Upload folder using huggingface_hub

checkpoint-26/config.json

@@ -0,0 +1,46 @@
+{
+  "add_cross_attention": false,
+  "architectures": [
+    "BertForTokenClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "bos_token_id": null,
+  "classifier_dropout": null,
+  "dtype": "float32",
+  "eos_token_id": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "B-ADE",
+    "1": "B-AGE",
+    "2": "B-DRUG",
+    "3": "I-ADE",
+    "4": "I-AGE",
+    "5": "I-DRUG",
+    "6": "O"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "is_decoder": false,
+  "label2id": {
+    "B-ADE": 0,
+    "B-AGE": 1,
+    "B-DRUG": 2,
+    "I-ADE": 3,
+    "I-AGE": 4,
+    "I-DRUG": 5,
+    "O": 6
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "tie_word_embeddings": true,
+  "transformers_version": "5.3.0",
+  "type_vocab_size": 2,
+  "use_cache": false,
+  "vocab_size": 28996
+}

checkpoint-26/model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d9c2496469f79c1fb87c1591444607745d8e6108ca4adb7d45140bf2dff46af5
+size 430923564

checkpoint-26/optimizer.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:845bc460a8c73f457650d48c009c3db103f3efc570a6bf9285776f8bb6992256
+size 861970123

checkpoint-26/rng_state.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3a5a7422dbe51806d882a2479da08afcb5a46f17dd87b6371d4e78b65d56b8ea
+size 14645

checkpoint-26/scheduler.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4ebfcfb4944bd4fb2e03e1e04992fc304c0f65cf8dd985b64119612b6df24f2d
+size 1465

checkpoint-26/tokenizer_config.json

@@ -0,0 +1,14 @@
+{
+  "backend": "tokenizers",
+  "cls_token": "[CLS]",
+  "do_lower_case": true,
+  "is_local": false,
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}

checkpoint-26/trainer_state.json

@@ -0,0 +1,45 @@
+{
+  "best_global_step": 26,
+  "best_metric": 0.06289733201265335,
+  "best_model_checkpoint": "/content/drive/MyDrive/ADEGuard/ner_biobert_final/checkpoint-26",
+  "epoch": 1.0,
+  "eval_steps": 500,
+  "global_step": 26,
+  "is_hyper_param_search": false,
+  "is_local_process_zero": true,
+  "is_world_process_zero": true,
+  "log_history": [
+    {
+      "epoch": 1.0,
+      "eval_f1": 0.0,
+      "eval_loss": 0.06289733201265335,
+      "eval_precision": 0.0,
+      "eval_recall": 0.0,
+      "eval_runtime": 0.7698,
+      "eval_samples_per_second": 33.775,
+      "eval_steps_per_second": 5.196,
+      "step": 26
+    }
+  ],
+  "logging_steps": 50,
+  "max_steps": 78,
+  "num_input_tokens_seen": 0,
+  "num_train_epochs": 3,
+  "save_steps": 500,
+  "stateful_callbacks": {
+    "TrainerControl": {
+      "args": {
+        "should_epoch_stop": false,
+        "should_evaluate": false,
+        "should_log": false,
+        "should_save": true,
+        "should_training_stop": false
+      },
+      "attributes": {}
+    }
+  },
+  "total_flos": 27176091131904.0,
+  "train_batch_size": 4,
+  "trial_name": null,
+  "trial_params": null
+}

checkpoint-26/training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b2e33e0687b2225b37b3b842824292cee58a877110d3e61b73275919a0a2f4b1
+size 5201

checkpoint-52/config.json

@@ -0,0 +1,46 @@
+{
+  "add_cross_attention": false,
+  "architectures": [
+    "BertForTokenClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "bos_token_id": null,
+  "classifier_dropout": null,
+  "dtype": "float32",
+  "eos_token_id": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "B-ADE",
+    "1": "B-AGE",
+    "2": "B-DRUG",
+    "3": "I-ADE",
+    "4": "I-AGE",
+    "5": "I-DRUG",
+    "6": "O"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "is_decoder": false,
+  "label2id": {
+    "B-ADE": 0,
+    "B-AGE": 1,
+    "B-DRUG": 2,
+    "I-ADE": 3,
+    "I-AGE": 4,
+    "I-DRUG": 5,
+    "O": 6
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "tie_word_embeddings": true,
+  "transformers_version": "5.3.0",
+  "type_vocab_size": 2,
+  "use_cache": false,
+  "vocab_size": 28996
+}

checkpoint-52/model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:06f3e92579bd3ee0f5b4a8dc8d5709068f2ef100851ffb0bba272814494b1170
+size 430923564

checkpoint-52/optimizer.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:356b5d063ccb0d1429b245b503f250811f8e547f4d06bc214165902cb83c3524
+size 861970123

checkpoint-52/rng_state.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c7e6c0e8e273c2f6b50af5caac50a1b7f627da4cf5222dd263a292a90c1d573e
+size 14645

checkpoint-52/scheduler.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bea3c51af45d25a7261b4b0df286c324e8be04554f45df38e96d91bc84fdda87
+size 1465

checkpoint-52/tokenizer_config.json

@@ -0,0 +1,14 @@
+{
+  "backend": "tokenizers",
+  "cls_token": "[CLS]",
+  "do_lower_case": true,
+  "is_local": false,
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}

checkpoint-52/trainer_state.json

@@ -0,0 +1,63 @@
+{
+  "best_global_step": 52,
+  "best_metric": 0.049389105290174484,
+  "best_model_checkpoint": "/content/drive/MyDrive/ADEGuard/ner_biobert_final/checkpoint-52",
+  "epoch": 2.0,
+  "eval_steps": 500,
+  "global_step": 52,
+  "is_hyper_param_search": false,
+  "is_local_process_zero": true,
+  "is_world_process_zero": true,
+  "log_history": [
+    {
+      "epoch": 1.0,
+      "eval_f1": 0.0,
+      "eval_loss": 0.06289733201265335,
+      "eval_precision": 0.0,
+      "eval_recall": 0.0,
+      "eval_runtime": 0.7698,
+      "eval_samples_per_second": 33.775,
+      "eval_steps_per_second": 5.196,
+      "step": 26
+    },
+    {
+      "epoch": 1.9230769230769231,
+      "grad_norm": 0.09649301320314407,
+      "learning_rate": 1.858974358974359e-05,
+      "loss": 0.15085140228271485,
+      "step": 50
+    },
+    {
+      "epoch": 2.0,
+      "eval_f1": 0.1904761904761905,
+      "eval_loss": 0.049389105290174484,
+      "eval_precision": 1.0,
+      "eval_recall": 0.10526315789473684,
+      "eval_runtime": 0.7878,
+      "eval_samples_per_second": 33.002,
+      "eval_steps_per_second": 5.077,
+      "step": 52
+    }
+  ],
+  "logging_steps": 50,
+  "max_steps": 78,
+  "num_input_tokens_seen": 0,
+  "num_train_epochs": 3,
+  "save_steps": 500,
+  "stateful_callbacks": {
+    "TrainerControl": {
+      "args": {
+        "should_epoch_stop": false,
+        "should_evaluate": false,
+        "should_log": false,
+        "should_save": true,
+        "should_training_stop": false
+      },
+      "attributes": {}
+    }
+  },
+  "total_flos": 54352182263808.0,
+  "train_batch_size": 4,
+  "trial_name": null,
+  "trial_params": null
+}

checkpoint-52/training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b2e33e0687b2225b37b3b842824292cee58a877110d3e61b73275919a0a2f4b1
+size 5201

checkpoint-78/config.json

@@ -0,0 +1,46 @@
+{
+  "add_cross_attention": false,
+  "architectures": [
+    "BertForTokenClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "bos_token_id": null,
+  "classifier_dropout": null,
+  "dtype": "float32",
+  "eos_token_id": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "B-ADE",
+    "1": "B-AGE",
+    "2": "B-DRUG",
+    "3": "I-ADE",
+    "4": "I-AGE",
+    "5": "I-DRUG",
+    "6": "O"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "is_decoder": false,
+  "label2id": {
+    "B-ADE": 0,
+    "B-AGE": 1,
+    "B-DRUG": 2,
+    "I-ADE": 3,
+    "I-AGE": 4,
+    "I-DRUG": 5,
+    "O": 6
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "tie_word_embeddings": true,
+  "transformers_version": "5.3.0",
+  "type_vocab_size": 2,
+  "use_cache": false,
+  "vocab_size": 28996
+}

checkpoint-78/model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a4d7f02d1f3246386da560af52aee7ca7aecdb423d0707a4c5b6dd8eef7dabcc
+size 430923564

checkpoint-78/optimizer.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:90c4a48b2641c9e4428ed7beef0d4df29041494b046b605b0b37dbe3fd833630
+size 861970123

checkpoint-78/rng_state.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:79ed8d45a4499bcffc47aab390786f5185fc3d7b706539fb18806d87c243fb0d
+size 14645

checkpoint-78/scheduler.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1bf819bf62e0d94d7d30d87fe36e9317a4be1fad217925e872ff99a8214e2e9d
+size 1465

checkpoint-78/tokenizer_config.json

@@ -0,0 +1,14 @@
+{
+  "backend": "tokenizers",
+  "cls_token": "[CLS]",
+  "do_lower_case": true,
+  "is_local": false,
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}

checkpoint-78/trainer_state.json

@@ -0,0 +1,74 @@
+{
+  "best_global_step": 78,
+  "best_metric": 0.04243722930550575,
+  "best_model_checkpoint": "/content/drive/MyDrive/ADEGuard/ner_biobert_final/checkpoint-78",
+  "epoch": 3.0,
+  "eval_steps": 500,
+  "global_step": 78,
+  "is_hyper_param_search": false,
+  "is_local_process_zero": true,
+  "is_world_process_zero": true,
+  "log_history": [
+    {
+      "epoch": 1.0,
+      "eval_f1": 0.0,
+      "eval_loss": 0.06289733201265335,
+      "eval_precision": 0.0,
+      "eval_recall": 0.0,
+      "eval_runtime": 0.7698,
+      "eval_samples_per_second": 33.775,
+      "eval_steps_per_second": 5.196,
+      "step": 26
+    },
+    {
+      "epoch": 1.9230769230769231,
+      "grad_norm": 0.09649301320314407,
+      "learning_rate": 1.858974358974359e-05,
+      "loss": 0.15085140228271485,
+      "step": 50
+    },
+    {
+      "epoch": 2.0,
+      "eval_f1": 0.1904761904761905,
+      "eval_loss": 0.049389105290174484,
+      "eval_precision": 1.0,
+      "eval_recall": 0.10526315789473684,
+      "eval_runtime": 0.7878,
+      "eval_samples_per_second": 33.002,
+      "eval_steps_per_second": 5.077,
+      "step": 52
+    },
+    {
+      "epoch": 3.0,
+      "eval_f1": 0.1904761904761905,
+      "eval_loss": 0.04243722930550575,
+      "eval_precision": 1.0,
+      "eval_recall": 0.10526315789473684,
+      "eval_runtime": 0.8159,
+      "eval_samples_per_second": 31.867,
+      "eval_steps_per_second": 4.903,
+      "step": 78
+    }
+  ],
+  "logging_steps": 50,
+  "max_steps": 78,
+  "num_input_tokens_seen": 0,
+  "num_train_epochs": 3,
+  "save_steps": 500,
+  "stateful_callbacks": {
+    "TrainerControl": {
+      "args": {
+        "should_epoch_stop": false,
+        "should_evaluate": false,
+        "should_log": false,
+        "should_save": true,
+        "should_training_stop": true
+      },
+      "attributes": {}
+    }
+  },
+  "total_flos": 81528273395712.0,
+  "train_batch_size": 4,
+  "trial_name": null,
+  "trial_params": null
+}

checkpoint-78/training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b2e33e0687b2225b37b3b842824292cee58a877110d3e61b73275919a0a2f4b1
+size 5201

config.json

@@ -0,0 +1,46 @@
+{
+  "add_cross_attention": false,
+  "architectures": [
+    "BertForTokenClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "bos_token_id": null,
+  "classifier_dropout": null,
+  "dtype": "float32",
+  "eos_token_id": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "B-ADE",
+    "1": "B-AGE",
+    "2": "B-DRUG",
+    "3": "I-ADE",
+    "4": "I-AGE",
+    "5": "I-DRUG",
+    "6": "O"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "is_decoder": false,
+  "label2id": {
+    "B-ADE": 0,
+    "B-AGE": 1,
+    "B-DRUG": 2,
+    "I-ADE": 3,
+    "I-AGE": 4,
+    "I-DRUG": 5,
+    "O": 6
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "tie_word_embeddings": true,
+  "transformers_version": "5.3.0",
+  "type_vocab_size": 2,
+  "use_cache": false,
+  "vocab_size": 28996
+}

model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a4d7f02d1f3246386da560af52aee7ca7aecdb423d0707a4c5b6dd8eef7dabcc
+size 430923564

tokenizer_config.json

@@ -0,0 +1,14 @@
+{
+  "backend": "tokenizers",
+  "cls_token": "[CLS]",
+  "do_lower_case": true,
+  "is_local": false,
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}

training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b2e33e0687b2225b37b3b842824292cee58a877110d3e61b73275919a0a2f4b1
+size 5201