Upload Splicebert
#2
by
qrodenas - opened
- multimolecule-splicebert-finetuned/eval_metrics_splicebert.csv +28 -0
- multimolecule-splicebert-finetuned/final_model/config.json +52 -0
- multimolecule-splicebert-finetuned/final_model/model.safetensors +3 -0
- multimolecule-splicebert-finetuned/final_model/special_tokens_map.json +54 -0
- multimolecule-splicebert-finetuned/final_model/tokenizer_config.json +68 -0
- multimolecule-splicebert-finetuned/final_model/training_args.bin +3 -0
- multimolecule-splicebert-finetuned/final_model/vocab.txt +26 -0
multimolecule-splicebert-finetuned/eval_metrics_splicebert.csv
ADDED
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@@ -0,0 +1,28 @@
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,step,eval_loss,eval_seq_accuracy,eval_F1,eval_ideal_threshold
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7,8000,0.002569204429164529,0.735277816267147,0.7846375222694258,0.4193652868270874
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10,11000,0.002500804141163826,0.7438686434806706,0.792448951623955,0.4591529965400696
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11,12000,0.0024977801367640495,0.7506581682139393,0.7933212996389891,0.5195016264915466
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12,13000,0.002506256103515625,0.750519606484689,0.7949502408833562,0.5634196996688843
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13,14000,0.002466367557644844,0.750173202161563,0.7933188390792698,0.47746482491493225
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14,15000,0.0024979824665933847,0.7483026188166828,0.7927380664756842,0.5055601596832275
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15,16000,0.0024439790286123753,0.7586254676458363,0.7993190188312139,0.5041056871414185
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16,17000,0.0024133624974638224,0.7607038935845919,0.8025286392847164,0.5179569125175476
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17,18000,0.0023823431693017483,0.7622973534709713,0.8020388483262157,0.46387553215026855
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18,19000,0.0023969090543687344,0.7575862546764583,0.8003836141937252,0.4617359936237335
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19,20000,0.0023910230956971645,0.7623666343355965,0.8018734717773874,0.4711677134037018
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20,21000,0.0023792830761522055,0.7651378689206041,0.8037143550119539,0.4961932897567749
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21,22000,0.002382500097155571,0.7649993071913538,0.8038154699965314,0.4926639199256897
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22,23000,0.002373825293034315,0.7658306775668561,0.8052274792088895,0.506659209728241
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23,24000,0.0023699423763900995,0.7652071497852293,0.8055755827925979,0.46972033381462097
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24,25000,0.002361688995733857,0.7708188998198697,0.8070101647388713,0.5162570476531982
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| 27 |
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25,26000,0.00235151220113039,0.768740473881114,0.8066535256077739,0.48440903425216675
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| 28 |
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26,27000,0.0023619181010872126,0.7682555078287377,0.8066019819757605,0.4802227020263672
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multimolecule-splicebert-finetuned/final_model/config.json
ADDED
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@@ -0,0 +1,52 @@
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{
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"_name_or_path": "multimolecule/splicebert",
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"architectures": [
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"SpliceBertForTokenPrediction"
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],
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"attention_dropout": 0.1,
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"bos_token_id": 1,
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"eos_token_id": 2,
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"head": {
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"act": null,
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"bias": true,
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"dropout": 0.0,
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"hidden_size": 512,
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"layer_norm_eps": 1e-12,
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"num_labels": 2,
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"output_name": null,
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"problem_type": "single_label_classification",
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"transform": null,
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"transform_act": "gelu"
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},
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"hidden_act": "gelu",
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"hidden_dropout": 0.1,
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"hidden_size": 512,
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"initializer_range": 0.02,
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"intermediate_size": 2048,
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"layer_norm_eps": 1e-12,
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"lm_head": {
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"act": null,
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"bias": true,
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"dropout": 0.0,
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"hidden_size": null,
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"layer_norm_eps": 1e-12,
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"output_name": null,
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"transform": "nonlinear",
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"transform_act": "gelu"
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},
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"mask_token_id": 4,
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"max_position_embeddings": 1026,
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"model_type": "splicebert",
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"null_token_id": 5,
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"num_attention_heads": 16,
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"num_hidden_layers": 6,
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"pad_token_id": 0,
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"position_embedding_type": "absolute",
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"problem_type": "single_label_classification",
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"torch_dtype": "float32",
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"transformers_version": "4.46.3",
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"type_vocab_size": 2,
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| 49 |
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"unk_token_id": 3,
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"use_cache": true,
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"vocab_size": 26
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}
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multimolecule-splicebert-finetuned/final_model/model.safetensors
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version https://git-lfs.github.com/spec/v1
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oid sha256:a7285e3200d1b8a727c904eabee8190dbff4eecc090be018200ef726cc13c0ee
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size 78887280
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multimolecule-splicebert-finetuned/final_model/special_tokens_map.json
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{
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"additional_special_tokens": [
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"<null>"
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],
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"bos_token": {
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| 6 |
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"content": "<cls>",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"cls_token": {
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"content": "<cls>",
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| 14 |
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"lstrip": false,
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| 15 |
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"normalized": false,
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| 16 |
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"rstrip": false,
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| 17 |
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"single_word": false
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},
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| 19 |
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"eos_token": {
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| 20 |
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"content": "<eos>",
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| 21 |
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"lstrip": false,
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| 22 |
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"normalized": false,
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| 23 |
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"rstrip": false,
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"single_word": false
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},
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| 26 |
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"mask_token": {
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| 27 |
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"content": "<mask>",
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| 28 |
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"lstrip": false,
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| 29 |
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"normalized": false,
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| 30 |
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"rstrip": false,
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| 31 |
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"single_word": false
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| 32 |
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},
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| 33 |
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"pad_token": {
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| 34 |
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"content": "<pad>",
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| 35 |
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"lstrip": false,
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| 36 |
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"normalized": false,
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| 37 |
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"rstrip": false,
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| 38 |
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"single_word": false
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},
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| 40 |
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"sep_token": {
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| 41 |
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"content": "<eos>",
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| 42 |
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"lstrip": false,
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| 43 |
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"normalized": false,
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| 44 |
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"rstrip": false,
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| 45 |
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"single_word": false
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| 46 |
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},
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| 47 |
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"unk_token": {
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| 48 |
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"content": "<unk>",
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| 49 |
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"lstrip": false,
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| 50 |
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"normalized": false,
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| 51 |
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"rstrip": false,
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| 52 |
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"single_word": false
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| 53 |
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}
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| 54 |
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}
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multimolecule-splicebert-finetuned/final_model/tokenizer_config.json
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{
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"added_tokens_decoder": {
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"0": {
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"content": "<pad>",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"1": {
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"content": "<cls>",
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"lstrip": false,
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"normalized": false,
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| 15 |
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"rstrip": false,
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| 16 |
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"single_word": false,
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"special": true
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| 18 |
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},
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| 19 |
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"2": {
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| 20 |
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"content": "<eos>",
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| 21 |
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"lstrip": false,
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| 22 |
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"normalized": false,
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| 23 |
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"rstrip": false,
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| 24 |
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"single_word": false,
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| 25 |
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"special": true
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| 26 |
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},
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| 27 |
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"3": {
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| 28 |
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"content": "<unk>",
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| 29 |
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"lstrip": false,
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| 30 |
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"normalized": false,
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| 31 |
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"rstrip": false,
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| 32 |
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"single_word": false,
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| 33 |
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"special": true
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| 34 |
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},
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| 35 |
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"4": {
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| 36 |
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"content": "<mask>",
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| 37 |
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"lstrip": false,
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| 38 |
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"normalized": false,
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| 39 |
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"rstrip": false,
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| 40 |
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"single_word": false,
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| 41 |
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"special": true
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| 42 |
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},
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| 43 |
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"5": {
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| 44 |
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"content": "<null>",
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| 45 |
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"lstrip": false,
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| 46 |
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"normalized": false,
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| 47 |
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"rstrip": false,
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| 48 |
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"single_word": false,
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| 49 |
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"special": true
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| 50 |
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}
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| 51 |
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},
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| 52 |
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"additional_special_tokens": [
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| 53 |
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"<null>"
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| 54 |
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],
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| 55 |
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"bos_token": "<cls>",
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| 56 |
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"clean_up_tokenization_spaces": true,
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| 57 |
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"cls_token": "<cls>",
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| 58 |
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"codon": false,
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| 59 |
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"eos_token": "<eos>",
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| 60 |
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"mask_token": "<mask>",
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| 61 |
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"model_max_length": 1026,
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| 62 |
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"nmers": 1,
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| 63 |
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"pad_token": "<pad>",
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| 64 |
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"replace_T_with_U": true,
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| 65 |
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"sep_token": "<eos>",
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| 66 |
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"tokenizer_class": "RnaTokenizer",
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| 67 |
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"unk_token": "<unk>"
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| 68 |
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}
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multimolecule-splicebert-finetuned/final_model/training_args.bin
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version https://git-lfs.github.com/spec/v1
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oid sha256:ce47261154b49be1dcb1e977db3183bb281e4c8a0cc142d3caa177772d66d24a
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| 3 |
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size 5368
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multimolecule-splicebert-finetuned/final_model/vocab.txt
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<pad>
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<cls>
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<eos>
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<unk>
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<mask>
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<null>
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A
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C
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G
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U
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N
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R
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Y
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S
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W
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K
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M
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B
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D
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H
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*
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-
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