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Files for Jiarui's DTR classifier with PubMedBert as a starting point, with continued fine tuning on THYME and ChemoTimelines SharedTask data.

README.md

@@ -1,3 +1,55 @@
 ---
-license: apache-2.0
+tags:
+- generated_from_trainer
+metrics:
+- accuracy
+model-index:
+- name: pubmedBertTHYME2
+  results: []
 ---
+
+<!-- This model card has been generated automatically according to the information the Trainer had access to. You
+should probably proofread and complete it, then remove this comment. -->
+
+# pubmedBertTHYME2
+
+This model is a fine-tuned version of [../deepphe_timeline_v1/glue_output/myProcessedData/dtr_pubmedbert](https://huggingface.co/../deepphe_timeline_v1/glue_output/myProcessedData/dtr_pubmedbert) on an unknown dataset.
+It achieves the following results on the evaluation set:
+- Loss: 1.3263
+- Accuracy: 0.7169
+
+## Model description
+
+More information needed
+
+## Intended uses & limitations
+
+More information needed
+
+## Training and evaluation data
+
+More information needed
+
+## Training procedure
+
+### Training hyperparameters
+
+The following hyperparameters were used during training:
+- learning_rate: 3e-05
+- train_batch_size: 16
+- eval_batch_size: 16
+- seed: 42
+- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
+- lr_scheduler_type: linear
+- num_epochs: 3.0
+
+### Training results
+
+
+
+### Framework versions
+
+- Transformers 4.24.0
+- Pytorch 2.0.1+cu117
+- Datasets 2.12.0
+- Tokenizers 0.11.0

all_results.json

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+{
+    "epoch": 3.0,
+    "eval_accuracy": 0.7168998718261719,
+    "eval_loss": 1.326256513595581,
+    "eval_runtime": 40.7056,
+    "eval_samples": 1858,
+    "eval_samples_per_second": 45.645,
+    "eval_steps_per_second": 2.874,
+    "train_loss": 0.3852307585631909,
+    "train_runtime": 523.2251,
+    "train_samples": 2338,
+    "train_samples_per_second": 13.405,
+    "train_steps_per_second": 0.843
+}

config.json

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+{
+  "_name_or_path": "../deepphe_timeline_v1/glue_output/myProcessedData/dtr_pubmedbert",
+  "architectures": [
+    "BertForSequenceClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "AFTER",
+    "1": "BEFORE",
+    "2": "BEFORE/OVERLAP",
+    "3": "None",
+    "4": "OVERLAP"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "label2id": {
+    "AFTER": 0,
+    "BEFORE": 1,
+    "BEFORE/OVERLAP": 2,
+    "None": 3,
+    "OVERLAP": 4
+  },
+  "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",
+  "problem_type": "single_label_classification",
+  "torch_dtype": "float32",
+  "transformers_version": "4.24.0",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 30522
+}

eval_results.json

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+{
+    "epoch": 3.0,
+    "eval_accuracy": 0.7168998718261719,
+    "eval_loss": 1.326256513595581,
+    "eval_runtime": 40.7056,
+    "eval_samples": 1858,
+    "eval_samples_per_second": 45.645,
+    "eval_steps_per_second": 2.874
+}

predict_results_None.txt

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+index	prediction
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