|
| 414 |
-
"\\Si": 314,
|
| 415 |
-
"/S-1": 315,
|
| 416 |
-
"=PH2": 316,
|
| 417 |
-
"14C@H1": 317,
|
| 418 |
-
"NH3+1": 318,
|
| 419 |
-
"#14C": 319,
|
| 420 |
-
"#O+1": 320,
|
| 421 |
-
"-3": 321,
|
| 422 |
-
"22": 322,
|
| 423 |
-
"4H": 323,
|
| 424 |
-
"5Se": 324,
|
| 425 |
-
"5Sr+2": 325,
|
| 426 |
-
"75Se": 326,
|
| 427 |
-
"85Sr+2": 327,
|
| 428 |
-
"=B-1": 328,
|
| 429 |
-
"=13C": 329,
|
| 430 |
-
"@-1": 330,
|
| 431 |
-
"Be": 331,
|
| 432 |
-
"B@@": 332,
|
| 433 |
-
"B@-1": 333,
|
| 434 |
-
"Ca": 334,
|
| 435 |
-
"CH1": 335,
|
| 436 |
-
"I+3": 336,
|
| 437 |
-
"KH1": 337,
|
| 438 |
-
"OH1+1": 338,
|
| 439 |
-
"Ra+2": 339,
|
| 440 |
-
"SH1-1": 340,
|
| 441 |
-
"\\PH1": 341,
|
| 442 |
-
"\\123I": 342,
|
| 443 |
-
"=Ca": 343,
|
| 444 |
-
"\\CH1-1": 344,
|
| 445 |
-
"=S@": 345,
|
| 446 |
-
"\\SeH1": 346,
|
| 447 |
-
"/SeH1": 347,
|
| 448 |
-
"Se-1": 348,
|
| 449 |
-
"LiH1": 349,
|
| 450 |
-
"18F-1": 350,
|
| 451 |
-
"125IH1": 351,
|
| 452 |
-
"11CH1": 352,
|
| 453 |
-
"TeH1": 353,
|
| 454 |
-
"Zn+1": 354,
|
| 455 |
-
"Zn-2": 355,
|
| 456 |
-
"Al-3": 356,
|
| 457 |
-
"13CH3": 357,
|
| 458 |
-
"15N": 358,
|
| 459 |
-
"Be+2": 359,
|
| 460 |
-
"B@@-1": 360,
|
| 461 |
-
"#P": 361,
|
| 462 |
-
"#S": 362,
|
| 463 |
-
"-4": 363,
|
| 464 |
-
"/PH1": 364,
|
| 465 |
-
"/P@@": 365,
|
| 466 |
-
"/As": 366,
|
| 467 |
-
"/14C": 367,
|
| 468 |
-
"/14CH1": 368,
|
| 469 |
-
"2K+1": 369,
|
| 470 |
-
"2Rb+1": 370,
|
| 471 |
-
"3Se": 371,
|
| 472 |
-
"3Ra+2": 372,
|
| 473 |
-
"45": 373,
|
| 474 |
-
"47": 374,
|
| 475 |
-
"42K+1": 375,
|
| 476 |
-
"5I-1": 376,
|
| 477 |
-
"73Se": 377,
|
| 478 |
-
"89": 378,
|
| 479 |
-
"82Rb+1": 379,
|
| 480 |
-
"=32": 380,
|
| 481 |
-
"=32P": 381,
|
| 482 |
-
"CH0": 382,
|
| 483 |
-
"CH2": 383,
|
| 484 |
-
"I+2": 384,
|
| 485 |
-
"NH0": 385,
|
| 486 |
-
"NH4": 386,
|
| 487 |
-
"OH1": 387,
|
| 488 |
-
"PH2+1": 388,
|
| 489 |
-
"SH0": 389,
|
| 490 |
-
"SH2": 390,
|
| 491 |
-
"\\3H": 391,
|
| 492 |
-
"\\11CH3": 392,
|
| 493 |
-
"\\C-1": 393,
|
| 494 |
-
"\\Se": 394,
|
| 495 |
-
"Si@": 395,
|
| 496 |
-
"Si-1": 396,
|
| 497 |
-
"SiH1-1": 397,
|
| 498 |
-
"SiH3-1": 398,
|
| 499 |
-
"/Se": 399,
|
| 500 |
-
"Se-2": 400,
|
| 501 |
-
"\\NH1-1": 401,
|
| 502 |
-
"18FH1": 402,
|
| 503 |
-
"125I-1": 403,
|
| 504 |
-
"11C@@H1": 404,
|
| 505 |
-
"11C-1": 405,
|
| 506 |
-
"AsH1": 406,
|
| 507 |
-
"As-1": 407,
|
| 508 |
-
"14C@@": 408,
|
| 509 |
-
"Te-1": 409,
|
| 510 |
-
"Mg+1": 410,
|
| 511 |
-
"123I-1": 411,
|
| 512 |
-
"123Te": 412,
|
| 513 |
-
"123IH1": 413,
|
| 514 |
-
"135I": 414,
|
| 515 |
-
"131I-1": 415,
|
| 516 |
-
"Ag-4": 416,
|
| 517 |
-
"124I-1": 417,
|
| 518 |
-
"76BrH1": 418,
|
| 519 |
-
"18OH1": 419,
|
| 520 |
-
"22Na+1": 420,
|
| 521 |
-
"223Ra+2": 421,
|
| 522 |
-
"CaH2": 422,
|
| 523 |
-
"45Ca+2": 423,
|
| 524 |
-
"47Ca+2": 424,
|
| 525 |
-
"89Sr+2": 425,
|
| 526 |
-
"=32PH1": 426,
|
| 527 |
-
"NH4+1": 427
|
| 528 |
-
},
|
| 529 |
-
"merges": [
|
| 530 |
-
"B r",
|
| 531 |
-
"a n",
|
| 532 |
-
"c h",
|
| 533 |
-
"Br an",
|
| 534 |
-
"Bran ch",
|
| 535 |
-
"Branch 1",
|
| 536 |
-
"= C",
|
| 537 |
-
"R i",
|
| 538 |
-
"n g",
|
| 539 |
-
"Ri ng",
|
| 540 |
-
"Ring 1",
|
| 541 |
-
"= Branch1",
|
| 542 |
-
"Branch 2",
|
| 543 |
-
"= O",
|
| 544 |
-
"Ring 2",
|
| 545 |
-
"H 1",
|
| 546 |
-
"C @",
|
| 547 |
-
"= N",
|
| 548 |
-
"# Branch1",
|
| 549 |
-
"C@ @",
|
| 550 |
-
"= Branch2",
|
| 551 |
-
"C@ H1",
|
| 552 |
-
"C@@ H1",
|
| 553 |
-
"# Branch2",
|
| 554 |
-
"# C",
|
| 555 |
-
"C l",
|
| 556 |
-
"/ C",
|
| 557 |
-
"N H1",
|
| 558 |
-
"= Ring1",
|
| 559 |
-
"+ 1",
|
| 560 |
-
"- 1",
|
| 561 |
-
"O -1",
|
| 562 |
-
"N +1",
|
| 563 |
-
"\\ C",
|
| 564 |
-
"# N",
|
| 565 |
-
"/ N",
|
| 566 |
-
"= Ring2",
|
| 567 |
-
"= S",
|
| 568 |
-
"=N +1",
|
| 569 |
-
"\\ N",
|
| 570 |
-
"N a",
|
| 571 |
-
"Na +1",
|
| 572 |
-
"/ O",
|
| 573 |
-
"\\ O",
|
| 574 |
-
"Br -1",
|
| 575 |
-
"Branch 3",
|
| 576 |
-
"\\ S",
|
| 577 |
-
"S +1",
|
| 578 |
-
"Cl -1",
|
| 579 |
-
"I -1",
|
| 580 |
-
"/ C@@H1",
|
| 581 |
-
"S i",
|
| 582 |
-
"/ C@H1",
|
| 583 |
-
"/ S",
|
| 584 |
-
"=N -1",
|
| 585 |
-
"S e",
|
| 586 |
-
"= P",
|
| 587 |
-
"N -1",
|
| 588 |
-
"Ring 3",
|
| 589 |
-
"2 H",
|
| 590 |
-
"P +1",
|
| 591 |
-
"K +1",
|
| 592 |
-
"\\ C@@H1",
|
| 593 |
-
"\\ C@H1",
|
| 594 |
-
"/ N+1",
|
| 595 |
-
"@ @",
|
| 596 |
-
"C -1",
|
| 597 |
-
"# N+1",
|
| 598 |
-
"B -1",
|
| 599 |
-
"+ 3",
|
| 600 |
-
"Cl +3",
|
| 601 |
-
"\\ NH1",
|
| 602 |
-
"L i",
|
| 603 |
-
"Li +1",
|
| 604 |
-
"P H1",
|
| 605 |
-
"1 8",
|
| 606 |
-
"18 F",
|
| 607 |
-
"@ +1",
|
| 608 |
-
"3 H",
|
| 609 |
-
"P @@",
|
| 610 |
-
"H 0",
|
| 611 |
-
"O H0",
|
| 612 |
-
"1 2",
|
| 613 |
-
"P @",
|
| 614 |
-
"+ 2",
|
| 615 |
-
"@@ +1",
|
| 616 |
-
"S -1",
|
| 617 |
-
"/ Br",
|
| 618 |
-
"- /",
|
| 619 |
-
"\\ Cl",
|
| 620 |
-
"-/ Ring2",
|
| 621 |
-
"\\ O-1",
|
| 622 |
-
"1 1",
|
| 623 |
-
"5 I",
|
| 624 |
-
"12 5I",
|
| 625 |
-
"11 C",
|
| 626 |
-
"H 3",
|
| 627 |
-
"\\ N+1",
|
| 628 |
-
"- \\",
|
| 629 |
-
"/ C@@",
|
| 630 |
-
"S @+1",
|
| 631 |
-
"A s",
|
| 632 |
-
"/ Cl",
|
| 633 |
-
"11C H3",
|
| 634 |
-
"=S e",
|
| 635 |
-
"S @@+1",
|
| 636 |
-
"N @+1",
|
| 637 |
-
"1 4",
|
| 638 |
-
"-\\ Ring2",
|
| 639 |
-
"14 C",
|
| 640 |
-
"\\ F",
|
| 641 |
-
"/ C@",
|
| 642 |
-
"T e",
|
| 643 |
-
"H 2",
|
| 644 |
-
"H1 -1",
|
| 645 |
-
"=O +1",
|
| 646 |
-
"N @@+1",
|
| 647 |
-
"C +1",
|
| 648 |
-
"=S +1",
|
| 649 |
-
"Z n",
|
| 650 |
-
"/ P",
|
| 651 |
-
"a +2",
|
| 652 |
-
"/ I",
|
| 653 |
-
"O H1-1",
|
| 654 |
-
"C a+2",
|
| 655 |
-
"\\ Br",
|
| 656 |
-
"M g",
|
| 657 |
-
"Zn +2",
|
| 658 |
-
"A l",
|
| 659 |
-
"/ F",
|
| 660 |
-
"Mg +2",
|
| 661 |
-
"12 3",
|
| 662 |
-
"123 I",
|
| 663 |
-
"1 3",
|
| 664 |
-
"I +1",
|
| 665 |
-
"/ O-1",
|
| 666 |
-
"-\\ Ring1",
|
| 667 |
-
"B H2",
|
| 668 |
-
"BH2 -1",
|
| 669 |
-
"\\ I",
|
| 670 |
-
"/ NH1",
|
| 671 |
-
"O +1",
|
| 672 |
-
"13 1",
|
| 673 |
-
"131 I",
|
| 674 |
-
"= 14C",
|
| 675 |
-
"/ S+1",
|
| 676 |
-
"= Ring3",
|
| 677 |
-
"\\ C@@",
|
| 678 |
-
"H2 +1",
|
| 679 |
-
"\\ C@",
|
| 680 |
-
"A g",
|
| 681 |
-
"= As",
|
| 682 |
-
"=Se +1",
|
| 683 |
-
"N H2+1",
|
| 684 |
-
"Se H1",
|
| 685 |
-
"-/ Ring1",
|
| 686 |
-
"= Te",
|
| 687 |
-
"Al +3",
|
| 688 |
-
"Na H1",
|
| 689 |
-
"=Te +1",
|
| 690 |
-
"NH1 +1",
|
| 691 |
-
"Ag +1",
|
| 692 |
-
"H1 +1",
|
| 693 |
-
"NH1 -1",
|
| 694 |
-
"\\ P",
|
| 695 |
-
"14C H2",
|
| 696 |
-
"13 C",
|
| 697 |
-
"14C H1",
|
| 698 |
-
"= 11C",
|
| 699 |
-
"S @@",
|
| 700 |
-
"=P @@",
|
| 701 |
-
"Si H2",
|
| 702 |
-
"H3 -1",
|
| 703 |
-
"14C H3",
|
| 704 |
-
"B H3-1",
|
| 705 |
-
"S @",
|
| 706 |
-
"=14C H1",
|
| 707 |
-
"=P H1",
|
| 708 |
-
"=P @",
|
| 709 |
-
"=N H1+1",
|
| 710 |
-
"\\S +1",
|
| 711 |
-
"12 4",
|
| 712 |
-
"C H1-1",
|
| 713 |
-
"S r",
|
| 714 |
-
"=S i",
|
| 715 |
-
"124 I",
|
| 716 |
-
"Sr +2",
|
| 717 |
-
"#C -1",
|
| 718 |
-
"/C -1",
|
| 719 |
-
"N @",
|
| 720 |
-
"/N -1",
|
| 721 |
-
"13C H1",
|
| 722 |
-
"/ B",
|
| 723 |
-
"1 9",
|
| 724 |
-
"B a+2",
|
| 725 |
-
"H 4",
|
| 726 |
-
"S H1+1",
|
| 727 |
-
"Se +1",
|
| 728 |
-
"19 F",
|
| 729 |
-
"/ 125I",
|
| 730 |
-
"P @+1",
|
| 731 |
-
"R b",
|
| 732 |
-
"Cl +1",
|
| 733 |
-
"Si H4",
|
| 734 |
-
"Rb +1",
|
| 735 |
-
"= Branch3",
|
| 736 |
-
"N @@",
|
| 737 |
-
"As +1",
|
| 738 |
-
"/ Si",
|
| 739 |
-
"B H1-1",
|
| 740 |
-
"S H1",
|
| 741 |
-
"/ 123I",
|
| 742 |
-
"3 2",
|
| 743 |
-
"= Mg",
|
| 744 |
-
"H +1",
|
| 745 |
-
"\\ B",
|
| 746 |
-
"Si H1",
|
| 747 |
-
"P@@ +1",
|
| 748 |
-
"- 2",
|
| 749 |
-
"1 5",
|
| 750 |
-
"1 7",
|
| 751 |
-
"3 5",
|
| 752 |
-
"= 13CH1",
|
| 753 |
-
"C s",
|
| 754 |
-
"=N H2+1",
|
| 755 |
-
"=S H1",
|
| 756 |
-
"Mg H2",
|
| 757 |
-
"32 P",
|
| 758 |
-
"17 F",
|
| 759 |
-
"35 S",
|
| 760 |
-
"Cs +1",
|
| 761 |
-
"# 11C",
|
| 762 |
-
"/ 131I",
|
| 763 |
-
"B i",
|
| 764 |
-
"\\ 125I",
|
| 765 |
-
"=S @@",
|
| 766 |
-
"\\S -1",
|
| 767 |
-
"6 Br",
|
| 768 |
-
"7 I",
|
| 769 |
-
"7 6Br",
|
| 770 |
-
"= B",
|
| 771 |
-
"e H1",
|
| 772 |
-
"\\N -1",
|
| 773 |
-
"18 O",
|
| 774 |
-
"12 7I",
|
| 775 |
-
"11C H2",
|
| 776 |
-
"14 C@@H1",
|
| 777 |
-
"Te H2",
|
| 778 |
-
"15 NH1",
|
| 779 |
-
"Bi +3",
|
| 780 |
-
"/ P+1",
|
| 781 |
-
"/ 13C",
|
| 782 |
-
"/ 13CH1",
|
| 783 |
-
"0 B",
|
| 784 |
-
"1 0B",
|
| 785 |
-
"= Al",
|
| 786 |
-
"= 18O",
|
| 787 |
-
"B H0",
|
| 788 |
-
"F -1",
|
| 789 |
-
"N H3",
|
| 790 |
-
"S -2",
|
| 791 |
-
"Br +2",
|
| 792 |
-
"Cl +2",
|
| 793 |
-
"\\S i",
|
| 794 |
-
"/S -1",
|
| 795 |
-
"=P H2",
|
| 796 |
-
"14 C@H1",
|
| 797 |
-
"NH3 +1",
|
| 798 |
-
"# 14C",
|
| 799 |
-
"# O+1",
|
| 800 |
-
"- 3",
|
| 801 |
-
"2 2",
|
| 802 |
-
"4 H",
|
| 803 |
-
"5 Se",
|
| 804 |
-
"5 Sr+2",
|
| 805 |
-
"7 5Se",
|
| 806 |
-
"8 5Sr+2",
|
| 807 |
-
"= B-1",
|
| 808 |
-
"= 13C",
|
| 809 |
-
"@ -1",
|
| 810 |
-
"B e",
|
| 811 |
-
"B @@",
|
| 812 |
-
"B @-1",
|
| 813 |
-
"C a",
|
| 814 |
-
"C H1",
|
| 815 |
-
"I +3",
|
| 816 |
-
"K H1",
|
| 817 |
-
"O H1+1",
|
| 818 |
-
"R a+2",
|
| 819 |
-
"S H1-1",
|
| 820 |
-
"\\ PH1",
|
| 821 |
-
"\\ 123I",
|
| 822 |
-
"=C a",
|
| 823 |
-
"\\C H1-1",
|
| 824 |
-
"=S @",
|
| 825 |
-
"\\S eH1",
|
| 826 |
-
"/S eH1",
|
| 827 |
-
"Se -1",
|
| 828 |
-
"Li H1",
|
| 829 |
-
"18F -1",
|
| 830 |
-
"125I H1",
|
| 831 |
-
"11C H1",
|
| 832 |
-
"Te H1",
|
| 833 |
-
"Zn +1",
|
| 834 |
-
"Zn -2",
|
| 835 |
-
"Al -3",
|
| 836 |
-
"13C H3",
|
| 837 |
-
"15 N",
|
| 838 |
-
"Be +2",
|
| 839 |
-
"B@@ -1",
|
| 840 |
-
"# P",
|
| 841 |
-
"# S",
|
| 842 |
-
"- 4",
|
| 843 |
-
"/ PH1",
|
| 844 |
-
"/ P@@",
|
| 845 |
-
"/ As",
|
| 846 |
-
"/ 14C",
|
| 847 |
-
"/ 14CH1",
|
| 848 |
-
"2 K+1",
|
| 849 |
-
"2 Rb+1",
|
| 850 |
-
"3 Se",
|
| 851 |
-
"3 Ra+2",
|
| 852 |
-
"4 5",
|
| 853 |
-
"4 7",
|
| 854 |
-
"4 2K+1",
|
| 855 |
-
"5 I-1",
|
| 856 |
-
"7 3Se",
|
| 857 |
-
"8 9",
|
| 858 |
-
"8 2Rb+1",
|
| 859 |
-
"= 32",
|
| 860 |
-
"= 32P",
|
| 861 |
-
"C H0",
|
| 862 |
-
"C H2",
|
| 863 |
-
"I +2",
|
| 864 |
-
"N H0",
|
| 865 |
-
"N H4",
|
| 866 |
-
"O H1",
|
| 867 |
-
"P H2+1",
|
| 868 |
-
"S H0",
|
| 869 |
-
"S H2",
|
| 870 |
-
"\\ 3H",
|
| 871 |
-
"\\ 11CH3",
|
| 872 |
-
"\\C -1",
|
| 873 |
-
"\\S e",
|
| 874 |
-
"Si @",
|
| 875 |
-
"Si -1",
|
| 876 |
-
"Si H1-1",
|
| 877 |
-
"Si H3-1",
|
| 878 |
-
"/S e",
|
| 879 |
-
"Se -2",
|
| 880 |
-
"\\NH1 -1",
|
| 881 |
-
"18F H1",
|
| 882 |
-
"12 5I-1",
|
| 883 |
-
"11 C@@H1",
|
| 884 |
-
"11 C-1",
|
| 885 |
-
"As H1",
|
| 886 |
-
"As -1",
|
| 887 |
-
"14 C@@",
|
| 888 |
-
"Te -1",
|
| 889 |
-
"Mg +1",
|
| 890 |
-
"123 I-1",
|
| 891 |
-
"123 Te",
|
| 892 |
-
"123I H1",
|
| 893 |
-
"13 5I",
|
| 894 |
-
"131 I-1",
|
| 895 |
-
"Ag -4",
|
| 896 |
-
"124 I-1",
|
| 897 |
-
"76Br H1",
|
| 898 |
-
"18O H1",
|
| 899 |
-
"22 Na+1",
|
| 900 |
-
"22 3Ra+2",
|
| 901 |
-
"Ca H2",
|
| 902 |
-
"45 Ca+2",
|
| 903 |
-
"47 Ca+2",
|
| 904 |
-
"89 Sr+2",
|
| 905 |
-
"=32 PH1",
|
| 906 |
-
"NH4 +1"
|
| 907 |
-
]
|
| 908 |
-
}
|
| 909 |
-
}
|
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models/finetuned/hiv/tokenizer_config.json
DELETED
|
@@ -1,65 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"add_prefix_space": false,
|
| 3 |
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"bos_token": {
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| 4 |
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| 5 |
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| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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| 11 |
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"cls_token": {
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| 12 |
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"__type": "AddedToken",
|
| 13 |
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"content": "<s>",
|
| 14 |
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"lstrip": false,
|
| 15 |
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"normalized": true,
|
| 16 |
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"rstrip": false,
|
| 17 |
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"single_word": false
|
| 18 |
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},
|
| 19 |
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"eos_token": {
|
| 20 |
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"__type": "AddedToken",
|
| 21 |
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"content": "</s>",
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| 22 |
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"lstrip": false,
|
| 23 |
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"normalized": true,
|
| 24 |
-
"rstrip": false,
|
| 25 |
-
"single_word": false
|
| 26 |
-
},
|
| 27 |
-
"errors": "replace",
|
| 28 |
-
"mask_token": {
|
| 29 |
-
"__type": "AddedToken",
|
| 30 |
-
"content": "<mask>",
|
| 31 |
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"lstrip": true,
|
| 32 |
-
"normalized": true,
|
| 33 |
-
"rstrip": false,
|
| 34 |
-
"single_word": false
|
| 35 |
-
},
|
| 36 |
-
"model_max_length": 1000000000000000019884624838656,
|
| 37 |
-
"name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
|
| 38 |
-
"pad_token": {
|
| 39 |
-
"__type": "AddedToken",
|
| 40 |
-
"content": "<pad>",
|
| 41 |
-
"lstrip": false,
|
| 42 |
-
"normalized": true,
|
| 43 |
-
"rstrip": false,
|
| 44 |
-
"single_word": false
|
| 45 |
-
},
|
| 46 |
-
"sep_token": {
|
| 47 |
-
"__type": "AddedToken",
|
| 48 |
-
"content": "</s>",
|
| 49 |
-
"lstrip": false,
|
| 50 |
-
"normalized": true,
|
| 51 |
-
"rstrip": false,
|
| 52 |
-
"single_word": false
|
| 53 |
-
},
|
| 54 |
-
"special_tokens_map_file": null,
|
| 55 |
-
"tokenizer_class": "RobertaTokenizer",
|
| 56 |
-
"trim_offsets": true,
|
| 57 |
-
"unk_token": {
|
| 58 |
-
"__type": "AddedToken",
|
| 59 |
-
"content": "<unk>",
|
| 60 |
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"lstrip": false,
|
| 61 |
-
"normalized": true,
|
| 62 |
-
"rstrip": false,
|
| 63 |
-
"single_word": false
|
| 64 |
-
}
|
| 65 |
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models/finetuned/hiv/vocab.json
DELETED
|
@@ -1 +0,0 @@
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|
| 1 |
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models/finetuned/lipo/config.json
DELETED
|
@@ -1,28 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "data/epoch_267/hf",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"RobertaForMaskedLM"
|
| 5 |
-
],
|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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"hidden_act": "gelu",
|
| 11 |
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|
| 12 |
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"hidden_size": 768,
|
| 13 |
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|
| 14 |
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|
| 15 |
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"layer_norm_eps": 1e-12,
|
| 16 |
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|
| 17 |
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"model_type": "roberta",
|
| 18 |
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"num_attention_heads": 4,
|
| 19 |
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"num_hidden_layers": 12,
|
| 20 |
-
"output_hidden_states": true,
|
| 21 |
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"pad_token_id": 1,
|
| 22 |
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"position_embedding_type": "absolute",
|
| 23 |
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"torch_dtype": "float32",
|
| 24 |
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"transformers_version": "4.26.1",
|
| 25 |
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"type_vocab_size": 1,
|
| 26 |
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"use_cache": true,
|
| 27 |
-
"vocab_size": 800
|
| 28 |
-
}
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models/finetuned/lipo/finetuning_optimized_config.json
DELETED
|
@@ -1,24 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"dataset_meta_csv": "data/finetuning_datasets/regression/lipo/lipo.csv",
|
| 3 |
-
"dataset_embs_npz": "data/finetuning_datasets/regression/lipo/lipo_embs.npz",
|
| 4 |
-
"use_scaffold": 0,
|
| 5 |
-
"seed": 42,
|
| 6 |
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"train_frac": 0.8,
|
| 7 |
-
"val_frac": 0.1,
|
| 8 |
-
"test_frac": 0.1,
|
| 9 |
-
"model_path": "HUBioDataLab/SELFormer",
|
| 10 |
-
"tokenizer_path": "HUBioDataLab/SELFormer",
|
| 11 |
-
"pretrained_multimodal_dir": "data/models/SELFormerMM",
|
| 12 |
-
"task_type": "regression",
|
| 13 |
-
"label_column": "lipo",
|
| 14 |
-
"num_labels": 1,
|
| 15 |
-
"batch_size": 32,
|
| 16 |
-
"max_len": 128,
|
| 17 |
-
"epochs": 100,
|
| 18 |
-
"backbone_lr": 5e-05,
|
| 19 |
-
"head_lr": 5e-06,
|
| 20 |
-
"weight_decay": 0.1,
|
| 21 |
-
"checkpoint_every": 25,
|
| 22 |
-
"test_eval_every": 0,
|
| 23 |
-
"save_dir": "data/models/finetuned/lipo"
|
| 24 |
-
}
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models/finetuned/lipo/merges.txt
DELETED
|
@@ -1,162 +0,0 @@
|
|
| 1 |
-
#version: 0.2 - Trained by `huggingface/tokenizers`
|
| 2 |
-
B r
|
| 3 |
-
a n
|
| 4 |
-
c h
|
| 5 |
-
Br an
|
| 6 |
-
Bran ch
|
| 7 |
-
Branch 1
|
| 8 |
-
= C
|
| 9 |
-
R i
|
| 10 |
-
n g
|
| 11 |
-
Ri ng
|
| 12 |
-
Ring 1
|
| 13 |
-
= Branch1
|
| 14 |
-
Branch 2
|
| 15 |
-
= O
|
| 16 |
-
Ring 2
|
| 17 |
-
H 1
|
| 18 |
-
C @
|
| 19 |
-
= N
|
| 20 |
-
# Branch1
|
| 21 |
-
C@ @
|
| 22 |
-
= Branch2
|
| 23 |
-
C@ H1
|
| 24 |
-
C@@ H1
|
| 25 |
-
# Branch2
|
| 26 |
-
C l
|
| 27 |
-
# C
|
| 28 |
-
/ C
|
| 29 |
-
N H1
|
| 30 |
-
+ 1
|
| 31 |
-
- 1
|
| 32 |
-
= Ring1
|
| 33 |
-
O -1
|
| 34 |
-
N +1
|
| 35 |
-
\ C
|
| 36 |
-
/ N
|
| 37 |
-
# N
|
| 38 |
-
= Ring2
|
| 39 |
-
= S
|
| 40 |
-
=N +1
|
| 41 |
-
N a
|
| 42 |
-
Na +1
|
| 43 |
-
\ N
|
| 44 |
-
S +1
|
| 45 |
-
/ O
|
| 46 |
-
\ S
|
| 47 |
-
\ O
|
| 48 |
-
Br -1
|
| 49 |
-
I -1
|
| 50 |
-
Cl -1
|
| 51 |
-
/ C@H1
|
| 52 |
-
Branch 3
|
| 53 |
-
/ C@@H1
|
| 54 |
-
= P
|
| 55 |
-
/ S
|
| 56 |
-
=N -1
|
| 57 |
-
S i
|
| 58 |
-
K +1
|
| 59 |
-
N -1
|
| 60 |
-
S e
|
| 61 |
-
L i
|
| 62 |
-
Li +1
|
| 63 |
-
+ 3
|
| 64 |
-
Cl +3
|
| 65 |
-
\ C@H1
|
| 66 |
-
Ring 3
|
| 67 |
-
\ C@@H1
|
| 68 |
-
/ N+1
|
| 69 |
-
/ P
|
| 70 |
-
\ F
|
| 71 |
-
P @
|
| 72 |
-
2 H
|
| 73 |
-
P H1
|
| 74 |
-
/ Br
|
| 75 |
-
N @
|
| 76 |
-
P +1
|
| 77 |
-
/ Cl
|
| 78 |
-
\ NH1
|
| 79 |
-
\ Br
|
| 80 |
-
@ +1
|
| 81 |
-
/ I
|
| 82 |
-
/ C@
|
| 83 |
-
T e
|
| 84 |
-
\ N+1
|
| 85 |
-
P@ @
|
| 86 |
-
1 2
|
| 87 |
-
5 I
|
| 88 |
-
\ O-1
|
| 89 |
-
12 5I
|
| 90 |
-
/ F
|
| 91 |
-
# N+1
|
| 92 |
-
\ Cl
|
| 93 |
-
N@ +1
|
| 94 |
-
\ I
|
| 95 |
-
- /
|
| 96 |
-
/ C@@
|
| 97 |
-
N@ @
|
| 98 |
-
N@ @+1
|
| 99 |
-
-/ Ring2
|
| 100 |
-
- \
|
| 101 |
-
1 4
|
| 102 |
-
B -1
|
| 103 |
-
C -1
|
| 104 |
-
S @+1
|
| 105 |
-
14 C
|
| 106 |
-
H 2
|
| 107 |
-
H 4
|
| 108 |
-
I +1
|
| 109 |
-
S -1
|
| 110 |
-
\ P
|
| 111 |
-
=S +1
|
| 112 |
-
=P @
|
| 113 |
-
Si H4
|
| 114 |
-
+ 2
|
| 115 |
-
3 H
|
| 116 |
-
@ @+1
|
| 117 |
-
A g
|
| 118 |
-
C +1
|
| 119 |
-
S @@+1
|
| 120 |
-
Cl +1
|
| 121 |
-
=S e
|
| 122 |
-
-\ Ring1
|
| 123 |
-
H 0
|
| 124 |
-
O H0
|
| 125 |
-
1 1
|
| 126 |
-
= Branch3
|
| 127 |
-
= Te
|
| 128 |
-
M g
|
| 129 |
-
O +1
|
| 130 |
-
Z n
|
| 131 |
-
\ C@
|
| 132 |
-
\ S+1
|
| 133 |
-
H1 -1
|
| 134 |
-
Se H1
|
| 135 |
-
P@ +1
|
| 136 |
-
-\ Ring2
|
| 137 |
-
11 C
|
| 138 |
-
=Te +1
|
| 139 |
-
Zn +2
|
| 140 |
-
/ NH1
|
| 141 |
-
1 8
|
| 142 |
-
A s
|
| 143 |
-
B H2
|
| 144 |
-
B H1-1
|
| 145 |
-
C a
|
| 146 |
-
H 3
|
| 147 |
-
O H1-1
|
| 148 |
-
S H2
|
| 149 |
-
=O +1
|
| 150 |
-
Se +1
|
| 151 |
-
Te H2
|
| 152 |
-
125I H1
|
| 153 |
-
-/ Ring1
|
| 154 |
-
14C H2
|
| 155 |
-
Ag +1
|
| 156 |
-
=Se +1
|
| 157 |
-
Mg H2
|
| 158 |
-
Mg +2
|
| 159 |
-
11C H3
|
| 160 |
-
18 F
|
| 161 |
-
BH2 -1
|
| 162 |
-
Ca +2
|
|
|
|
|
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models/finetuned/lipo/model.pt
DELETED
|
@@ -1,3 +0,0 @@
|
|
| 1 |
-
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:1b92b270751c67da0e55692cd40d5d0aa33e73b669f41e5f1e920b4ca1e3735a
|
| 3 |
-
size 1022843005
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models/finetuned/lipo/special_tokens_map.json
DELETED
|
@@ -1,51 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"bos_token": {
|
| 3 |
-
"content": "<s>",
|
| 4 |
-
"lstrip": false,
|
| 5 |
-
"normalized": true,
|
| 6 |
-
"rstrip": false,
|
| 7 |
-
"single_word": false
|
| 8 |
-
},
|
| 9 |
-
"cls_token": {
|
| 10 |
-
"content": "<s>",
|
| 11 |
-
"lstrip": false,
|
| 12 |
-
"normalized": true,
|
| 13 |
-
"rstrip": false,
|
| 14 |
-
"single_word": false
|
| 15 |
-
},
|
| 16 |
-
"eos_token": {
|
| 17 |
-
"content": "</s>",
|
| 18 |
-
"lstrip": false,
|
| 19 |
-
"normalized": true,
|
| 20 |
-
"rstrip": false,
|
| 21 |
-
"single_word": false
|
| 22 |
-
},
|
| 23 |
-
"mask_token": {
|
| 24 |
-
"content": "<mask>",
|
| 25 |
-
"lstrip": true,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"rstrip": false,
|
| 28 |
-
"single_word": false
|
| 29 |
-
},
|
| 30 |
-
"pad_token": {
|
| 31 |
-
"content": "<pad>",
|
| 32 |
-
"lstrip": false,
|
| 33 |
-
"normalized": true,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"single_word": false
|
| 36 |
-
},
|
| 37 |
-
"sep_token": {
|
| 38 |
-
"content": "</s>",
|
| 39 |
-
"lstrip": false,
|
| 40 |
-
"normalized": true,
|
| 41 |
-
"rstrip": false,
|
| 42 |
-
"single_word": false
|
| 43 |
-
},
|
| 44 |
-
"unk_token": {
|
| 45 |
-
"content": "<unk>",
|
| 46 |
-
"lstrip": false,
|
| 47 |
-
"normalized": true,
|
| 48 |
-
"rstrip": false,
|
| 49 |
-
"single_word": false
|
| 50 |
-
}
|
| 51 |
-
}
|
|
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|
models/finetuned/lipo/tokenizer.json
DELETED
|
@@ -1,473 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"version": "1.0",
|
| 3 |
-
"truncation": {
|
| 4 |
-
"direction": "Right",
|
| 5 |
-
"max_length": 128,
|
| 6 |
-
"strategy": "LongestFirst",
|
| 7 |
-
"stride": 0
|
| 8 |
-
},
|
| 9 |
-
"padding": {
|
| 10 |
-
"strategy": {
|
| 11 |
-
"Fixed": 128
|
| 12 |
-
},
|
| 13 |
-
"direction": "Right",
|
| 14 |
-
"pad_to_multiple_of": null,
|
| 15 |
-
"pad_id": 3,
|
| 16 |
-
"pad_type_id": 0,
|
| 17 |
-
"pad_token": "<pad>"
|
| 18 |
-
},
|
| 19 |
-
"added_tokens": [
|
| 20 |
-
{
|
| 21 |
-
"id": 0,
|
| 22 |
-
"content": "<unk>",
|
| 23 |
-
"single_word": false,
|
| 24 |
-
"lstrip": false,
|
| 25 |
-
"rstrip": false,
|
| 26 |
-
"normalized": true,
|
| 27 |
-
"special": true
|
| 28 |
-
},
|
| 29 |
-
{
|
| 30 |
-
"id": 1,
|
| 31 |
-
"content": "<s>",
|
| 32 |
-
"single_word": false,
|
| 33 |
-
"lstrip": false,
|
| 34 |
-
"rstrip": false,
|
| 35 |
-
"normalized": true,
|
| 36 |
-
"special": true
|
| 37 |
-
},
|
| 38 |
-
{
|
| 39 |
-
"id": 2,
|
| 40 |
-
"content": "</s>",
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"lstrip": false,
|
| 43 |
-
"rstrip": false,
|
| 44 |
-
"normalized": true,
|
| 45 |
-
"special": true
|
| 46 |
-
},
|
| 47 |
-
{
|
| 48 |
-
"id": 3,
|
| 49 |
-
"content": "<pad>",
|
| 50 |
-
"single_word": false,
|
| 51 |
-
"lstrip": false,
|
| 52 |
-
"rstrip": false,
|
| 53 |
-
"normalized": true,
|
| 54 |
-
"special": true
|
| 55 |
-
},
|
| 56 |
-
{
|
| 57 |
-
"id": 4,
|
| 58 |
-
"content": "<mask>",
|
| 59 |
-
"single_word": false,
|
| 60 |
-
"lstrip": true,
|
| 61 |
-
"rstrip": false,
|
| 62 |
-
"normalized": true,
|
| 63 |
-
"special": true
|
| 64 |
-
}
|
| 65 |
-
],
|
| 66 |
-
"normalizer": null,
|
| 67 |
-
"pre_tokenizer": {
|
| 68 |
-
"type": "ByteLevel",
|
| 69 |
-
"add_prefix_space": false,
|
| 70 |
-
"trim_offsets": true,
|
| 71 |
-
"use_regex": true
|
| 72 |
-
},
|
| 73 |
-
"post_processor": {
|
| 74 |
-
"type": "RobertaProcessing",
|
| 75 |
-
"sep": [
|
| 76 |
-
"</s>",
|
| 77 |
-
2
|
| 78 |
-
],
|
| 79 |
-
"cls": [
|
| 80 |
-
"<s>",
|
| 81 |
-
1
|
| 82 |
-
],
|
| 83 |
-
"trim_offsets": true,
|
| 84 |
-
"add_prefix_space": false
|
| 85 |
-
},
|
| 86 |
-
"decoder": {
|
| 87 |
-
"type": "ByteLevel",
|
| 88 |
-
"add_prefix_space": true,
|
| 89 |
-
"trim_offsets": true,
|
| 90 |
-
"use_regex": true
|
| 91 |
-
},
|
| 92 |
-
"model": {
|
| 93 |
-
"type": "BPE",
|
| 94 |
-
"dropout": null,
|
| 95 |
-
"unk_token": null,
|
| 96 |
-
"continuing_subword_prefix": "",
|
| 97 |
-
"end_of_word_suffix": "",
|
| 98 |
-
"fuse_unk": false,
|
| 99 |
-
"vocab": {
|
| 100 |
-
"<unk>": 0,
|
| 101 |
-
"<s>": 1,
|
| 102 |
-
"</s>": 2,
|
| 103 |
-
"<pad>": 3,
|
| 104 |
-
"<mask>": 4,
|
| 105 |
-
"\n": 5,
|
| 106 |
-
"#": 6,
|
| 107 |
-
"+": 7,
|
| 108 |
-
"-": 8,
|
| 109 |
-
".": 9,
|
| 110 |
-
"/": 10,
|
| 111 |
-
"0": 11,
|
| 112 |
-
"1": 12,
|
| 113 |
-
"2": 13,
|
| 114 |
-
"3": 14,
|
| 115 |
-
"4": 15,
|
| 116 |
-
"5": 16,
|
| 117 |
-
"8": 17,
|
| 118 |
-
"=": 18,
|
| 119 |
-
"@": 19,
|
| 120 |
-
"A": 20,
|
| 121 |
-
"B": 21,
|
| 122 |
-
"C": 22,
|
| 123 |
-
"F": 23,
|
| 124 |
-
"H": 24,
|
| 125 |
-
"I": 25,
|
| 126 |
-
"K": 26,
|
| 127 |
-
"L": 27,
|
| 128 |
-
"M": 28,
|
| 129 |
-
"N": 29,
|
| 130 |
-
"O": 30,
|
| 131 |
-
"P": 31,
|
| 132 |
-
"R": 32,
|
| 133 |
-
"S": 33,
|
| 134 |
-
"T": 34,
|
| 135 |
-
"Z": 35,
|
| 136 |
-
"\\": 36,
|
| 137 |
-
"a": 37,
|
| 138 |
-
"c": 38,
|
| 139 |
-
"e": 39,
|
| 140 |
-
"g": 40,
|
| 141 |
-
"h": 41,
|
| 142 |
-
"i": 42,
|
| 143 |
-
"l": 43,
|
| 144 |
-
"n": 44,
|
| 145 |
-
"r": 45,
|
| 146 |
-
"s": 46,
|
| 147 |
-
"Br": 47,
|
| 148 |
-
"an": 48,
|
| 149 |
-
"ch": 49,
|
| 150 |
-
"Bran": 50,
|
| 151 |
-
"Branch": 51,
|
| 152 |
-
"Branch1": 52,
|
| 153 |
-
"=C": 53,
|
| 154 |
-
"Ri": 54,
|
| 155 |
-
"ng": 55,
|
| 156 |
-
"Ring": 56,
|
| 157 |
-
"Ring1": 57,
|
| 158 |
-
"=Branch1": 58,
|
| 159 |
-
"Branch2": 59,
|
| 160 |
-
"=O": 60,
|
| 161 |
-
"Ring2": 61,
|
| 162 |
-
"H1": 62,
|
| 163 |
-
"C@": 63,
|
| 164 |
-
"=N": 64,
|
| 165 |
-
"#Branch1": 65,
|
| 166 |
-
"C@@": 66,
|
| 167 |
-
"=Branch2": 67,
|
| 168 |
-
"C@H1": 68,
|
| 169 |
-
"C@@H1": 69,
|
| 170 |
-
"#Branch2": 70,
|
| 171 |
-
"Cl": 71,
|
| 172 |
-
"#C": 72,
|
| 173 |
-
"/C": 73,
|
| 174 |
-
"NH1": 74,
|
| 175 |
-
"+1": 75,
|
| 176 |
-
"-1": 76,
|
| 177 |
-
"=Ring1": 77,
|
| 178 |
-
"O-1": 78,
|
| 179 |
-
"N+1": 79,
|
| 180 |
-
"\\C": 80,
|
| 181 |
-
"/N": 81,
|
| 182 |
-
"#N": 82,
|
| 183 |
-
"=Ring2": 83,
|
| 184 |
-
"=S": 84,
|
| 185 |
-
"=N+1": 85,
|
| 186 |
-
"Na": 86,
|
| 187 |
-
"Na+1": 87,
|
| 188 |
-
"\\N": 88,
|
| 189 |
-
"S+1": 89,
|
| 190 |
-
"/O": 90,
|
| 191 |
-
"\\S": 91,
|
| 192 |
-
"\\O": 92,
|
| 193 |
-
"Br-1": 93,
|
| 194 |
-
"I-1": 94,
|
| 195 |
-
"Cl-1": 95,
|
| 196 |
-
"/C@H1": 96,
|
| 197 |
-
"Branch3": 97,
|
| 198 |
-
"/C@@H1": 98,
|
| 199 |
-
"=P": 99,
|
| 200 |
-
"/S": 100,
|
| 201 |
-
"=N-1": 101,
|
| 202 |
-
"Si": 102,
|
| 203 |
-
"K+1": 103,
|
| 204 |
-
"N-1": 104,
|
| 205 |
-
"Se": 105,
|
| 206 |
-
"Li": 106,
|
| 207 |
-
"Li+1": 107,
|
| 208 |
-
"+3": 108,
|
| 209 |
-
"Cl+3": 109,
|
| 210 |
-
"\\C@H1": 110,
|
| 211 |
-
"Ring3": 111,
|
| 212 |
-
"\\C@@H1": 112,
|
| 213 |
-
"/N+1": 113,
|
| 214 |
-
"/P": 114,
|
| 215 |
-
"\\F": 115,
|
| 216 |
-
"P@": 116,
|
| 217 |
-
"2H": 117,
|
| 218 |
-
"PH1": 118,
|
| 219 |
-
"/Br": 119,
|
| 220 |
-
"N@": 120,
|
| 221 |
-
"P+1": 121,
|
| 222 |
-
"/Cl": 122,
|
| 223 |
-
"\\NH1": 123,
|
| 224 |
-
"\\Br": 124,
|
| 225 |
-
"@+1": 125,
|
| 226 |
-
"/I": 126,
|
| 227 |
-
"/C@": 127,
|
| 228 |
-
"Te": 128,
|
| 229 |
-
"\\N+1": 129,
|
| 230 |
-
"P@@": 130,
|
| 231 |
-
"12": 131,
|
| 232 |
-
"5I": 132,
|
| 233 |
-
"\\O-1": 133,
|
| 234 |
-
"125I": 134,
|
| 235 |
-
"/F": 135,
|
| 236 |
-
"#N+1": 136,
|
| 237 |
-
"\\Cl": 137,
|
| 238 |
-
"N@+1": 138,
|
| 239 |
-
"\\I": 139,
|
| 240 |
-
"-/": 140,
|
| 241 |
-
"/C@@": 141,
|
| 242 |
-
"N@@": 142,
|
| 243 |
-
"N@@+1": 143,
|
| 244 |
-
"-/Ring2": 144,
|
| 245 |
-
"-\\": 145,
|
| 246 |
-
"14": 146,
|
| 247 |
-
"B-1": 147,
|
| 248 |
-
"C-1": 148,
|
| 249 |
-
"S@+1": 149,
|
| 250 |
-
"14C": 150,
|
| 251 |
-
"H2": 151,
|
| 252 |
-
"H4": 152,
|
| 253 |
-
"I+1": 153,
|
| 254 |
-
"S-1": 154,
|
| 255 |
-
"\\P": 155,
|
| 256 |
-
"=S+1": 156,
|
| 257 |
-
"=P@": 157,
|
| 258 |
-
"SiH4": 158,
|
| 259 |
-
"+2": 159,
|
| 260 |
-
"3H": 160,
|
| 261 |
-
"@@+1": 161,
|
| 262 |
-
"Ag": 162,
|
| 263 |
-
"C+1": 163,
|
| 264 |
-
"S@@+1": 164,
|
| 265 |
-
"Cl+1": 165,
|
| 266 |
-
"=Se": 166,
|
| 267 |
-
"-\\Ring1": 167,
|
| 268 |
-
"H0": 168,
|
| 269 |
-
"OH0": 169,
|
| 270 |
-
"11": 170,
|
| 271 |
-
"=Branch3": 171,
|
| 272 |
-
"=Te": 172,
|
| 273 |
-
"Mg": 173,
|
| 274 |
-
"O+1": 174,
|
| 275 |
-
"Zn": 175,
|
| 276 |
-
"\\C@": 176,
|
| 277 |
-
"\\S+1": 177,
|
| 278 |
-
"H1-1": 178,
|
| 279 |
-
"SeH1": 179,
|
| 280 |
-
"P@+1": 180,
|
| 281 |
-
"-\\Ring2": 181,
|
| 282 |
-
"11C": 182,
|
| 283 |
-
"=Te+1": 183,
|
| 284 |
-
"Zn+2": 184,
|
| 285 |
-
"/NH1": 185,
|
| 286 |
-
"18": 186,
|
| 287 |
-
"As": 187,
|
| 288 |
-
"BH2": 188,
|
| 289 |
-
"BH1-1": 189,
|
| 290 |
-
"Ca": 190,
|
| 291 |
-
"H3": 191,
|
| 292 |
-
"OH1-1": 192,
|
| 293 |
-
"SH2": 193,
|
| 294 |
-
"=O+1": 194,
|
| 295 |
-
"Se+1": 195,
|
| 296 |
-
"TeH2": 196,
|
| 297 |
-
"125IH1": 197,
|
| 298 |
-
"-/Ring1": 198,
|
| 299 |
-
"14CH2": 199,
|
| 300 |
-
"Ag+1": 200,
|
| 301 |
-
"=Se+1": 201,
|
| 302 |
-
"MgH2": 202,
|
| 303 |
-
"Mg+2": 203,
|
| 304 |
-
"11CH3": 204,
|
| 305 |
-
"18F": 205,
|
| 306 |
-
"BH2-1": 206,
|
| 307 |
-
"Ca+2": 207
|
| 308 |
-
},
|
| 309 |
-
"merges": [
|
| 310 |
-
"B r",
|
| 311 |
-
"a n",
|
| 312 |
-
"c h",
|
| 313 |
-
"Br an",
|
| 314 |
-
"Bran ch",
|
| 315 |
-
"Branch 1",
|
| 316 |
-
"= C",
|
| 317 |
-
"R i",
|
| 318 |
-
"n g",
|
| 319 |
-
"Ri ng",
|
| 320 |
-
"Ring 1",
|
| 321 |
-
"= Branch1",
|
| 322 |
-
"Branch 2",
|
| 323 |
-
"= O",
|
| 324 |
-
"Ring 2",
|
| 325 |
-
"H 1",
|
| 326 |
-
"C @",
|
| 327 |
-
"= N",
|
| 328 |
-
"# Branch1",
|
| 329 |
-
"C@ @",
|
| 330 |
-
"= Branch2",
|
| 331 |
-
"C@ H1",
|
| 332 |
-
"C@@ H1",
|
| 333 |
-
"# Branch2",
|
| 334 |
-
"C l",
|
| 335 |
-
"# C",
|
| 336 |
-
"/ C",
|
| 337 |
-
"N H1",
|
| 338 |
-
"+ 1",
|
| 339 |
-
"- 1",
|
| 340 |
-
"= Ring1",
|
| 341 |
-
"O -1",
|
| 342 |
-
"N +1",
|
| 343 |
-
"\\ C",
|
| 344 |
-
"/ N",
|
| 345 |
-
"# N",
|
| 346 |
-
"= Ring2",
|
| 347 |
-
"= S",
|
| 348 |
-
"=N +1",
|
| 349 |
-
"N a",
|
| 350 |
-
"Na +1",
|
| 351 |
-
"\\ N",
|
| 352 |
-
"S +1",
|
| 353 |
-
"/ O",
|
| 354 |
-
"\\ S",
|
| 355 |
-
"\\ O",
|
| 356 |
-
"Br -1",
|
| 357 |
-
"I -1",
|
| 358 |
-
"Cl -1",
|
| 359 |
-
"/ C@H1",
|
| 360 |
-
"Branch 3",
|
| 361 |
-
"/ C@@H1",
|
| 362 |
-
"= P",
|
| 363 |
-
"/ S",
|
| 364 |
-
"=N -1",
|
| 365 |
-
"S i",
|
| 366 |
-
"K +1",
|
| 367 |
-
"N -1",
|
| 368 |
-
"S e",
|
| 369 |
-
"L i",
|
| 370 |
-
"Li +1",
|
| 371 |
-
"+ 3",
|
| 372 |
-
"Cl +3",
|
| 373 |
-
"\\ C@H1",
|
| 374 |
-
"Ring 3",
|
| 375 |
-
"\\ C@@H1",
|
| 376 |
-
"/ N+1",
|
| 377 |
-
"/ P",
|
| 378 |
-
"\\ F",
|
| 379 |
-
"P @",
|
| 380 |
-
"2 H",
|
| 381 |
-
"P H1",
|
| 382 |
-
"/ Br",
|
| 383 |
-
"N @",
|
| 384 |
-
"P +1",
|
| 385 |
-
"/ Cl",
|
| 386 |
-
"\\ NH1",
|
| 387 |
-
"\\ Br",
|
| 388 |
-
"@ +1",
|
| 389 |
-
"/ I",
|
| 390 |
-
"/ C@",
|
| 391 |
-
"T e",
|
| 392 |
-
"\\ N+1",
|
| 393 |
-
"P@ @",
|
| 394 |
-
"1 2",
|
| 395 |
-
"5 I",
|
| 396 |
-
"\\ O-1",
|
| 397 |
-
"12 5I",
|
| 398 |
-
"/ F",
|
| 399 |
-
"# N+1",
|
| 400 |
-
"\\ Cl",
|
| 401 |
-
"N@ +1",
|
| 402 |
-
"\\ I",
|
| 403 |
-
"- /",
|
| 404 |
-
"/ C@@",
|
| 405 |
-
"N@ @",
|
| 406 |
-
"N@ @+1",
|
| 407 |
-
"-/ Ring2",
|
| 408 |
-
"- \\",
|
| 409 |
-
"1 4",
|
| 410 |
-
"B -1",
|
| 411 |
-
"C -1",
|
| 412 |
-
"S @+1",
|
| 413 |
-
"14 C",
|
| 414 |
-
"H 2",
|
| 415 |
-
"H 4",
|
| 416 |
-
"I +1",
|
| 417 |
-
"S -1",
|
| 418 |
-
"\\ P",
|
| 419 |
-
"=S +1",
|
| 420 |
-
"=P @",
|
| 421 |
-
"Si H4",
|
| 422 |
-
"+ 2",
|
| 423 |
-
"3 H",
|
| 424 |
-
"@ @+1",
|
| 425 |
-
"A g",
|
| 426 |
-
"C +1",
|
| 427 |
-
"S @@+1",
|
| 428 |
-
"Cl +1",
|
| 429 |
-
"=S e",
|
| 430 |
-
"-\\ Ring1",
|
| 431 |
-
"H 0",
|
| 432 |
-
"O H0",
|
| 433 |
-
"1 1",
|
| 434 |
-
"= Branch3",
|
| 435 |
-
"= Te",
|
| 436 |
-
"M g",
|
| 437 |
-
"O +1",
|
| 438 |
-
"Z n",
|
| 439 |
-
"\\ C@",
|
| 440 |
-
"\\ S+1",
|
| 441 |
-
"H1 -1",
|
| 442 |
-
"Se H1",
|
| 443 |
-
"P@ +1",
|
| 444 |
-
"-\\ Ring2",
|
| 445 |
-
"11 C",
|
| 446 |
-
"=Te +1",
|
| 447 |
-
"Zn +2",
|
| 448 |
-
"/ NH1",
|
| 449 |
-
"1 8",
|
| 450 |
-
"A s",
|
| 451 |
-
"B H2",
|
| 452 |
-
"B H1-1",
|
| 453 |
-
"C a",
|
| 454 |
-
"H 3",
|
| 455 |
-
"O H1-1",
|
| 456 |
-
"S H2",
|
| 457 |
-
"=O +1",
|
| 458 |
-
"Se +1",
|
| 459 |
-
"Te H2",
|
| 460 |
-
"125I H1",
|
| 461 |
-
"-/ Ring1",
|
| 462 |
-
"14C H2",
|
| 463 |
-
"Ag +1",
|
| 464 |
-
"=Se +1",
|
| 465 |
-
"Mg H2",
|
| 466 |
-
"Mg +2",
|
| 467 |
-
"11C H3",
|
| 468 |
-
"18 F",
|
| 469 |
-
"BH2 -1",
|
| 470 |
-
"Ca +2"
|
| 471 |
-
]
|
| 472 |
-
}
|
| 473 |
-
}
|
|
|
|
|
|
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models/finetuned/lipo/tokenizer_config.json
DELETED
|
@@ -1,59 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"add_prefix_space": false,
|
| 3 |
-
"added_tokens_decoder": {
|
| 4 |
-
"0": {
|
| 5 |
-
"content": "<unk>",
|
| 6 |
-
"lstrip": false,
|
| 7 |
-
"normalized": true,
|
| 8 |
-
"rstrip": false,
|
| 9 |
-
"single_word": false,
|
| 10 |
-
"special": true
|
| 11 |
-
},
|
| 12 |
-
"1": {
|
| 13 |
-
"content": "<s>",
|
| 14 |
-
"lstrip": false,
|
| 15 |
-
"normalized": true,
|
| 16 |
-
"rstrip": false,
|
| 17 |
-
"single_word": false,
|
| 18 |
-
"special": true
|
| 19 |
-
},
|
| 20 |
-
"2": {
|
| 21 |
-
"content": "</s>",
|
| 22 |
-
"lstrip": false,
|
| 23 |
-
"normalized": true,
|
| 24 |
-
"rstrip": false,
|
| 25 |
-
"single_word": false,
|
| 26 |
-
"special": true
|
| 27 |
-
},
|
| 28 |
-
"3": {
|
| 29 |
-
"content": "<pad>",
|
| 30 |
-
"lstrip": false,
|
| 31 |
-
"normalized": true,
|
| 32 |
-
"rstrip": false,
|
| 33 |
-
"single_word": false,
|
| 34 |
-
"special": true
|
| 35 |
-
},
|
| 36 |
-
"4": {
|
| 37 |
-
"content": "<mask>",
|
| 38 |
-
"lstrip": true,
|
| 39 |
-
"normalized": true,
|
| 40 |
-
"rstrip": false,
|
| 41 |
-
"single_word": false,
|
| 42 |
-
"special": true
|
| 43 |
-
}
|
| 44 |
-
},
|
| 45 |
-
"bos_token": "<s>",
|
| 46 |
-
"clean_up_tokenization_spaces": true,
|
| 47 |
-
"cls_token": "<s>",
|
| 48 |
-
"eos_token": "</s>",
|
| 49 |
-
"errors": "replace",
|
| 50 |
-
"mask_token": "<mask>",
|
| 51 |
-
"model_max_length": 1000000000000000019884624838656,
|
| 52 |
-
"name_or_path": "data/epoch_267/hf",
|
| 53 |
-
"pad_token": "<pad>",
|
| 54 |
-
"sep_token": "</s>",
|
| 55 |
-
"special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
|
| 56 |
-
"tokenizer_class": "RobertaTokenizer",
|
| 57 |
-
"trim_offsets": true,
|
| 58 |
-
"unk_token": "<unk>"
|
| 59 |
-
}
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models/finetuned/lipo/vocab.json
DELETED
|
@@ -1 +0,0 @@
|
|
| 1 |
-
{"<unk>":0,"<s>":1,"</s>":2,"<pad>":3,"<mask>":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
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|
models/finetuned/pdbbind_full/config.json
DELETED
|
@@ -1,28 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"_name_or_path": "data/epoch_267/hf",
|
| 3 |
-
"architectures": [
|
| 4 |
-
"RobertaForMaskedLM"
|
| 5 |
-
],
|
| 6 |
-
"attention_probs_dropout_prob": 0.1,
|
| 7 |
-
"bos_token_id": 0,
|
| 8 |
-
"classifier_dropout": null,
|
| 9 |
-
"eos_token_id": 2,
|
| 10 |
-
"hidden_act": "gelu",
|
| 11 |
-
"hidden_dropout_prob": 0.1,
|
| 12 |
-
"hidden_size": 768,
|
| 13 |
-
"initializer_range": 0.02,
|
| 14 |
-
"intermediate_size": 3072,
|
| 15 |
-
"layer_norm_eps": 1e-12,
|
| 16 |
-
"max_position_embeddings": 514,
|
| 17 |
-
"model_type": "roberta",
|
| 18 |
-
"num_attention_heads": 4,
|
| 19 |
-
"num_hidden_layers": 12,
|
| 20 |
-
"output_hidden_states": true,
|
| 21 |
-
"pad_token_id": 1,
|
| 22 |
-
"position_embedding_type": "absolute",
|
| 23 |
-
"torch_dtype": "float32",
|
| 24 |
-
"transformers_version": "4.26.1",
|
| 25 |
-
"type_vocab_size": 1,
|
| 26 |
-
"use_cache": true,
|
| 27 |
-
"vocab_size": 800
|
| 28 |
-
}
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models/finetuned/pdbbind_full/finetuning_optimized_config.json
DELETED
|
@@ -1,24 +0,0 @@
|
|
| 1 |
-
{
|
| 2 |
-
"dataset_meta_csv": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full.csv",
|
| 3 |
-
"dataset_embs_npz": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full_embs.npz",
|
| 4 |
-
"use_scaffold": 0,
|
| 5 |
-
"seed": 42,
|
| 6 |
-
"train_frac": 0.8,
|
| 7 |
-
"val_frac": 0.1,
|
| 8 |
-
"test_frac": 0.1,
|
| 9 |
-
"model_path": "HUBioDataLab/SELFormer",
|
| 10 |
-
"tokenizer_path": "HUBioDataLab/SELFormer",
|
| 11 |
-
"pretrained_multimodal_dir": "data/models/SELFormerMM",
|
| 12 |
-
"task_type": "regression",
|
| 13 |
-
"label_column": "-logKd/Ki",
|
| 14 |
-
"num_labels": 1,
|
| 15 |
-
"batch_size": 32,
|
| 16 |
-
"max_len": 128,
|
| 17 |
-
"epochs": 75,
|
| 18 |
-
"backbone_lr": 5e-05,
|
| 19 |
-
"head_lr": 1e-06,
|
| 20 |
-
"weight_decay": 0.01,
|
| 21 |
-
"checkpoint_every": 25,
|
| 22 |
-
"test_eval_every": 0,
|
| 23 |
-
"save_dir": "data/models/finetuned/pdbbind_full"
|
| 24 |
-
}
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