Upload folder using huggingface_hub
Browse files- config.json +34 -0
- model.safetensors +3 -0
- optimizer_state_dict.pth +3 -0
- special_tokens_map.json +37 -0
- tokenizer.json +0 -0
- tokenizer_config.json +53 -0
- trainer_state.json +96 -0
- training_args.bin +3 -0
config.json
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{
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"_name_or_path": "zhihan1996/DNABERT-2-117M",
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"alibi_starting_size": 512,
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"architectures": [
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"BertForSequenceClassification"
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],
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"attention_probs_dropout_prob": 0.0,
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"auto_map": {
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"AutoConfig": "zhihan1996/DNABERT-2-117M--configuration_bert.BertConfig",
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"AutoModel": "zhihan1996/DNABERT-2-117M--bert_layers.BertModel",
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"AutoModelForMaskedLM": "zhihan1996/DNABERT-2-117M--bert_layers.BertForMaskedLM",
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"AutoModelForSequenceClassification": "zhihan1996/DNABERT-2-117M--bert_layers.BertForSequenceClassification"
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},
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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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"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": 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": "4.45.2",
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"type_vocab_size": 2,
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"use_cache": true,
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"vocab_size": 4096
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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 sha256:50ed8e4236840c8739550987ab1f190c2d7716dfdbb94472150a975a0c1fe891
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size 468296408
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optimizer_state_dict.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:48625cac3b92d149691171d37d7b23d87724f77bee6344b6d270d323093d64fa
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size 936682546
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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
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{
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"added_tokens_decoder": {
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"0": {
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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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"1": {
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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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"2": {
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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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"3": {
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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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"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": false,
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"cls_token": "[CLS]",
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"mask_token": "[MASK]",
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"model_max_length": 256,
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"pad_token": "[PAD]",
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"padding_side": "right",
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"sep_token": "[SEP]",
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"tokenizer_class": "PreTrainedTokenizerFast",
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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": 0.43876591324806213,
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"best_model_checkpoint": "output_pipe/0/origin/checkpoint-400",
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"epoch": 4.0,
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| 5 |
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"eval_steps": 200,
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| 6 |
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"global_step": 408,
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| 7 |
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"is_hyper_param_search": false,
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| 8 |
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"is_local_process_zero": true,
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| 9 |
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"is_world_process_zero": true,
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| 10 |
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"log_history": [
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{
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| 12 |
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"epoch": 0.9803921568627451,
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| 13 |
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"grad_norm": 4.340454578399658,
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| 14 |
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"learning_rate": 2.6061452513966484e-05,
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| 15 |
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"loss": 0.6743,
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| 16 |
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"step": 100
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},
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{
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"epoch": 1.9607843137254903,
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| 20 |
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"grad_norm": 4.347059726715088,
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| 21 |
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"learning_rate": 1.7681564245810057e-05,
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| 22 |
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"loss": 0.4757,
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| 23 |
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"step": 200
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},
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{
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"epoch": 1.9607843137254903,
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| 27 |
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"eval_accuracy": 0.8098765432098766,
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"eval_f1": 0.8095002474022761,
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| 29 |
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"eval_loss": 0.45168113708496094,
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| 30 |
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"eval_matthews_correlation": 0.626803554022576,
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| 31 |
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"eval_precision": 0.8153468923901698,
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| 32 |
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"eval_recall": 0.8114686594479182,
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| 33 |
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"eval_runtime": 0.1311,
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| 34 |
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"eval_samples_per_second": 6180.527,
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"eval_steps_per_second": 99.194,
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| 36 |
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"step": 200
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},
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{
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| 39 |
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"epoch": 2.9411764705882355,
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| 40 |
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"grad_norm": 6.6639485359191895,
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| 41 |
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"learning_rate": 9.301675977653631e-06,
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| 42 |
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"loss": 0.3291,
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| 43 |
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"step": 300
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},
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{
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| 46 |
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"epoch": 3.9215686274509802,
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| 47 |
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"grad_norm": 6.7193684577941895,
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| 48 |
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"learning_rate": 9.217877094972066e-07,
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| 49 |
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"loss": 0.2513,
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| 50 |
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"step": 400
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| 51 |
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},
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| 52 |
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{
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| 53 |
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"epoch": 3.9215686274509802,
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| 54 |
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"eval_accuracy": 0.8333333333333334,
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| 55 |
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"eval_f1": 0.8333025904792685,
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| 56 |
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"eval_loss": 0.43876591324806213,
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| 57 |
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"eval_matthews_correlation": 0.669050678827637,
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| 58 |
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"eval_precision": 0.8348738262910798,
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| 59 |
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"eval_recall": 0.8341772151898734,
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| 60 |
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"eval_runtime": 0.1238,
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| 61 |
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"eval_samples_per_second": 6544.22,
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| 62 |
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"eval_steps_per_second": 105.031,
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| 63 |
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"step": 400
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| 64 |
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},
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| 65 |
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{
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| 66 |
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"epoch": 4.0,
|
| 67 |
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"step": 408,
|
| 68 |
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"total_flos": 531354250802880.0,
|
| 69 |
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"train_loss": 0.4285174494280535,
|
| 70 |
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"train_runtime": 23.4588,
|
| 71 |
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"train_samples_per_second": 1104.575,
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| 72 |
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"train_steps_per_second": 17.392
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| 73 |
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}
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| 74 |
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],
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| 75 |
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"logging_steps": 100,
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| 76 |
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"max_steps": 408,
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| 77 |
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"num_input_tokens_seen": 0,
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| 78 |
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"num_train_epochs": 4,
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| 79 |
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"save_steps": 200,
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| 80 |
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"stateful_callbacks": {
|
| 81 |
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"TrainerControl": {
|
| 82 |
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"args": {
|
| 83 |
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"should_epoch_stop": false,
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| 84 |
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"should_evaluate": false,
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| 85 |
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"should_log": false,
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| 86 |
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"should_save": true,
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| 87 |
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"should_training_stop": true
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| 88 |
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},
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| 89 |
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"attributes": {}
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| 90 |
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}
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| 91 |
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},
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| 92 |
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"total_flos": 531354250802880.0,
|
| 93 |
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"train_batch_size": 64,
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| 94 |
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"trial_name": null,
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| 95 |
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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 sha256:1f5b87f984dc290198519933dbb3d3673d556d0ccad7a7bb47f705d449ca00bd
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size 5368
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