Finetuned BioLinkBERT model with capition only dataset
Browse files- config.json +35 -0
- model.safetensors +3 -0
- optimizer.pt +3 -0
- rng_state.pth +3 -0
- scheduler.pt +3 -0
- special_tokens_map.json +37 -0
- tokenizer.json +0 -0
- tokenizer_config.json +57 -0
- trainer_state.json +89 -0
- training_args.bin +3 -0
- vocab.txt +0 -0
config.json
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{
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"_name_or_path": "michiyasunaga/BioLinkBERT-base",
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"architectures": [
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"BertForSequenceClassification"
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],
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"attention_probs_dropout_prob": 0.1,
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"classifier_dropout": null,
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"gradient_checkpointing": false,
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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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"id2label": {
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"0": "medical",
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"1": "non-medical"
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},
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"initializer_range": 0.02,
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"intermediate_size": 3072,
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"label2id": {
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"false": 0,
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"true": 1
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},
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"layer_norm_eps": 1e-12,
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"max_position_embeddings": 512,
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"model_type": "bert",
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"num_attention_heads": 12,
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"num_hidden_layers": 12,
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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": "4.42.4",
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"type_vocab_size": 2,
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"use_cache": true,
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"vocab_size": 28895
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}
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model.safetensors
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version https://git-lfs.github.com/spec/v1
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oid sha256:d0053d738de021785173e3c42fb33ff25767fcf569bed973338b550b328819da
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size 432960488
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optimizer.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:17ba94fded14153bccf3bfe347fc0cc39b4e560dfbed0ec68fec8a788cef669d
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size 866042106
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rng_state.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:5cb3fc6616906193af26a015a56b8fa278ab16ebe538d37a58ec341a3bff2f40
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size 14244
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scheduler.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:fbc8cfc3c0c7c3e9ca7a2f291ecebb32099d3d2a715930cba68b5e931884385b
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size 1064
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special_tokens_map.json
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{
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"cls_token": {
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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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"mask_token": {
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"content": "[MASK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"pad_token": {
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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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},
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"sep_token": {
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"content": "[SEP]",
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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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"unk_token": {
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"content": "[UNK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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}
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}
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tokenizer.json
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tokenizer_config.json
ADDED
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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": "[UNK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"2": {
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"content": "[CLS]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"3": {
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"content": "[SEP]",
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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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"4": {
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"content": "[MASK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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}
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},
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"clean_up_tokenization_spaces": true,
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"cls_token": "[CLS]",
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"do_basic_tokenize": true,
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"do_lower_case": true,
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"mask_token": "[MASK]",
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"model_max_length": 1000000000000000019884624838656,
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"never_split": null,
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"pad_token": "[PAD]",
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"sep_token": "[SEP]",
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"strip_accents": null,
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"tokenize_chinese_chars": true,
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"tokenizer_class": "BertTokenizer",
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"unk_token": "[UNK]"
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}
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trainer_state.json
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{
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"best_metric": 0.18062713742256165,
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"best_model_checkpoint": "biolinkbert_caption_RTX6000/checkpoint-1230",
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"epoch": 2.0,
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"eval_steps": 500,
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"global_step": 2460,
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"is_hyper_param_search": false,
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"is_local_process_zero": true,
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"is_world_process_zero": true,
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"log_history": [
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{
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"learning_rate": 2.75609756097561e-05,
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"step": 500
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},
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{
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"learning_rate": 2.5121951219512197e-05,
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"step": 1000
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},
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{
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"epoch": 1.0,
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"eval_accuracy": 0.9264901339331356,
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"eval_f1": 0.9205521585884222,
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"eval_f1_medical": 0.9422721798474508,
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"eval_f1_non_medical": 0.8988321373293936,
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"eval_loss": 0.18062713742256165,
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"eval_precision": 0.9294423823345337,
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"eval_recall": 0.913885790809698,
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"eval_runtime": 68.9283,
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"eval_samples_per_second": 141.901,
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"eval_steps_per_second": 4.439,
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"step": 1230
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},
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{
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"loss": 0.1479,
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"step": 1500
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},
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{
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"learning_rate": 2.024390243902439e-05,
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"loss": 0.1218,
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"step": 2000
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},
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{
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"epoch": 2.0,
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"eval_accuracy": 0.9329311931295369,
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"eval_f1": 0.928538519062421,
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"eval_f1_medical": 0.946255939701786,
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"eval_f1_non_medical": 0.910821098423056,
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"eval_loss": 0.20084594190120697,
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"eval_precision": 0.9298713253776563,
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"eval_recall": 0.9272784207124916,
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"eval_runtime": 68.7943,
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"eval_samples_per_second": 142.177,
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"eval_steps_per_second": 4.448,
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"step": 2460
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}
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],
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"logging_steps": 500,
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"max_steps": 6150,
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"num_input_tokens_seen": 0,
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"num_train_epochs": 5,
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"save_steps": 500,
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"stateful_callbacks": {
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"TrainerControl": {
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"args": {
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"should_epoch_stop": false,
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"should_evaluate": false,
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"should_log": false,
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"should_save": true,
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"should_training_stop": false
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},
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"attributes": {}
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}
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},
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"total_flos": 1.749629318156544e+16,
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"train_batch_size": 32,
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"trial_name": null,
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"trial_params": null
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}
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training_args.bin
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version https://git-lfs.github.com/spec/v1
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oid sha256:e3e23d54205f780b66c0714d738488989517bb4e7a0aafc5bbf5336dc8ba830b
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size 5176
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vocab.txt
ADDED
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