Upload 11 files

checkpoint-11915/config.json

@@ -0,0 +1,35 @@
+{
+  "_name_or_path": "microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract",
+  "architectures": [
+    "BertForTokenClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "gradient_checkpointing": false,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "O",
+    "1": "B",
+    "2": "I"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "label2id": {
+    "B": "1",
+    "I": "2",
+    "O": "0"
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "torch_dtype": "float32",
+  "transformers_version": "4.9.0",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 30522
+}

checkpoint-11915/optimizer.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bbb485a6579f5db32427bc6fd7f142e558859132b6aa8fbbdd95ffddeca84dab
+size 871267045

checkpoint-11915/pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b656312521d69b8a006dc0094343d54c401a35909edd7ca43a4a4a0ec1bd71c6
+size 435659249

checkpoint-11915/rng_state.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bdedc1d574e8fabf4db555ce5a0ba3b08f56163798433ea90bd35b3e49fc6e36
+size 17563

checkpoint-11915/scheduler.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:016e1255ae87f86ba423afc33cb7c20bb77df9d205269949849a26d18d1f1686
+size 623

checkpoint-11915/special_tokens_map.json

@@ -0,0 +1 @@
+{"unk_token": "[UNK]", "sep_token": "[SEP]", "pad_token": "[PAD]", "cls_token": "[CLS]", "mask_token": "[MASK]"}

checkpoint-11915/tokenizer_config.json

@@ -0,0 +1 @@
+{"do_lower_case": true, "unk_token": "[UNK]", "sep_token": "[SEP]", "pad_token": "[PAD]", "cls_token": "[CLS]", "mask_token": "[MASK]", "tokenize_chinese_chars": true, "strip_accents": null, "special_tokens_map_file": null, "name_or_path": "microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract", "do_basic_tokenize": true, "never_split": null, "tokenizer_class": "BertTokenizer"}

checkpoint-11915/trainer_state.json

@@ -0,0 +1,166 @@
+{
+  "best_metric": 0.09137263894081116,
+  "best_model_checkpoint": "data/models/gene/final/checkpoint-11915",
+  "epoch": 1.0,
+  "global_step": 11915,
+  "is_hyper_param_search": false,
+  "is_local_process_zero": true,
+  "is_world_process_zero": true,
+  "log_history": [
+    {
+      "epoch": 0.04,
+      "learning_rate": 9.082182123373897e-05,
+      "loss": 0.1639,
+      "step": 500
+    },
+    {
+      "epoch": 0.08,
+      "learning_rate": 8.684364246747798e-05,
+      "loss": 0.1393,
+      "step": 1000
+    },
+    {
+      "epoch": 0.13,
+      "learning_rate": 8.286546370121695e-05,
+      "loss": 0.1309,
+      "step": 1500
+    },
+    {
+      "epoch": 0.17,
+      "learning_rate": 7.888728493495594e-05,
+      "loss": 0.1286,
+      "step": 2000
+    },
+    {
+      "epoch": 0.21,
+      "learning_rate": 7.490910616869493e-05,
+      "loss": 0.1222,
+      "step": 2500
+    },
+    {
+      "epoch": 0.25,
+      "learning_rate": 7.093092740243391e-05,
+      "loss": 0.1202,
+      "step": 3000
+    },
+    {
+      "epoch": 0.29,
+      "learning_rate": 6.695274863617289e-05,
+      "loss": 0.1166,
+      "step": 3500
+    },
+    {
+      "epoch": 0.34,
+      "learning_rate": 6.297456986991188e-05,
+      "loss": 0.1164,
+      "step": 4000
+    },
+    {
+      "epoch": 0.38,
+      "learning_rate": 5.8996391103650865e-05,
+      "loss": 0.1099,
+      "step": 4500
+    },
+    {
+      "epoch": 0.42,
+      "learning_rate": 5.501821233738984e-05,
+      "loss": 0.1101,
+      "step": 5000
+    },
+    {
+      "epoch": 0.46,
+      "learning_rate": 5.1040033571128834e-05,
+      "loss": 0.1096,
+      "step": 5500
+    },
+    {
+      "epoch": 0.5,
+      "learning_rate": 4.7061854804867815e-05,
+      "loss": 0.1088,
+      "step": 6000
+    },
+    {
+      "epoch": 0.55,
+      "learning_rate": 4.3083676038606796e-05,
+      "loss": 0.1055,
+      "step": 6500
+    },
+    {
+      "epoch": 0.59,
+      "learning_rate": 3.9105497272345784e-05,
+      "loss": 0.1027,
+      "step": 7000
+    },
+    {
+      "epoch": 0.63,
+      "learning_rate": 3.512731850608477e-05,
+      "loss": 0.0961,
+      "step": 7500
+    },
+    {
+      "epoch": 0.67,
+      "learning_rate": 3.114913973982375e-05,
+      "loss": 0.1026,
+      "step": 8000
+    },
+    {
+      "epoch": 0.71,
+      "learning_rate": 2.7170960973562734e-05,
+      "loss": 0.1005,
+      "step": 8500
+    },
+    {
+      "epoch": 0.76,
+      "learning_rate": 2.3192782207301722e-05,
+      "loss": 0.1002,
+      "step": 9000
+    },
+    {
+      "epoch": 0.8,
+      "learning_rate": 1.9214603441040703e-05,
+      "loss": 0.1008,
+      "step": 9500
+    },
+    {
+      "epoch": 0.84,
+      "learning_rate": 1.523642467477969e-05,
+      "loss": 0.0947,
+      "step": 10000
+    },
+    {
+      "epoch": 0.88,
+      "learning_rate": 1.1258245908518674e-05,
+      "loss": 0.0935,
+      "step": 10500
+    },
+    {
+      "epoch": 0.92,
+      "learning_rate": 7.2800671422576585e-06,
+      "loss": 0.0961,
+      "step": 11000
+    },
+    {
+      "epoch": 0.97,
+      "learning_rate": 3.301888375996643e-06,
+      "loss": 0.0926,
+      "step": 11500
+    },
+    {
+      "epoch": 1.0,
+      "eval_accuracy": 0.9433962264150944,
+      "eval_f1": 0.6666666666666666,
+      "eval_loss": 0.09137263894081116,
+      "eval_precision": 0.5,
+      "eval_recall": 1.0,
+      "eval_runtime": 1.5459,
+      "eval_samples_per_second": 1.294,
+      "eval_steps_per_second": 0.647,
+      "step": 11915
+    }
+  ],
+  "max_steps": 11915,
+  "num_train_epochs": 1,
+  "total_flos": 4.981092847655731e+16,
+  "trial_name": null,
+  "trial_params": null
+}

checkpoint-11915/training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4e40086fb494d27319fad58db81cad2dbd1c40bc0f4dbabb543a1ce4e5aa4339
+size 2607