biobert-variant-lora

README.md

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+---
+library_name: transformers
+base_model: dmis-lab/biobert-base-cased-v1.1
+tags:
+- generated_from_trainer
+metrics:
+- accuracy
+model-index:
+- name: results
+  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. -->
+
+# results
+
+This model is a fine-tuned version of [dmis-lab/biobert-base-cased-v1.1](https://huggingface.co/dmis-lab/biobert-base-cased-v1.1) on the None dataset.
+It achieves the following results on the evaluation set:
+- Loss: 3.2504
+- Accuracy: 0.0909
+
+## 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: 2e-05
+- train_batch_size: 16
+- eval_batch_size: 16
+- seed: 42
+- optimizer: Use OptimizerNames.ADAMW_TORCH_FUSED with betas=(0.9,0.999) and epsilon=1e-08 and optimizer_args=No additional optimizer arguments
+- lr_scheduler_type: linear
+- num_epochs: 3
+
+### Training results
+
+
+
+### Framework versions
+
+- Transformers 4.57.1
+- Pytorch 2.8.0+cu126
+- Datasets 4.0.0
+- Tokenizers 0.22.1

config.json

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+{
+  "architectures": [
+    "BertForSequenceClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "dtype": "float32",
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "Benign; No actionable therapy. [COSMIC]",
+    "1": "Benign; No actionable therapy. [ClinVar]",
+    "2": "Benign; No actionable therapy. [OncoKB]",
+    "3": "Founder mutation; Genetic counseling required. [COSMIC]",
+    "4": "Founder mutation; Genetic counseling required. [ClinVar]",
+    "5": "Founder mutation; Genetic counseling required. [OncoKB]",
+    "6": "Likely oncogenic; Chemo to moderate extent. [COSMIC]",
+    "7": "Likely oncogenic; Chemo to moderate extent. [ClinVar]",
+    "8": "Likely oncogenic; Chemo to moderate extent. [OncoKB]",
+    "9": "Likely pathogenic; PARP inhibitors recommended. [COSMIC]",
+    "10": "Likely pathogenic; PARP inhibitors recommended. [ClinVar]",
+    "11": "Likely pathogenic; PARP inhibitors recommended. [OncoKB]",
+    "12": "Oncogenic; TKI therapy (osimertinib). [COSMIC]",
+    "13": "Oncogenic; TKI therapy (osimertinib). [ClinVar]",
+    "14": "Oncogenic; TKI therapy (osimertinib). [OncoKB]",
+    "15": "Pathogenic; Immunotherapy (pembrolizumab) advised. [COSMIC]",
+    "16": "Pathogenic; Immunotherapy (pembrolizumab) advised. [ClinVar]",
+    "17": "Pathogenic; Immunotherapy (pembrolizumab) advised. [OncoKB]",
+    "18": "Pathogenic; Level 1 evidence for olaparib. [COSMIC]",
+    "19": "Pathogenic; Level 1 evidence for olaparib. [ClinVar]",
+    "20": "Pathogenic; Level 1 evidence for olaparib. [OncoKB]",
+    "21": "Resistance mutation; Switch to alternative TKI. [COSMIC]",
+    "22": "Resistance mutation; Switch to alternative TKI. [ClinVar]",
+    "23": "Resistance mutation; Switch to alternative TKI. [OncoKB]",
+    "24": "Truncating variant; Radiation not advised. [COSMIC]",
+    "25": "Truncating variant; Radiation not advised. [ClinVar]",
+    "26": "Truncating variant; Radiation not advised. [OncoKB]",
+    "27": "VUS; Monitor and consider trials. [COSMIC]",
+    "28": "VUS; Monitor and consider trials. [ClinVar]",
+    "29": "VUS; Monitor and consider trials. [OncoKB]"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "label2id": {
+    "Benign; No actionable therapy. [COSMIC]": 0,
+    "Benign; No actionable therapy. [ClinVar]": 1,
+    "Benign; No actionable therapy. [OncoKB]": 2,
+    "Founder mutation; Genetic counseling required. [COSMIC]": 3,
+    "Founder mutation; Genetic counseling required. [ClinVar]": 4,
+    "Founder mutation; Genetic counseling required. [OncoKB]": 5,
+    "Likely oncogenic; Chemo to moderate extent. [COSMIC]": 6,
+    "Likely oncogenic; Chemo to moderate extent. [ClinVar]": 7,
+    "Likely oncogenic; Chemo to moderate extent. [OncoKB]": 8,
+    "Likely pathogenic; PARP inhibitors recommended. [COSMIC]": 9,
+    "Likely pathogenic; PARP inhibitors recommended. [ClinVar]": 10,
+    "Likely pathogenic; PARP inhibitors recommended. [OncoKB]": 11,
+    "Oncogenic; TKI therapy (osimertinib). [COSMIC]": 12,
+    "Oncogenic; TKI therapy (osimertinib). [ClinVar]": 13,
+    "Oncogenic; TKI therapy (osimertinib). [OncoKB]": 14,
+    "Pathogenic; Immunotherapy (pembrolizumab) advised. [COSMIC]": 15,
+    "Pathogenic; Immunotherapy (pembrolizumab) advised. [ClinVar]": 16,
+    "Pathogenic; Immunotherapy (pembrolizumab) advised. [OncoKB]": 17,
+    "Pathogenic; Level 1 evidence for olaparib. [COSMIC]": 18,
+    "Pathogenic; Level 1 evidence for olaparib. [ClinVar]": 19,
+    "Pathogenic; Level 1 evidence for olaparib. [OncoKB]": 20,
+    "Resistance mutation; Switch to alternative TKI. [COSMIC]": 21,
+    "Resistance mutation; Switch to alternative TKI. [ClinVar]": 22,
+    "Resistance mutation; Switch to alternative TKI. [OncoKB]": 23,
+    "Truncating variant; Radiation not advised. [COSMIC]": 24,
+    "Truncating variant; Radiation not advised. [ClinVar]": 25,
+    "Truncating variant; Radiation not advised. [OncoKB]": 26,
+    "VUS; Monitor and consider trials. [COSMIC]": 27,
+    "VUS; Monitor and consider trials. [ClinVar]": 28,
+    "VUS; Monitor and consider trials. [OncoKB]": 29
+  },
+  "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",
+  "transformers_version": "4.57.1",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 28996
+}

model.safetensors

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+oid sha256:ff22039834cf46a0321c68a650c7d7cf8d64f6246d13a55f484416110b84abe5
+size 433356896

special_tokens_map.json

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

tokenizer_config.json

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+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "100": {
+      "content": "[UNK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "101": {
+      "content": "[CLS]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+    "102": {
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+      "lstrip": false,
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+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+    "103": {
+      "content": "[MASK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "clean_up_tokenization_spaces": true,
+  "cls_token": "[CLS]",
+  "do_basic_tokenize": true,
+  "do_lower_case": true,
+  "extra_special_tokens": {},
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "never_split": null,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}

training_args.bin

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+oid sha256:765d43690aa93aff13622db2c66d8f4f27efdc182b04d60f4a523f3d00731775
+size 5777