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

README.md

@@ -1,3 +1,46 @@
 ---
-license: apache-2.0
+tags:
+- generated_from_trainer
+model-index:
+- name: pubmed_thyme_deepphe_no_crc
+  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. -->
+
+# pubmed_thyme_deepphe_no_crc
+
+This model is a fine-tuned version of [tlink_shared_task_weights/pubmed_thyme_deepphe_no_crc](https://huggingface.co/tlink_shared_task_weights/pubmed_thyme_deepphe_no_crc) on an unknown dataset.
+
+## 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: 62
+- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
+- lr_scheduler_type: linear
+- num_epochs: 10.0
+
+### Framework versions
+
+- Transformers 4.24.0
+- Pytorch 2.0.1+cu117
+- Datasets 2.12.0
+- Tokenizers 0.11.0

all_results.json

@@ -0,0 +1,14 @@
+{
+    "epoch": 10.0,
+    "eval_accuracy": 0.8376963138580322,
+    "eval_loss": 1.120042324066162,
+    "eval_runtime": 0.7684,
+    "eval_samples": 1146,
+    "eval_samples_per_second": 1491.385,
+    "eval_steps_per_second": 93.7,
+    "train_loss": 0.09304492578171847,
+    "train_runtime": 41.8899,
+    "train_samples": 1812,
+    "train_samples_per_second": 432.562,
+    "train_steps_per_second": 27.214
+}

config.json

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+{
+  "_name_or_path": "tlink_shared_task_weights/pubmed_thyme",
+  "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": "begins-on",
+    "3": "contains",
+    "4": "contains-1",
+    "5": "contains-subevent",
+    "6": "contains-subevent-1",
+    "7": "ends-on",
+    "8": "none",
+    "9": "noted-on",
+    "10": "noted-on-1",
+    "11": "overlap"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "label2id": {
+    "after": 0,
+    "before": 1,
+    "begins-on": 2,
+    "contains": 3,
+    "contains-1": 4,
+    "contains-subevent": 5,
+    "contains-subevent-1": 6,
+    "ends-on": 7,
+    "none": 8,
+    "noted-on": 9,
+    "noted-on-1": 10,
+    "overlap": 11
+  },
+  "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

@@ -0,0 +1,9 @@
+{
+    "epoch": 10.0,
+    "eval_accuracy": 0.8376963138580322,
+    "eval_loss": 1.120042324066162,
+    "eval_runtime": 0.7684,
+    "eval_samples": 1146,
+    "eval_samples_per_second": 1491.385,
+    "eval_steps_per_second": 93.7
+}

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